432 research outputs found
The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary
Harmful blooms of the cyanobacterium Microcystis sp. have become increasingly pervasive in the San Francisco Estuary Delta (USA) since the early 2000s and their rise has coincided with substantial decreases in several important fish species. Direct and indirect effects Microcystis blooms may have on the Delta food web were investigated. The Microcystis population was tracked for 2 years at six sites throughout the Delta using quantitative PCR. High-throughput amplicon sequencing and colony PCR sequencing revealed the presence of 10 different strains of Microcystis, including 6 different microcystin-producing strains. Shotgun metagenomic analysis identified a variety of Microcystis secondary metabolite pathways, including those for the biosynthesis of: aeruginosin, cyanopeptolin, microginin, microviridin and piricyclamide. A sizable reduction was observed in microbial community diversity during a large Microcystis bloom (H′ = 0.61) relative to periods preceding (H′ = 2.32) or following (H′ = 3.71) the bloom. Physicochemical conditions of the water column were stable throughout the bloom period. The elevated abundance of a cyanomyophage with high similarity to previously sequenced isolates known to infect Microcystis sp. was implicated in the bloom's collapse. Network analysis was employed to elucidate synergistic and antagonistic relationships between Microcystis and other bacteria and indicated that only very few taxa were positively correlated with Microcystis
FAS and NF-κB signalling modulate dependence of lung cancers on mutant EGFR
Human lung adenocarcinomas with activating mutations in EGFR (epidermal growth factor receptor) often respond to treatment with EGFR tyrosine kinase inhibitors (TKIs), but the magnitude of tumour regression is variable and transient. This heterogeneity in treatment response could result from genetic modifiers that regulate the degree to which tumour cells are dependent on mutant EGFR. Through a pooled RNA interference screen, we show that knockdown of FAS and several components of the NF-κB pathway specifically enhanced cell death induced by the EGFR TKI erlotinib in EGFR-mutant lung cancer cells. Activation of NF-κB through overexpression of c-FLIP or IKK (also known as CFLAR and IKBKB, respectively), or silencing of IκB (also known as NFKBIA), rescued EGFR-mutant lung cancer cells from EGFR TKI treatment. Genetic or pharmacologic inhibition of NF-κB enhanced erlotinib-induced apoptosis in erlotinib-sensitive and erlotinib-resistant EGFR-mutant lung cancer models. Increased expression of the NF-κB inhibitor IκB predicted for improved response and survival in EGFR-mutant lung cancer patients treated with EGFR TKI. These data identify NF-κB as a potential companion drug target, together with EGFR, in EGFR-mutant lung cancers and provide insight into the mechanisms by which tumour cells escape from oncogene dependence
Magnetohydrodynamics and Plasma Cosmology
We study the linear magnetohydrodynamic (MHD) equations, both in the
Newtonian and the general-relativistic limit, as regards a viscous magnetized
fluid of finite conductivity and discuss instability criteria. In addition, we
explore the excitation of cosmological perturbations in anisotropic spacetimes,
in the presence of an ambient magnetic field. Acoustic, electromagnetic (e/m)
and fast-magnetosonic modes, propagating normal to the magnetic field, can be
excited, resulting in several implications of cosmological significance.Comment: 9 pages, RevTeX, To appear in the Proceedings of the Peyresq X
Meeting, IJTP Conference Serie
A Quantitative Model of Energy Release and Heating by Time-dependent, Localized Reconnection in a Flare with a Thermal Loop-top X-ray Source
We present a quantitative model of the magnetic energy stored and then
released through magnetic reconnection for a flare on 26 Feb 2004. This flare,
well observed by RHESSI and TRACE, shows evidence of non-thermal electrons only
for a brief, early phase. Throughout the main period of energy release there is
a super-hot (T>30 MK) plasma emitting thermal bremsstrahlung atop the flare
loops. Our model describes the heating and compression of such a source by
localized, transient magnetic reconnection. It is a three-dimensional
generalization of the Petschek model whereby Alfven-speed retraction following
reconnection drives supersonic inflows parallel to the field lines, which form
shocks heating, compressing, and confining a loop-top plasma plug. The
confining inflows provide longer life than a freely-expanding or
conductively-cooling plasma of similar size and temperature. Superposition of
successive transient episodes of localized reconnection across a current sheet
produces an apparently persistent, localized source of high-temperature
emission. The temperature of the source decreases smoothly on a time scale
consistent with observations, far longer than the cooling time of a single
plug. Built from a disordered collection of small plugs, the source need not
have the coherent jet-like structure predicted by steady-state reconnection
models. This new model predicts temperatures and emission measure consistent
with the observations of 26 Feb 2004. Furthermore, the total energy released by
the flare is found to be roughly consistent with that predicted by the model.
Only a small fraction of the energy released appears in the super-hot source at
any one time, but roughly a quarter of the flare energy is thermalized by the
reconnection shocks over the course of the flare. All energy is presumed to
ultimately appear in the lower-temperature T<20 MK, post-flare loops
Simulations of galactic dynamos
We review our current understanding of galactic dynamo theory, paying
particular attention to numerical simulations both of the mean-field equations
and the original three-dimensional equations relevant to describing the
magnetic field evolution for a turbulent flow. We emphasize the theoretical
difficulties in explaining non-axisymmetric magnetic fields in galaxies and
discuss the observational basis for such results in terms of rotation measure
analysis. Next, we discuss nonlinear theory, the role of magnetic helicity
conservation and magnetic helicity fluxes. This leads to the possibility that
galactic magnetic fields may be bi-helical, with opposite signs of helicity and
large and small length scales. We discuss their observational signatures and
close by discussing the possibilities of explaining the origin of primordial
magnetic fields.Comment: 28 pages, 15 figure, to appear in Lecture Notes in Physics "Magnetic
fields in diffuse media", Eds. E. de Gouveia Dal Pino and A. Lazaria
3D Coronal Density Reconstruction and Retrieving the Magnetic Field Structure during Solar Minimum
Measurement of the coronal magnetic field is a crucial ingredient in
understanding the nature of solar coronal phenomena at all scales. We employed
STEREO/COR1 data obtained during a deep minimum of solar activity in February
2008 (Carrington rotation CR 2066) to retrieve and analyze the
three-dimensional (3D) coronal electron density in the range of heights from
1.5 to 4 Rsun using a tomography method. With this, we qualitatively deduced
structures of the coronal magnetic field. The 3D electron density analysis is
complemented by the 3D STEREO/EUVI emissivity in the 195 A band obtained by
tomography for the same CR. A global 3D MHD model of the solar corona was used
to relate the reconstructed 3D density and emissivity to open/closed magnetic
field structures. We show that the density maximum locations can serve as an
indicator of current sheet position, while the locations of the density
gradient maximum can be a reliable indicator of coronal hole boundaries. We
find that the magnetic field configuration during CR 2066 has a tendency to
become radially open at heliocentric distances greater than 2.5 Rsun. We also
find that the potential field model with a fixed source surface (PFSS) is
inconsistent with the boundaries between the regions with open and closed
magnetic field structures. This indicates that the assumption of the potential
nature of the coronal global magnetic field is not satisfied even during the
deep solar minimum. Results of our 3D density reconstruction will help to
constrain solar coronal field models and test the accuracy of the magnetic
field approximations for coronal modeling.Comment: Published in "Solar Physics
75th Anniversary of ‘Existence of Electromagnetic-Hydrodynamic Waves’
We have recently passed the 75th anniversary of one of the most important
results in solar and space physics: Hannes Alfv\'en's discovery of Alfv\'en
waves and the Alfv\'en speed. To celebrate the anniversary, this article
recounts some major episodes in the history of MHD waves. Following an
initially cool reception, Alfv\'en's ideas were propelled into the spotlight by
Fermi's work on cosmic rays, the new mystery of coronal heating and, as
scientific perception of interplanetary space shifted dramatically and the
space race started, detection of Alfv\'en waves in the solar wind. From then
on, interest in MHD waves boomed, laying the foundations for modern remote
observations of MHD waves in the Sun, coronal seismology and some of today's
leading theories of coronal heating and solar wind acceleration. In 1970,
Alfv\'en received the Nobel Prize for his work in MHD, including these
discoveries. The article concludes with some reflection about what the history
implies about the way we do science, especially the advantages and pitfalls of
idealised mathematical models.Comment: 10 pages, accepted by Solar Physic
PIK3CA mutation in HPV-associated OPSCC patients receiving deintensified chemoradiation
PIK3CA is the most frequently mutated gene in human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC). Prognostic implications of such mutations remain unknown. We sought to elucidate the clinical significance of PIK3CA mutations in HPV-associated OPSCC patients treated with definitive chemoradiation (CRT). Seventyseven patients with HPV-associated OPSCC were enrolled on two phase II clinical trials of deintensified CRT (60 Gy intensitymodulated radiotherapy with concurrent weekly cisplatin). Targeted next-generation sequencing was performed. Of the 77 patients, nine had disease recurrence (two regional, four distant, three regional and distant). Thirty-four patients had mutation( s) identified; 16 had PIK3CA mutations. Patients with wild-type-PIK3CA had statistically significantly higher 3-year disease-free survival than PIK3CA-mutant patients (93.4%, 95% confidence interval [CI] = 85.0% to 99.9% vs 68.8%, 95% CI = 26.7% to 89.8%; P=.004). On multivariate analysis, PIK3CA mutation was the only variable statistically significantly associated with disease recurrence (hazard ratio = 5.71, 95% CI = 1.53 to 21.3; P=.01). PIK3CA mutation is associated with worse diseasefree survival in a prospective cohort of newly diagnosed HPV-associated OPSCC patients treated with deintensified CRT
Modeling the Subsurface Structure of Sunspots
While sunspots are easily observed at the solar surface, determining their
subsurface structure is not trivial. There are two main hypotheses for the
subsurface structure of sunspots: the monolithic model and the cluster model.
Local helioseismology is the only means by which we can investigate
subphotospheric structure. However, as current linear inversion techniques do
not yet allow helioseismology to probe the internal structure with sufficient
confidence to distinguish between the monolith and cluster models, the
development of physically realistic sunspot models are a priority for
helioseismologists. This is because they are not only important indicators of
the variety of physical effects that may influence helioseismic inferences in
active regions, but they also enable detailed assessments of the validity of
helioseismic interpretations through numerical forward modeling. In this paper,
we provide a critical review of the existing sunspot models and an overview of
numerical methods employed to model wave propagation through model sunspots. We
then carry out an helioseismic analysis of the sunspot in Active Region 9787
and address the serious inconsistencies uncovered by
\citeauthor{gizonetal2009}~(\citeyear{gizonetal2009,gizonetal2009a}). We find
that this sunspot is most probably associated with a shallow, positive
wave-speed perturbation (unlike the traditional two-layer model) and that
travel-time measurements are consistent with a horizontal outflow in the
surrounding moat.Comment: 73 pages, 19 figures, accepted by Solar Physic
Stellar structure and compact objects before 1940: Towards relativistic astrophysics
Since the mid-1920s, different strands of research used stars as "physics
laboratories" for investigating the nature of matter under extreme densities
and pressures, impossible to realize on Earth. To trace this process this paper
is following the evolution of the concept of a dense core in stars, which was
important both for an understanding of stellar evolution and as a testing
ground for the fast-evolving field of nuclear physics. In spite of the divide
between physicists and astrophysicists, some key actors working in the
cross-fertilized soil of overlapping but different scientific cultures
formulated models and tentative theories that gradually evolved into more
realistic and structured astrophysical objects. These investigations culminated
in the first contact with general relativity in 1939, when J. Robert
Oppenheimer and his students George Volkoff and Hartland Snyder systematically
applied the theory to the dense core of a collapsing neutron star. This
pioneering application of Einstein's theory to an astrophysical compact object
can be regarded as a milestone in the path eventually leading to the emergence
of relativistic astrophysics in the early 1960s.Comment: 83 pages, 4 figures, submitted to the European Physical Journal
- …