1,278 research outputs found
Local rewiring of genome-nuclear lamina interactions by transcription
Transcriptionally inactive genes are often positioned at the nuclear lamina (NL), as part of large lamina-associated domains (LADs). Activation of such genes is often accompanied by repositioning toward the nuclear interior. How this process works and how it impacts flanking chromosomal regions are poorly understood. We addressed these questions by systematic activation or inactivation of individual genes, followed by detailed genome-wide analysis of NL interactions, replication timing, and transcription patterns. Gene activation inside LADs typically causes NL detachment of the entire transcription unit, but rarely more than 50-100Â kb of flanking DNA, even when multiple neighboring genes are activated. The degree of detachment depends on the expression level and the length of the activated gene. Loss of NL interactions coincides with a switch from late to early replication timing, but the latter can involve longer stretches of DNA. Inactivation of active genes can lead to increased NL contacts. These extensive datasets are a resource for the analysis of LAD rewiring by transcription and reveal a remarkable flexibility of interphase chromosomes
Large-scale Bright Fronts in the Solar Corona: A Review of "EIT waves"
``EIT waves" are large-scale coronal bright fronts (CBFs) that were first
observed in 195 \AA\ images obtained using the Extreme-ultraviolet Imaging
Telescope (EIT) onboard the \emph{Solar and Heliospheric Observatory (SOHO)}.
Commonly called ``EIT waves", CBFs typically appear as diffuse fronts that
propagate pseudo-radially across the solar disk at velocities of 100--700 km
s with front widths of 50-100 Mm. As their speed is greater than the
quiet coronal sound speed (200 km s) and comparable to the
local Alfv\'{e}n speed (1000 km s), they were initially
interpreted as fast-mode magnetoacoustic waves ().
Their propagation is now known to be modified by regions where the magnetosonic
sound speed varies, such as active regions and coronal holes, but there is also
evidence for stationary CBFs at coronal hole boundaries. The latter has led to
the suggestion that they may be a manifestation of a processes such as Joule
heating or magnetic reconnection, rather than a wave-related phenomena. While
the general morphological and kinematic properties of CBFs and their
association with coronal mass ejections have now been well described, there are
many questions regarding their excitation and propagation. In particular, the
theoretical interpretation of these enigmatic events as magnetohydrodynamic
waves or due to changes in magnetic topology remains the topic of much debate.Comment: 34 pages, 19 figure
On the Nature and Genesis of EUV Waves: A Synthesis of Observations from SOHO, STEREO, SDO, and Hinode
A major, albeit serendipitous, discovery of the SOlar and Heliospheric
Observatory mission was the observation by the Extreme Ultraviolet Telescope
(EIT) of large-scale Extreme Ultraviolet (EUV) intensity fronts propagating
over a significant fraction of the Sun's surface. These so-called EIT or EUV
waves are associated with eruptive phenomena and have been studied intensely.
However, their wave nature has been challenged by non-wave (or pseudo-wave)
interpretations and the subject remains under debate. A string of recent solar
missions has provided a wealth of detailed EUV observations of these waves
bringing us closer to resolving their nature. With this review, we gather the
current state-of-art knowledge in the field and synthesize it into a picture of
an EUV wave driven by the lateral expansion of the CME. This picture can
account for both wave and pseudo-wave interpretations of the observations, thus
resolving the controversy over the nature of EUV waves to a large degree but
not completely. We close with a discussion of several remaining open questions
in the field of EUV waves research.Comment: Solar Physics, Special Issue "The Sun in 360",2012, accepted for
publicatio
Physics of Solar Prominences: II - Magnetic Structure and Dynamics
Observations and models of solar prominences are reviewed. We focus on
non-eruptive prominences, and describe recent progress in four areas of
prominence research: (1) magnetic structure deduced from observations and
models, (2) the dynamics of prominence plasmas (formation and flows), (3)
Magneto-hydrodynamic (MHD) waves in prominences and (4) the formation and
large-scale patterns of the filament channels in which prominences are located.
Finally, several outstanding issues in prominence research are discussed, along
with observations and models required to resolve them.Comment: 75 pages, 31 pictures, review pape
What is the Nature of EUV Waves? First STEREO 3D Observations and Comparison with Theoretical Models
One of the major discoveries of the Extreme ultraviolet Imaging Telescope
(EIT) on SOHO were intensity enhancements propagating over a large fraction of
the solar surface. The physical origin(s) of the so-called `EIT' waves is still
strongly debated. They are considered to be either wave (primarily fast-mode
MHD waves) or non-wave (pseudo-wave) interpretations. The difficulty in
understanding the nature of EUV waves lies with the limitations of the EIT
observations which have been used almost exclusively for their study. Their
limitations are largely overcome by the SECCHI/EUVI observations on-board the
STEREO mission. The EUVI telescopes provide high cadence, simultaneous
multi-temperature coverage, and two well-separated viewpoints. We present here
the first detailed analysis of an EUV wave observed by the EUVI disk imagers on
December 07, 2007 when the STEREO spacecraft separation was .
Both a small flare and a CME were associated with the wave cadence, and single
temperature and viewpoint coverage. These limitations are largely overcome by
the SECCHI/EUVI observations on-board the STEREO mission. The EUVI telescopes
provide high cadence, simultaneous multi-temperature coverage, and two
well-separated viewpoints. Our findings give significant support for a
fast-mode interpretation of EUV waves and indicate that they are probably
triggered by the rapid expansion of the loops associated with the CME.Comment: Solar Physics, 2009, Special STEREO Issue, in pres
Identifying genotype specific elevated-risk areas and associated herd risk factors for bovine tuberculosis spread in British cattle
Bovine tuberculosis (bTB) is a chronic zoonosis with major health and economic impact on the cattle industry. Despite extensive control measures in cattle and culling trials in wildlife, the reasons behind the expansion of areas with high incidence of bTB breakdowns in Great Britain remain unexplained. By balancing the importance of cattle movements and local transmission on the observed pattern of cattle outbreaks, we identify areas at elevated risk of infection from specific Mycobacterium bovis genotypes. We show that elevated-risk areas (ERAs) were historically more extensive than previously understood, and that cattle movements alone are insufficient for ERA spread, suggesting the involvement of other factors. For all genotypes, we find that, while the absolute risk of infection is higher in ERAs compared to areas with intermittent risk, the statistically significant risk factors are remarkably similar in both, suggesting that these risk factors can be used to identify incipient ERAs before this is indicated by elevated incidence alone. Our findings identify research priorities for understanding bTB dynamics, improving surveillance and guiding management to prevent further ERA expansion
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS
We present the results of a search for new, heavy particles that decay at a
significant distance from their production point into a final state containing
charged hadrons in association with a high-momentum muon. The search is
conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV
and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS
detector operating at the Large Hadron Collider. Production of such particles
is expected in various scenarios of physics beyond the standard model. We
observe no signal and place limits on the production cross-section of
supersymmetric particles in an R-parity-violating scenario as a function of the
neutralino lifetime. Limits are presented for different squark and neutralino
masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final
version to appear in Physics Letters
Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment
This paper describes an analysis of the angular distribution of W->enu and
W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with
the ATLAS detector at the LHC in 2010, corresponding to an integrated
luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and
the missing transverse energy, the W decay angular distribution projected onto
the transverse plane is obtained and analysed in terms of helicity fractions
f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV
and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw
> 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour,
are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017
+/- 0.030, where the first uncertainties are statistical, and the second
include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables,
revised author list, matches European Journal of Physics C versio
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