897 research outputs found
Co-option of a coordinate system defined by the EGFr and Dpp pathways in the evolution of a morphological novelty
Morphological innovation is an elusive and fascinating concept in evolutionary biology. A novel structure may open up an array of possibilities for adaptation, and thus is fundamental to the evolution of complex multicellular life. We use the respiratory appendages on the dorsal-anterior side of the Drosophila eggshell as a model system for morphological novelty. To study the co-option of genetic pathways in the evolution of this novelty we have compared oogenesis and eggshell patterning in Drosophila melanogaster with Ceratitis capitata, a dipteran whose eggs do not bear dorsal appendages.FCT fellowship: (SFRH/BD/33216/2007), Collaborative Research Centre 680 ‘Molecular Basis of Evolutionary Innovations (DFG grant), Fundação Calouste Gulbenkian, Instituto Gulbenkian de Ciência
Panchromatic Imaging of a Transitional Disk: The Disk of GM Aur in Optical and FUV Scattered Light
We have imaged GM Aur with HST, detected its disk in scattered light at 1400A
and 1650A, and compared these with observations at 3300A, 5550A, 1.1 microns,
and 1.6 microns. The scattered light increases at shorter wavelengths. The
radial surface brightness profile at 3300A shows no evidence of the 24AU radius
cavity that has been previously observed in sub-mm observations. Comparison
with dust grain opacity models indicates the surface of the entire disk is
populated with sub-micron grains. We have compiled an SED from 0.1 microns to 1
mm, and used it to constrain a model of the star+disk system that includes the
sub-mm cavity using the Monte Carlo Radiative Transfer code by Barbara Whitney.
The best-fit model image indicates that the cavity should be detectable in the
F330W bandpass if the cavity has been cleared of both large and small dust
grains, but we do not detect it. The lack of an observed cavity can be
explained by the presence of sub-microns grains interior to the sub-mm cavity
wall. We suggest one explanation for this which could be due to a planet of
mass <9 Jupiter masses interior to 24 AU. A unique cylindrical structure is
detected in the FUV data from the Advanced Camera for Surveys/Solar Blind
Channel. It is aligned along the system semi-minor axis, but does not resemble
an accretion-driven jet. The structure is limb-brightened and extends 190 +/-
35 AU above the disk midplane. The inner radius of the limb-brightening is 40
+/- 10 AU, just beyond the sub-millimeter cavity wall.Comment: 40 pages, 11 figures, 4 tables, accepted to Ap
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.
Illumina BeadArrays are among the most popular and reliable platforms for gene expression profiling. However, little external scrutiny has been given to the design, selection and annotation of BeadArray probes, which is a fundamental issue in data quality and interpretation. Here we present a pipeline for the complete genomic and transcriptomic re-annotation of Illumina probe sequences, also applicable to other platforms, with its output available through a Web interface and incorporated into Bioconductor packages. We have identified several problems with the design of individual probes and we show the benefits of probe re-annotation on the analysis of BeadArray gene expression data sets. We discuss the importance of aspects such as probe coverage of individual transcripts, alternative messenger RNA splicing, single-nucleotide polymorphisms, repeat sequences, RNA degradation biases and probes targeting genomic regions with no known transcription. We conclude that many of the Illumina probes have unreliable original annotation and that our re-annotation allows analyses to focus on the good quality probes, which form the majority, and also to expand the scope of biological information that can be extracted
A double ovulation protocol for Xenopus laevis produces doubled fertilisation yield and moderately transiently elevated corticosterone levels without loss of egg quality
The African claw-toed frog, Xenopus laevis, is a well-established laboratory model for the biology of vertebrate oogenesis, fertilisation, and development at embryonic, larval, and metamorphic stages. For ovulation, X. laevis females are usually injected with chorionic gonadotropin, whereupon they lay typically hundreds to thousands of eggs in a day. After being rested for a minimum of three months, animals are re-used. The literature suggests that adult females can lay much larger numbers of eggs in a short period. Here, we compared the standard “single ovulation” protocol with a “double ovulation” protocol, in which females were ovulated, then re-ovulated after seven days and then rested for three months before re-use. We quantified egg number, fertilisation rate (development to cleavage stage), and corticosterone secretion rate as a measure of stress response for the two protocol groups over seven 3-month cycles. We found no differences in egg number-per-ovulation or egg quality between the groups and no long-term changes in any measures over the 21-month trial period. Corticosterone secretion was elevated by ovulation, similarly for the single ovulation as for the first ovulation in the double-ovulation protocol, but more highly for the second ovulation (to a level comparable to that seen following shipment) in the latter. However, both groups exhibited the same baseline secretion rates by the time of the subsequent cycle. Double ovulation is thus transiently more stressful/demanding than single ovulation but within the levels routinely experienced by laboratory X. laevis. Noting that “stress hormone” corticosterone/cortisol secretion is linked to physiological processes, such as ovulation, that are not necessarily harmful to the individual, we suggest that the benefits of a doubling in egg yield-per-cycle per animal without loss of egg quality or signs of acute or long-term harm may outweigh the relatively modest and transient corticosterone elevation we observed. The double ovulation protocol therefore represents a potential new standard practice for promoting the “3Rs” (animal use reduction, refinement and replacement) mission for Xenopus research
Accurate brain-age models for routine clinical MRI examinations
Convolutional neural networks (CNN) can accurately predict chronological age in healthy individuals from structural MRI brain scans. Potentially, these models could be applied during routine clinical examinations to detect deviations from healthy ageing, including early-stage neurodegeneration. This could have important implications for patient care, drug development, and optimising MRI data collection. However, existing brain-age models are typically optimised for scans which are not part of routine examinations (e.g., volumetric T1-weighted scans), generalise poorly (e.g., to data from different scanner vendors and hospitals etc.), or rely on computationally expensive pre-processing steps which limit real-time clinical utility. Here, we sought to develop a brain-age framework suitable for use during routine clinical head MRI examinations. Using a deep learning-based neuroradiology report classifier, we generated a dataset of 23,302 'radiologically normal for age' head MRI examinations from two large UK hospitals for model training and testing (age range = 18-95 years), and demonstrate fast (< 5 seconds), accurate (mean absolute error [MAE] < 4 years) age prediction from clinical-grade, minimally processed axial T2-weighted and axial diffusion-weighted scans, with generalisability between hospitals and scanner vendors (Δ MAE < 1 year). The clinical relevance of these brain-age predictions was tested using 228 patients whose MRIs were reported independently by neuroradiologists as showing atrophy 'excessive for age'. These patients had systematically higher brain-predicted age than chronological age (mean predicted age difference = +5.89 years, 'radiologically normal for age' mean predicted age difference = +0.05 years, p < 0.0001). Our brain-age framework demonstrates feasibility for use as a screening tool during routine hospital examinations to automatically detect older-appearing brains in real-time, with relevance for clinical decision-making and optimising patient pathways.</p
Automated triaging of head MRI examinations using convolutional neural networks
The growing demand for head magnetic resonance imaging (MRI) examinations,
along with a global shortage of radiologists, has led to an increase in the
time taken to report head MRI scans around the world. For many neurological
conditions, this delay can result in increased morbidity and mortality. An
automated triaging tool could reduce reporting times for abnormal examinations
by identifying abnormalities at the time of imaging and prioritizing the
reporting of these scans. In this work, we present a convolutional neural
network for detecting clinically-relevant abnormalities in
-weighted head MRI scans. Using a validated neuroradiology report
classifier, we generated a labelled dataset of 43,754 scans from two large UK
hospitals for model training, and demonstrate accurate classification (area
under the receiver operating curve (AUC) = 0.943) on a test set of 800 scans
labelled by a team of neuroradiologists. Importantly, when trained on scans
from only a single hospital the model generalized to scans from the other
hospital (AUC 0.02). A simulation study demonstrated that our
model would reduce the mean reporting time for abnormal examinations from 28
days to 14 days and from 9 days to 5 days at the two hospitals, demonstrating
feasibility for use in a clinical triage environment.Comment: Accepted as an oral presentation at Medical Imaging with Deep
Learning (MIDL) 202
Labelling imaging datasets on the basis of neuroradiology reports: a validation study
Natural language processing (NLP) shows promise as a means to automate the
labelling of hospital-scale neuroradiology magnetic resonance imaging (MRI)
datasets for computer vision applications. To date, however, there has been no
thorough investigation into the validity of this approach, including
determining the accuracy of report labels compared to image labels as well as
examining the performance of non-specialist labellers. In this work, we draw on
the experience of a team of neuroradiologists who labelled over 5000 MRI
neuroradiology reports as part of a project to build a dedicated deep
learning-based neuroradiology report classifier. We show that, in our
experience, assigning binary labels (i.e. normal vs abnormal) to images from
reports alone is highly accurate. In contrast to the binary labels, however,
the accuracy of more granular labelling is dependent on the category, and we
highlight reasons for this discrepancy. We also show that downstream model
performance is reduced when labelling of training reports is performed by a
non-specialist. To allow other researchers to accelerate their research, we
make our refined abnormality definitions and labelling rules available, as well
as our easy-to-use radiology report labelling app which helps streamline this
process
Swift X-Ray Observations of Classical Novae. II. The Super Soft Source sample
The Swift GRB satellite is an excellent facility for studying novae. Its
rapid response time and sensitive X-ray detector provides an unparalleled
opportunity to investigate the previously poorly sampled evolution of novae in
the X-ray regime. This paper presents Swift observations of 52
Galactic/Magellanic Cloud novae. We included the XRT (0.3-10 keV) X-ray
instrument count rates and the UVOT (1700-8000 Angstroms) filter photometry.
Also included in the analysis are the publicly available pointed observations
of 10 additional novae the X-ray archives. This is the largest X-ray sample of
Galactic/Magellanic Cloud novae yet assembled and consists of 26 novae with
super soft X-ray emission, 19 from Swift observations. The data set shows that
the faster novae have an early hard X-ray phase that is usually missing in
slower novae. The Super Soft X-ray phase occurs earlier and does not last as
long in fast novae compared to slower novae. All the Swift novae with
sufficient observations show that novae are highly variable with rapid
variability and different periodicities. In the majority of cases, nuclear
burning ceases less than 3 years after the outburst begins. Previous
relationships, such as the nuclear burning duration vs. t_2 or the expansion
velocity of the eject and nuclear burning duration vs. the orbital period, are
shown to be poorly correlated with the full sample indicating that additional
factors beyond the white dwarf mass and binary separation play important roles
in the evolution of a nova outburst. Finally, we confirm two optical phenomena
that are correlated with strong, soft X-ray emission which can be used to
further increase the efficiency of X-ray campaigns.Comment: Accepted to ApJ Supplements. Full data for Table 2 and Figure 17
available in the electronic edition. New version of the previously posted
paper since the earlier version was all set in landscape mod
A double ovulation protocol for Xenopus laevis produces doubled fertilisation yield and moderately transiently elevated corticosterone levels without loss of egg quality
The African claw-toed frog, Xenopus laevis, is a well-established laboratory model for the biology of vertebrate oogenesis, fertilisation, and development at embryonic, larval, and metamorphic stages. For ovulation, X. laevis females are usually injected with chorionic gonadotropin, whereupon they lay typically hundreds to thousands of eggs in a day. After being rested for a minimum of three months, animals are re-used. The literature suggests that adult females can lay much larger numbers of eggs in a short period. Here, we compared the standard “single ovulation” protocol with a “double ovulation” protocol, in which females were ovulated, then re-ovulated after seven days and then rested for three months before re-use. We quantified egg number, fertilisation rate (development to cleavage stage), and corticosterone secretion rate as a measure of stress response for the two protocol groups over seven 3-month cycles. We found no differences in egg number-per-ovulation or egg quality between the groups and no long-term changes in any measures over the 21-month trial period. Corticosterone secretion was elevated by ovulation, similarly for the single ovulation as for the first ovulation in the double-ovulation protocol, but more highly for the second ovulation (to a level comparable to that seen following shipment) in the latter. However, both groups exhibited the same baseline secretion rates by the time of the subsequent cycle. Double ovulation is thus transiently more stressful/demanding than single ovulation but within the levels routinely experienced by laboratory X. laevis. Noting that “stress hormone” corticosterone/cortisol secretion is linked to physiological processes, such as ovulation, that are not necessarily harmful to the individual, we suggest that the benefits of a doubling in egg yield-per-cycle per animal without loss of egg quality or signs of acute or long-term harm may outweigh the relatively modest and transient corticosterone elevation we observed. The double ovulation protocol therefore represents a potential new standard practice for promoting the “3Rs” (animal use reduction, refinement and replacement) mission for Xenopus research.N/
The Phylogenetic Origin of oskar Coincided with the Origin of Maternally Provisioned Germ Plasm and Pole Cells at the Base of the Holometabola
The establishment of the germline is a critical, yet surprisingly evolutionarily
labile, event in the development of sexually reproducing animals. In the fly
Drosophila, germ cells acquire their fate early during
development through the inheritance of the germ plasm, a specialized maternal
cytoplasm localized at the posterior pole of the oocyte. The gene
oskar (osk) is both necessary and
sufficient for assembling this substance. Both maternal germ plasm and
oskar are evolutionary novelties within the insects, as the
germline is specified by zygotic induction in basally branching insects, and
osk has until now only been detected in dipterans. In order
to understand the origin of these evolutionary novelties, we used comparative
genomics, parental RNAi, and gene expression analyses in multiple insect
species. We have found that the origin of osk and its role in
specifying the germline coincided with the innovation of maternal germ plasm and
pole cells at the base of the holometabolous insects and that losses of
osk are correlated with changes in germline determination
strategies within the Holometabola. Our results indicate that the invention of
the novel gene osk was a key innovation that allowed the
transition from the ancestral late zygotic mode of germline induction to a
maternally controlled establishment of the germline found in many holometabolous
insect species. We propose that the ancestral role of osk was
to connect an upstream network ancestrally involved in mRNA localization and
translational control to a downstream regulatory network ancestrally involved in
executing the germ cell program
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