97 research outputs found
IR-correlated 31 GHz radio emission from Orion East
Lynds dark cloud LDN1622 represents one of the best examples of anomalous
dust emission, possibly originating from small spinning dust grains. We present
Cosmic Background Imager (CBI) 31 GHz data of LDN1621, a diffuse dark cloud to
the north of LDN1622 in a region known as Orion East. A broken ring with
diameter g\approx 20 arcmin of diffuse emission is detected at 31 GHz, at
\approx 20-30 mJy beam with an angular resolution of \approx 5 arcmin.
The ring-like structure is highly correlated with Far Infra-Red emission at
m with correlation coefficients of r \approx 0.7-0.8, significant
at . Multi-frequency data are used to place constraints on other
components of emission that could be contributing to the 31 GHz flux. An
analysis of the GB6 survey maps at 4.85 GHz yields a upper limit on
free-free emission of 7.2 mJy beam (\la 30 per cent of the observed
flux) at the CBI resolution. The bulk of the 31 GHz flux therefore appears to
be mostly due to dust radiation. Aperture photometry, at an angular resolution
of 13 arcmin and with an aperture of diameter 30 arcmin, allowed the use of
IRAS maps and the {\it WMAP} 5-year W-band map at 93.5 GHz. A single modified
blackbody model was fitted to the data to estimate the contribution from
thermal dust, which amounts to \sim\sim100 \mu18.1\pm4.4 \mu^{-1}$, consistent with the values found for
LDN1622.Comment: 8 pages, 3 figures, 3 tables, submitted to MNRA
Follow-up observations at 16 and 33 GHz of extragalactic sources from WMAP 3-year data: I - Spectral properties
We present follow-up observations of 97 point sources from the Wilkinson
Microwave Anisotropy Probe (WMAP) 3-year data, contained within the New
Extragalactic WMAP Point Source (NEWPS) catalogue between declinations of -4
and +60 degrees; the sources form a flux-density-limited sample complete to 1.1
Jy (approximately 5 sigma) at 33 GHz. Our observations were made at 16 GHz
using the Arcminute Microkelvin Imager (AMI) and at 33 GHz with the Very Small
Array (VSA). 94 of the sources have reliable, simultaneous -- typically a few
minutes apart -- observations with both telescopes. The spectra between 13.9
and 33.75 GHz are very different from those of bright sources at low frequency:
44 per cent have rising spectra (alpha < 0.0), where flux density is
proportional to frequency^-alpha, and 93 per cent have spectra with alpha <
0.5; the median spectral index is 0.04. For the brighter sources, the agreement
between VSA and WMAP 33-GHz flux densities averaged over sources is very good.
However, for the fainter sources, the VSA tends to measure lower values for the
flux densities than WMAP. We suggest that the main cause of this effect is
Eddington bias arising from variability.Comment: 12 pages, 13 figures, submitted to MNRA
Functional polymorphisms in the promoter regions of MMP2 and MMP3 are not associated with melanoma progression
<p>Abstract</p> <p>Background</p> <p>The matrix metalloproteinases (MMPs) are enzymes that cleave various components of the extracellular matrix (ECM) and basement membranes. MMPs are expressed in melanocytes and their overexpression has been linked to tumor development, progression and metastasis. At the genetic level, the following functional promoter polymorphisms are known to modify the gene transcription: -1306 C/T and -735 C/T in the MMP2 gene, and -1171 5A/6A in the MMP3 gene. Functional polymorphisms in MMP genes' promoter regions may modulate the risk for melanoma progression.</p> <p>Methods</p> <p>We evaluated MMP2 and MMP3 germline polymorphisms in a group of 1002 melanoma patients using PCR-based methods, including fragment size analysis and melting temperature profiles. Two-sided Chi-Square, Cochran-Armitage tests for trend, Fisher's exact tests, and Kendall's Tau tests were performed to evaluate the associations between genotype and various clinical and epidemiologic factors. Multivariate analyses were conducted using logistic regression, adjusting for known melanoma confounders such as age, sex, phenotypic index, moles, freckles, and race. Survival estimates were computed using the Kaplan-Meier method and differences in survival were assessed using the log rank test.</p> <p>Results</p> <p>All genotypes were in Hardy-Weinberg equilibrium. After adjustment for age, sex and phenotypic characteristics of melanoma risk, no significant associations were identified with the clinical, pathological, and epidemiological variables studied. The melting profile for MMP2 -735 C/T identified a new change in one sample. A new PCR-amplification followed by direct sequencing confirmed a heterozygote G to A substitution at position -729.</p> <p>Conclusion</p> <p>This study does not provide strong evidence for further investigation into the role of the MMP2 and MMP3 variants in melanoma progression.</p
A systematic review of the impacts and management of introduced deer (family Cervidae) in Australia
MHC-IIB Filament Assembly and Cellular Localization Are Governed by the Rod Net Charge
Actin-dependent myosin II molecular motors form an integral part of the cell cytoskeleton. Myosin II molecules contain a long coiled-coil rod that mediates filament assembly required for myosin II to exert its full activity. The exact mechanisms orchestrating filament assembly are not fully understood., negatively-charged regions of the coiled-coil were found to play an important role by controlling the intracellular localization of native MHC-IIB. The entire positively-charged region is also important for intracellular localization of native MHC-IIB.A correct distribution of positive and negative charges along myosin II rod is a necessary component in proper filament assembly and intracellular localization of MHC-IIB
One Is Enough: In Vivo Effective Population Size Is Dose-Dependent for a Plant RNA Virus
Effective population size (Ne) determines the strength of genetic drift and the frequency of co-infection by multiple genotypes, making it a key factor in viral evolution. Experimental estimates of Ne for different plant viruses have, however, rendered diverging results. The independent action hypothesis (IAH) states that each virion has a probability of infection, and that virions act independent of one another during the infection process. A corollary of IAH is that Ne must be dose dependent. A test of IAH for a plant virus has not been reported yet. Here we perform a test of an IAH infection model using a plant RNA virus, Tobacco etch virus (TEV) variants carrying GFP or mCherry fluorescent markers, in Nicotiana tabacum and Capsicum annuum plants. The number of primary infection foci increased linearly with dose, and was similar to a Poisson distribution. At high doses, primary infection foci containing both genotypes were found at a low frequency (<2%). The probability that a genotype that infected the inoculated leaf would systemically infect that plant was near 1, although in a few rare cases genotypes could be trapped in the inoculated leaf by being physically surrounded by the other genotype. The frequency of mixed-genotype infection could be predicted from the mean number of primary infection foci using the independent-action model. Independent action appears to hold for TEV, and Ne is therefore dose-dependent for this plant RNA virus. The mean number of virions causing systemic infection can be very small, and approaches 1 at low doses. Dose-dependency in TEV suggests that comparison of Ne estimates for different viruses are not very meaningful unless dose effects are taken into consideration
Matrix Metalloproteinase-9 (MMP-9) polymorphisms in patients with cutaneous malignant melanoma
BACKGROUND: Cutaneous Malignant Melanoma causes over 75% of skin cancer-related deaths, and it is clear that many factors may contribute to the outcome. Matrix Metalloproteinases (MMPs) play an important role in the degradation and remodeling of the extracellular matrix and basement membrane that, in turn, modulate cell division, migration and angiogenesis. Some polymorphisms are known to influence gene expression, protein activity, stability, and interactions, and they were shown to be associated with certain tumor phenotypes and cancer risk. METHODS: We tested seven polymorphisms within the MMP-9 gene in 1002 patients with melanoma in order to evaluate germline genetic variants and their association with progression and known risk factors of melanoma. The polymorphisms were selected based on previously published reports and their known or potential functional relevance using in-silico methods. Germline DNA was then genotyped using pyrosequencing, melting temperature profiles, heteroduplex analysis, and fragment size analysis. RESULTS: We found that reference alleles were present in higher frequency in patients who tend to sunburn, have family history of melanoma, higher melanoma stage, intransit metastasis and desmoplastic melanomas among others. However, after adjustment for age, sex, phenotypic index, moles, and freckles only Q279R, P574R and R668Q had significant associations with intransit metastasis, propensity to tan/sunburn and primary melanoma site. CONCLUSION: This study does not provide strong evidence for further investigation into the role of the MMP-9 SNPs in melanoma progression
Dust-correlated cm-wavelength continuum emission on translucent clouds {\zeta} Oph and LDN 1780
The diffuse cm-wave IR-correlated signal, the "anomalous" CMB foreground, is
thought to arise in the dust in cirrus clouds. We present Cosmic Background
Imager (CBI) cm-wave data of two translucent clouds, {\zeta} Oph and LDN 1780
with the aim of characterising the anomalous emission in the translucent cloud
environment. In {\zeta} Oph, the measured brightness at 31 GHz is 2.4{\sigma}
higher than an extrapolation from 5 GHz measurements assuming a free-free
spectrum on 8 arcmin scales. The SED of this cloud on angular scales of
1{\odot} is dominated by free-free emission in the cm-range. In LDN 1780 we
detected a 3 {\sigma} excess in the SED on angular scales of 1{\odot} that can
be fitted using a spinning dust model. In this cloud, there is a spatial
correlation between the CBI data and IR images, which trace dust. The
correlation is better with near-IR templates (IRAS 12 and 25 {\mu}m) than with
IRAS 100 {\mu}m, which suggests a very small grain origin for the emission at
31 GHz. We calculated the 31 GHz emissivities in both clouds. They are similar
and have intermediate values between that of cirrus clouds and dark clouds.
Nevertheless, we found an indication of an inverse relationship between
emissivity and column density, which further supports the VSGs origin for the
cm-emission since the proportion of big relative to small grains is smaller in
diffuse clouds.Comment: 13 pages, 14 figures, 7 tables. Accepted for publication in MNRA
Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases
BACKGROUND: Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25–30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome. METHODS: We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants. RESULTS: Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving. CONCLUSIONS: Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing
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