410 research outputs found
Image patch analysis and clustering of sunspots: a dimensionality reduction approach
Sunspots, as seen in white light or continuum images, are associated with
regions of high magnetic activity on the Sun, visible on magnetogram images.
Their complexity is correlated with explosive solar activity and so classifying
these active regions is useful for predicting future solar activity. Current
classification of sunspot groups is visually based and suffers from bias.
Supervised learning methods can reduce human bias but fail to optimally
capitalize on the information present in sunspot images. This paper uses two
image modalities (continuum and magnetogram) to characterize the spatial and
modal interactions of sunspot and magnetic active region images and presents a
new approach to cluster the images. Specifically, in the framework of image
patch analysis, we estimate the number of intrinsic parameters required to
describe the spatial and modal dependencies, the correlation between the two
modalities and the corresponding spatial patterns, and examine the phenomena at
different scales within the images. To do this, we use linear and nonlinear
intrinsic dimension estimators, canonical correlation analysis, and
multiresolution analysis of intrinsic dimension.Comment: 5 pages, 7 figures, accepted to ICIP 201
Image patch analysis of sunspots and active regions. II. Clustering via matrix factorization
Separating active regions that are quiet from potentially eruptive ones is a
key issue in Space Weather applications. Traditional classification schemes
such as Mount Wilson and McIntosh have been effective in relating an active
region large scale magnetic configuration to its ability to produce eruptive
events. However, their qualitative nature prevents systematic studies of an
active region's evolution for example. We introduce a new clustering of active
regions that is based on the local geometry observed in Line of Sight
magnetogram and continuum images. We use a reduced-dimension representation of
an active region that is obtained by factoring the corresponding data matrix
comprised of local image patches. Two factorizations can be compared via the
definition of appropriate metrics on the resulting factors. The distances
obtained from these metrics are then used to cluster the active regions. We
find that these metrics result in natural clusterings of active regions. The
clusterings are related to large scale descriptors of an active region such as
its size, its local magnetic field distribution, and its complexity as measured
by the Mount Wilson classification scheme. We also find that including data
focused on the neutral line of an active region can result in an increased
correspondence between our clustering results and other active region
descriptors such as the Mount Wilson classifications and the value. We
provide some recommendations for which metrics, matrix factorization
techniques, and regions of interest to use to study active regions.Comment: Accepted for publication in the Journal of Space Weather and Space
Climate (SWSC). 33 pages, 12 figure
Image patch analysis of sunspots and active regions. I. Intrinsic dimension and correlation analysis
The flare-productivity of an active region is observed to be related to its
spatial complexity. Mount Wilson or McIntosh sunspot classifications measure
such complexity but in a categorical way, and may therefore not use all the
information present in the observations. Moreover, such categorical schemes
hinder a systematic study of an active region's evolution for example. We
propose fine-scale quantitative descriptors for an active region's complexity
and relate them to the Mount Wilson classification. We analyze the local
correlation structure within continuum and magnetogram data, as well as the
cross-correlation between continuum and magnetogram data. We compute the
intrinsic dimension, partial correlation, and canonical correlation analysis
(CCA) of image patches of continuum and magnetogram active region images taken
from the SOHO-MDI instrument. We use masks of sunspots derived from continuum
as well as larger masks of magnetic active regions derived from the magnetogram
to analyze separately the core part of an active region from its surrounding
part. We find the relationship between complexity of an active region as
measured by Mount Wilson and the intrinsic dimension of its image patches.
Partial correlation patterns exhibit approximately a third-order Markov
structure. CCA reveals different patterns of correlation between continuum and
magnetogram within the sunspots and in the region surrounding the sunspots.
These results also pave the way for patch-based dictionary learning with a view
towards automatic clustering of active regions.Comment: Accepted for publication in the Journal of Space Weather and Space
Climate (SWSC). 23 pages, 11 figure
Working with the homeless: The case of a non-profit organisation in Shanghai
This article addresses a two-pronged objective, namely to bring to the fore a much neglected social issue of homelessness, and to explore the dynamics of state-society relations in contemporary China, through a case study of a non-profit organisation (NPO) working with the homeless in Shanghai. It shows that the largely invisible homelessness in Chinese cities was substantially due to exclusionary institutions, such as the combined household registration and 'detention and deportation' systems. Official policy has become much more supportive since 2003 when the latter was replaced with government-run shelters, but we argue that the NPO case demonstrates the potential for enhanced longer-term support and enabling active citizenship for homeless people. By analysing the ways in which the NPO offers services through collaboration and partnership with the public (and private) actors, we also argue that the transformations in postreform China and the changes within the state and civil society have significantly blurred their boundaries, rendering state-society relations much more complex, dynamic, fluid and mutually embedded
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of file formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open XML file formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, and Waters Q-TOF instruments, and searched in turn using SEQUEST, Mascot, and COMET
Deriving a multivariate CO-to-H conversion function using the [CII]/CO(1-0) ratio and its application to molecular gas scaling relations
We present Herschel PACS observations of the [CII] 158 micron emission line
in a sample of 24 intermediate mass (9<logM/M<10) and low
metallicity (0.4< Z/Z<1.0) galaxies from the xCOLD GASS survey.
Combining them with IRAM CO(1-0) measurements, we establish scaling relations
between integrated and molecular region [CII]/CO(1-0) luminosity ratios as a
function of integrated galaxy properties. A Bayesian analysis reveals that only
two parameters, metallicity and offset from the star formation main sequence,
MS, are needed to quantify variations in the luminosity ratio;
metallicity describes the total dust content available to shield CO from UV
radiation, while MS describes the strength of this radiation field. We
connect the [CII]/CO luminosity ratio to the CO-to-H conversion factor and
find a multivariate conversion function , which can be used up to
z~2.5. This function depends primarily on metallicity, with a second order
dependence on MS. We apply this to the full xCOLD GASS and PHIBSS1
surveys and investigate molecular gas scaling relations. We find a flattening
of the relation between gas mass fraction and stellar mass at
logM/M<10. While the molecular gas depletion time varies with
sSFR, it is mostly independent of mass, indicating that the low L/SFR
ratios long observed in low mass galaxies are entirely due to photodissociation
of CO, and not to an enhanced star formation efficiency.Comment: Submitted to MNRAS, this version after referee comments. 21 page
The intestinal expulsion of the roundworm Ascaris suum is associated with eosinophils, intra-epithelial T cells and decreased intestinal transit time
Ascaris lumbricoides remains the most common endoparasite in humans, yet there is still very little information available about the immunological principles of protection, especially those directed against larval stages. Due to the natural host-parasite relationship, pigs infected with A. suum make an excellent model to study the mechanisms of protection against this nematode. In pigs, a self-cure reaction eliminates most larvae from the small intestine between 14 and 21 days post infection. In this study, we investigated the mucosal immune response leading to the expulsion of A. suum and the contribution of the hepato-tracheal migration. Self-cure was independent of previous passage through the liver or lungs, as infection with lung stage larvae did not impair self-cure. When animals were infected with 14-day-old intestinal larvae, the larvae were being driven distally in the small intestine around 7 days post infection but by 18 days post infection they re-inhabited the proximal part of the small intestine, indicating that more developed larvae can counter the expulsion mechanism. Self-cure was consistently associated with eosinophilia and intra-epithelial T cells in the jejunum. Furthermore, we identified increased gut movement as a possible mechanism of self-cure as the small intestinal transit time was markedly decreased at the time of expulsion of the worms. Taken together, these results shed new light on the mechanisms of self-cure that occur during A. suum infections
MicroRNAs targeting oncogenes are down-regulated in pancreatic malignant transformation from benign tumors
BACKGROUND
MicroRNA (miRNA) expression profiles have been described in pancreatic ductal adenocarcinoma (PDAC), but these have not been compared with pre-malignant pancreatic tumors. We wished to compare the miRNA expression signatures in pancreatic benign cystic tumors (BCT) of low and high malignant potential with PDAC, in order to identify miRNAs deregulated during PDAC development. The mechanistic consequences of miRNA dysregulation were further evaluated.
METHODS
Tissue samples were obtained at a tertiary pancreatic unit from individuals with BCT and PDAC. MiRNA profiling was performed using a custom microarray and results were validated using RT-qPCR prior to evaluation of miRNA targets.
RESULTS
Widespread miRNA down-regulation was observed in PDAC compared to low malignant potential BCT. We show that amongst those miRNAs down-regulated, miR-16, miR-126 and let-7d regulate known PDAC oncogenes (targeting BCL2, CRK and KRAS respectively). Notably, miR-126 also directly targets the KRAS transcript at a "seedless" binding site within its 3'UTR. In clinical specimens, miR-126 was strongly down-regulated in PDAC tissues, with an associated elevation in KRAS and CRK proteins. Furthermore, miR-21, a known oncogenic miRNA in pancreatic and other cancers, was not elevated in PDAC compared to serous microcystic adenoma (SMCA), but in both groups it was up-regulated compared to normal pancreas, implicating early up-regulation during malignant change.
CONCLUSIONS
Expression profiling revealed 21 miRNAs down-regulated in PDAC compared to SMCA, the most benign lesion that rarely progresses to invasive carcinoma. It appears that miR-21 up-regulation is an early event in the transformation from normal pancreatic tissue. MiRNA expression has the potential to distinguish PDAC from normal pancreas and BCT. Mechanistically the down-regulation of miR-16, miR-126 and let-7d promotes PDAC transformation by post-transcriptional up-regulation of crucial PDAC oncogenes. We show that miR-126 is able to directly target KRAS; re-expression has the potential as a therapeutic strategy against PDAC and other KRAS-driven cancers
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