1,490 research outputs found
Hypernetwork functional image representation
Motivated by the human way of memorizing images we introduce their functional
representation, where an image is represented by a neural network. For this
purpose, we construct a hypernetwork which takes an image and returns weights
to the target network, which maps point from the plane (representing positions
of the pixel) into its corresponding color in the image. Since the obtained
representation is continuous, one can easily inspect the image at various
resolutions and perform on it arbitrary continuous operations. Moreover, by
inspecting interpolations we show that such representation has some properties
characteristic to generative models. To evaluate the proposed mechanism
experimentally, we apply it to image super-resolution problem. Despite using a
single model for various scaling factors, we obtained results comparable to
existing super-resolution methods
The WiFeS S7 AGN survey: Current status and recent results on NGC 6300
The Siding Spring Southern Seyfert Spectroscopic Snapshot Survey (S7) is a
targeted survey probing the narrow-line regions (NLRs) of a representative
sample of ~140 nearby (z<0.02) Seyfert galaxies by means of optical integral
field spectroscopy. The survey is based on a homogeneous data set observed
using the Wide Field Spectrograph WiFeS. The data provide a 25x38 arcsec
field-of-view around the galaxy centre at typically ~1.5 arcsec spatial
resolution and cover a wavelength range between ~3400 - 7100 at spectral
resolutions of ~100 km s and ~50 km s in the blue and red parts,
respectively. The survey is primarily designed to study gas excitation and star
formation around AGN, with a special focus on the shape of the AGN ionising
continuum, the interaction between radio jets and the NLR gas, and the nature
of nuclear LINER emission. We provide an overview of the current status of
S7-based results and present new results for NGC 6300.Comment: 5 pages, 1 figure, Refereed Proceeding of the "The Universe of
Digital Sky Surveys" conference held at the INAF - Observatory of
Capodimonte, Naples, on 25th-28th november 2014, to be published on
Astrophysics and Space Science Proceedings, edited by Longo, Napolitano,
Marconi, Paolillo, Iodic
Radio Galaxy Zoo: Machine learning for radio source host galaxy cross-identification
We consider the problem of determining the host galaxies of radio sources by
cross-identification. This has traditionally been done manually, which will be
intractable for wide-area radio surveys like the Evolutionary Map of the
Universe (EMU). Automated cross-identification will be critical for these
future surveys, and machine learning may provide the tools to develop such
methods. We apply a standard approach from computer vision to
cross-identification, introducing one possible way of automating this problem,
and explore the pros and cons of this approach. We apply our method to the 1.4
GHz Australian Telescope Large Area Survey (ATLAS) observations of the Chandra
Deep Field South (CDFS) and the ESO Large Area ISO Survey South 1 (ELAIS-S1)
fields by cross-identifying them with the Spitzer Wide-area Infrared
Extragalactic (SWIRE) survey. We train our method with two sets of data: expert
cross-identifications of CDFS from the initial ATLAS data release and
crowdsourced cross-identifications of CDFS from Radio Galaxy Zoo. We found that
a simple strategy of cross-identifying a radio component with the nearest
galaxy performs comparably to our more complex methods, though our estimated
best-case performance is near 100 per cent. ATLAS contains 87 complex radio
sources that have been cross-identified by experts, so there are not enough
complex examples to learn how to cross-identify them accurately. Much larger
datasets are therefore required for training methods like ours. We also show
that training our method on Radio Galaxy Zoo cross-identifications gives
comparable results to training on expert cross-identifications, demonstrating
the value of crowdsourced training data
Examining the Polymorphisms in the Hypoxia Pathway Genes in Relation to Outcome in Colorectal Cancer
Introduction
Colorectal cancer is a common malignancy. Identification of genetic prognostic markers may help prognostic estimations in colorectal cancer. Genes that regulate response to hypoxia and other genes that are regulated under the hypoxic conditions have been shown to play roles in cancer progression. In this study, we hypothesized that genetic variations in the hypoxia pathway genes were associated with the risk of outcome in colorectal cancer patients.
Methods
This study was performed in two phases. In the first phase, 49 SNPs from six hypoxia pathway genes (HIF1A, HIF1B, HIF2A, LOX, MIF and CXCL12) in 272 colorectal cancer patients were analyzed. In the second phase, 77 SNPs from seven hypoxia pathway genes (HIF1A, HIF1B, HIF2A, HIF2B, HIF3A, LOX and CXCL12) were analyzed in an additional cohort of 535 patients. Kaplan Meier, Cox univariate and multivariable regression analyses were performed to analyze the relationship between the SNPs and overall survival (OS), disease free survival (DFS) or disease specific survival (DSS). Since this was a hypothesis-generating study, no correction for multiple testing was applied.
Results
In phase I, one SNP (HIF2A rs11125070) was found to be associated with DFS in multivariable analysis; yet association of a proxy polymorphism (HIF2A rs4953342) was not detected in the phase II patient cohort. In phase II, associations of two SNPs (HIF2A rs4953352 and HIF2B rs12593988) were significant in both OS and DFS multivariable analyses. However, association of HIF2A rs4953352 was not replicated in the phase I cohort using a proxy SNP (HIF2A rs6706003).
Conclusion
Overall, our study did not find a convincing evidence of association of the investigated polymorphisms with the disease outcomes in colorectal cance
Characterization of the hot Neptune GJ 436b with Spitzer and ground-based observations
We present Spitzer Space Telescope infrared photometry of a secondary eclipse
of the hot Neptune GJ436b. The observations were obtained using the 8-micron
band of the InfraRed Array Camera (IRAC). The data spanning the predicted time
of secondary eclipse show a clear flux decrement with the expected shape and
duration. The observed eclipse depth of 0.58 mmag allows us to estimate a
blackbody brightness temperature of T_p = 717 +- 35 K at 8 microns. We compare
this infrared flux measurement to a model of the planetary thermal emission,
and show that this model reproduces properly the observed flux decrement. The
timing of the secondary eclipse confirms the non-zero orbital eccentricity of
the planet, while also increasing its precision (e = 0.14 +- 0.01). Additional
new spectroscopic and photometric observations allow us to estimate the
rotational period of the star and to assess the potential presence of another
planet.Comment: Accepted for publication in A&A on 11/09/2007; 7 pages, 6 figure
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Observations of the martian atmosphere with the mars climate sounder
The Mars Climate Sounder (MCS) has obtained measurements of the Martian atmosphere for one Mars year. Onboard the Mars Reconnaissance Orbiter (MRO), MCS continues to acquire high vertical resolution profiles of temperature, dust, condensates of CO2 and H2O, and water vapor by observing the limb of the atmosphere from the surface to 80 km in the spectral intervals 0.3 – 3 ?m and 11.5 – 45 ?m [1]. This paper describes the investigation and introduces some of the observations being studied by the MCS science team. Other presentations by the team at this workshop will describe in greater detail results of ongoing research using MCS data
Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22
A substantial proportion of familial colorectal cancer (CRC) is not a consequence of known susceptibility loci, such as mismatch repair (MMR) genes, supporting the existence of additional loci. To identify novel CRC loci, we conducted a genome-wide linkage scan in 356 white families with no evidence of defective MMR (i.e., no loss of tumor expression of MMR proteins, no microsatellite instability (MSI)-high tumors, or no evidence of linkage to MMR genes). Families were ascertained via the Colon Cancer Family Registry multi-site NCI-supported consortium (Colon CFR), the City of Hope Comprehensive Cancer Center, and Memorial University of Newfoundland. A total of 1,612 individuals (average 5.0 per family including 2.2 affected) were genotyped using genome-wide single nucleotide polymorphism linkage arrays; parametric and non-parametric linkage analysis used MERLIN in a priori-defined family groups. Five lod scores greater than 3.0 were observed assuming heterogeneity. The greatest were among families with mean age of diagnosis less than 50 years at 4q21.1 (dominant HLOD = 4.51, α = 0.84, 145.40 cM, rs10518142) and among all families at 12q24.32 (dominant HLOD = 3.60, α = 0.48, 285.15 cM, rs952093). Among families with four or more affected individuals and among clinic-based families, a common peak was observed at 15q22.31 (101.40 cM, rs1477798; dominant HLOD = 3.07, α = 0.29; dominant HLOD = 3.03, α = 0.32, respectively). Analysis of families with only two affected individuals yielded a peak at 8q13.2 (recessive HLOD = 3.02, α = 0.51, 132.52 cM, rs1319036). These previously unreported linkage peaks demonstrate the continued utility of family-based data in complex traits and suggest that new CRC risk alleles remain to be elucidated. © 2012 Cicek et al
Use of a dual reporter plasmid to demonstrate bactofection with an attenuated aroa- derivative of Pasteurella multocida b:2
A reporter plasmid pSRG has been developed which expresses red fluorescent protein (RFP) from a constitutive prokaryotic promoter within Pasteurella multocida B:2 and green fluorescent protein (GFP) from a constitutive eukaryotic promoter within mammalian cells. This construct has been used to determine the location and viability of the bacteria when moving from the extracellular environment into the intracellular compartment of mammalian cells. Invasion assays with embryonic bovine lung (EBL) cells and an attenuated AroA- derivative of Pasteurella multocida B:2 (strain JRMT12), harbouring the plasmid pSRG, showed that RFP-expressing bacteria could be detected intracellularly at 3 h post-invasion. At this stage, some EBL cells harbouring RFP-expressing bacteria were observed to express GFP simultaneously, indicating release of the plasmid into the intracellular environment. At 5 h post-invasion, more EBL cells were expressing GFP, while still harbouring RFP-expressing bacteria. Concurrently, some EBL cells were shown to express only GFP, indicating loss of viable bacteria within these cells. These experiments proved the functionality of the pSRG dual reporter system and the potential of P. multocida B:2 JRMT12 for bactofection and delivery of a DNA vaccine
An Adaptive Interacting Wang-Landau Algorithm for Automatic Density Exploration
While statisticians are well-accustomed to performing exploratory analysis in
the modeling stage of an analysis, the notion of conducting preliminary
general-purpose exploratory analysis in the Monte Carlo stage (or more
generally, the model-fitting stage) of an analysis is an area which we feel
deserves much further attention. Towards this aim, this paper proposes a
general-purpose algorithm for automatic density exploration. The proposed
exploration algorithm combines and expands upon components from various
adaptive Markov chain Monte Carlo methods, with the Wang-Landau algorithm at
its heart. Additionally, the algorithm is run on interacting parallel chains --
a feature which both decreases computational cost as well as stabilizes the
algorithm, improving its ability to explore the density. Performance is studied
in several applications. Through a Bayesian variable selection example, the
authors demonstrate the convergence gains obtained with interacting chains. The
ability of the algorithm's adaptive proposal to induce mode-jumping is
illustrated through a trimodal density and a Bayesian mixture modeling
application. Lastly, through a 2D Ising model, the authors demonstrate the
ability of the algorithm to overcome the high correlations encountered in
spatial models.Comment: 33 pages, 20 figures (the supplementary materials are included as
appendices
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