Location Dependent Dirichlet Processes

Dirichlet processes (DP) are widely applied in Bayesian nonparametric modeling. However, in their basic form they do not directly integrate dependency information among data arising from space and time. In this paper, we propose location dependent Dirichlet processes (LDDP) which incorporate nonparametric Gaussian processes in the DP modeling framework to model such dependencies. We develop the LDDP in the context of mixture modeling, and develop a mean field variational inference algorithm for this mixture model. The effectiveness of the proposed modeling framework is shown on an image segmentation task

From Heisenberg matrix mechanics to EBK quantization: theory and first applications

Despite the seminal connection between classical multiply-periodic motion and Heisenberg matrix mechanics and the massive amount of work done on the associated problem of semiclassical (EBK) quantization of bound states, we show that there are, nevertheless, a number of previously unexploited aspects of this relationship that bear on the quantum-classical correspondence. In particular, we emphasize a quantum variational principle that implies the classical variational principle for invariant tori. We also expose the more indirect connection between commutation relations and quantization of action variables. With the help of several standard models with one or two degrees of freedom, we then illustrate how the methods of Heisenberg matrix mechanics described in this paper may be used to obtain quantum solutions with a modest increase in effort compared to semiclassical calculations. We also describe and apply a method for obtaining leading quantum corrections to EBK results. Finally, we suggest several new or modified applications of EBK quantization.Comment: 37 pages including 3 poscript figures, submitted to Phys. Rev.

The spectral action and cosmic topology

The spectral action functional, considered as a model of gravity coupled to matter, provides, in its non-perturbative form, a slow-roll potential for inflation, whose form and corresponding slow-roll parameters can be sensitive to the underlying cosmic topology. We explicitly compute the non-perturbative spectral action for some of the main candidates for cosmic topologies, namely the quaternionic space, the Poincare' dodecahedral space, and the flat tori. We compute the corresponding slow-roll parameters and see we check that the resulting inflation model behaves in the same way as for a simply-connected spherical topology in the case of the quaternionic space and the Poincare' homology sphere, while it behaves differently in the case of the flat tori. We add an appendix with a discussion of the case of lens spaces.Comment: 55 pages, LaTe

Constraining the LyC escape fraction from LEGUS star clusters with SIGNALS HII region observations: A pilot study of NGC 628

The ionising radiation of young and massive stars is a crucial form of stellar feedback. Most ionising (Lyman-continuum; LyC, $\lambda < 912A$) photons are absorbed close to the stars that produce them, forming compact HII regions, but some escape into the wider galaxy. Quantifying the fraction of LyC photons that escape is an open problem. In this work, we present a semi-novel method to estimate the escape fraction by combining broadband photometry of star clusters from the Legacy ExtraGalactic UV Survey (LEGUS) with HII regions observed by the Star formation, Ionized gas, and Nebular Abundances Legacy Survey (SIGNALS) in the nearby spiral galaxy NGC 628. We first assess the completeness of the combined catalogue, and find that 49\% of HII regions lack corresponding star clusters as a result of a difference in the sensitivities of the LEGUS and SIGNALS surveys. For HII regions that do have matching clusters, we infer the escape fraction from the difference between the ionising power required to produce the observed HII luminosity and the predicted ionising photon output of their host star clusters; the latter is computed using a combination of LEGUS photometric observations and a stochastic stellar population synthesis code SLUG (Stochastically Lighting Up Galaxies). Overall, we find an escape fraction of $f_{esc} = 0.09^{+0.06}_{-0.06}$ across our sample of 42 HII regions; in particular, we find HII regions with high $f_{esc}$ are predominantly regions with low H$\alpha$-luminosity. We also report possible correlation between $f_{esc}$ and the emission lines [O ii]/[N ii] and [O ii]/H$\beta$.Comment: Accepted for publication at MNRA

The impact of signal-to-noise ratio, diffusion-weighted directions and image resolution in cardiac diffusion tensor imaging - insights from the ex-vivo rat heart

Background: Cardiac diffusion tensor imaging (DTI) is limited by scan time and signal-to-noise (SNR) restrictions. This invariably leads to a trade-off between the number of averages, diffusion-weighted directions (ND), and image resolution. Systematic evaluation of these parameters is therefore important for adoption of cardiac DTI in clinical routine where time is a key constraint. Methods: High quality reference DTI data were acquired in five ex-vivo rat hearts. We then retrospectively set 2 ≤ SNR ≤ 97, 7 ≤ ND ≤ 61, varied the voxel volume by up to 192-fold and investigated the impact on the accuracy and precision of commonly derived parameters. Results: For maximal scan efficiency, the accuracy and precision of the mean diffusivity is optimised when SNR is maximised at the expense of ND. With typical parameter settings used clinically, we estimate that fractional anisotropy may be overestimated by up to 13% with an uncertainty of ±30%, while the precision of the sheetlet angles may be as poor as ±31°. Although the helix angle has better precision of ±14°, the transmural range of helix angles may be under-estimated by up to 30° in apical and basal slices, due to partial volume and tapering myocardial geometry. Conclusions: These findings inform a baseline of understanding upon which further issues inherent to in-vivo cardiac DTI, such as motion, strain and perfusion, can be considered. Furthermore, the reported bias and reproducibility provides a context in which to assess cardiac DTI biomarkers

Determination of energy-dependent neutron backgrounds using shadow bars

Understanding the neutron background is essential for determining the neutron yield from nuclear reactions. In the analysis presented here, the shadow bars are placed in front of neutron detectors to determine the energy dependent neutron background fractions. The measurement of neutron spectra with and without shadow bars is important to determine the neutron background more accurately. The neutron background, along with its sources and systematic uncertainties, are explored with a focus on the impact of background models and their dependence on neutron energy.Comment: 7 pages, 10 figure

Reconstruction of the equation of state for the cyclic universes in homogeneous and isotropic cosmology

We study the cosmological evolutions of the equation of state (EoS) for the universe in the homogeneous and isotropic Friedmann-Lema\^{i}tre-Robertson-Walker (FLRW) space-time. In particular, we reconstruct the cyclic universes by using the Weierstrass and Jacobian elliptic functions. It is explicitly illustrated that in several models the universe always stays in the non-phantom (quintessence) phase, whereas there also exist models in which the crossing of the phantom divide can be realized in the reconstructed cyclic universes.Comment: 29 pages, 8 figures, version accepted for publication in Central European Journal of Physic

FOXM1 Induces a Global Methylation Signature That Mimics the Cancer Epigenome in Head and Neck Squamous Cell Carcinoma

The oncogene FOXM1 has been implicated in all major types of human cancer. We recently showed that aberrant FOXM1 expression causes stem cell compartment expansion resulting in the initiation of hyperplasia. We have previously shown that FOXM1 regulates HELLS, a SNF2/helicase involved in DNA methylation, implicating FOXM1 in epigenetic regulation. Here, we have demonstrated using primary normal human oral keratinocytes (NOK) that upregulation of FOXM1 suppressed the tumour suppressor gene p16INK4A (CDKN2A) through promoter hypermethylation. Knockdown of HELLS using siRNA re-activated the mRNA expression of p16INK4A and concomitant downregulation of two DNA methyltransferases DNMT1 and DNMT3B. The dose-dependent upregulation of endogenous FOXM1 (isoform B) expression during tumour progression across a panel of normal primary NOK strains (n = 8), dysplasias (n = 5) and head and neck squamous cell carcinoma (HNSCC) cell lines (n = 11) correlated positively with endogenous expressions of HELLS, BMI1, DNMT1 and DNMT3B and negatively with p16INK4A and involucrin. Bisulfite modification and methylation-specific promoter analysis using absolute quantitative PCR (MS-qPCR) showed that upregulation of FOXM1 significantly induced p16INK4A promoter hypermethylation (10-fold, P<0.05) in primary NOK cells. Using a non-bias genome-wide promoter methylation microarray profiling method, we revealed that aberrant FOXM1 expression in primary NOK induced a global hypomethylation pattern similar to that found in an HNSCC (SCC15) cell line. Following validation experiments using absolute qPCR, we have identified a set of differentially methylated genes, found to be inversely correlated with in vivo mRNA expression levels of clinical HNSCC tumour biopsy samples. This study provided the first evidence, using primary normal human cells and tumour tissues, that aberrant upregulation of FOXM1 orchestrated a DNA methylation signature that mimics the cancer methylome landscape, from which we have identified a unique FOXM1-induced epigenetic signature which may have clinical translational potentials as biomarkers for early cancer screening, diagnostic and/or therapeutic interventions

Imaging assessment of children presenting with suspected or known juvenile idiopathic arthritis : ESSR-ESPR points to consider

Juvenile idiopathic arthritis (JIA) is the most common paediatric rheumatic disease. It represents a group of heterogenous inflammatory disorders with unknown origin and is a diagnosis of exclusion in which imaging plays an important role. JIA is defined as arthritis of one or more joints that begins before the age of 16 years, persists for more than 6 weeks and is of unknown aetiology and pathophysiology. The clinical goal is early suppression of inflammation to prevent irreversible joint damage which has shifted the emphasis from detecting established joint damage to proactively detecting inflammatory change. This drives the need for imaging techniques that are more sensitive than conventional radiography in the evaluation of inflammatory processes as well as early osteochondral change. Physical examination has limited reliability, even if performed by an experienced clinician, emphasising the importance of imaging to aid in clinical decision-making. On behalf of the European Society of Musculoskeletal Radiology (ESSR) arthritis subcommittee and the European Society of Paediatric Radiology (ESPR) musculoskeletal imaging taskforce, based on literature review and/or expert opinion, we discuss paediatric-specific imaging characteristics of the most commonly involved, in literature best documented and clinically important joints in JIA, namely the temporomandibular joints (TMJs), spine, sacroiliac (SI) joints, wrists, hips and knees, followed by a clinically applicable point to consider for each joint. We will also touch upon controversies in the current literature that remain to be resolved with ongoing research

Functional epigenomics approach to identify methylated candidate tumour suppressor genes in renal cell carcinoma

Promoter region hypermethylation and transcriptional silencing is a frequent cause of tumour suppressor gene (TSG) inactivation in many human cancers. Previously, to identify candidate epigenetically inactivated TSGs in renal cell carcinoma (RCC), we monitored changes in gene expression in four RCC cell lines after treatment with the demethylating agent 5-azacytidine. This enabled us to identify HAI-2/SPINT2 as a novel epigenetically inactivated candidate RCC TSG. To identify further candidate TSGs, we undertook bioinformatic and molecular genetic evaluation of a further 60 genes differentially expressed after demethylation. In addition to HAI-2/SPINT2, four genes (PLAU, CDH1, IGFB3 and MT1G) had previously been shown to undergo promoter methylation in RCC. After bioinformatic prioritisation, expression and/or methylation analysis of RCC cell lines±primary tumours was performed for 34 genes. KRT19 and CXCL16 were methylated in RCC cell lines and primary RCC; however, 22 genes were differentially expressed after demethylation but did not show primary tumour-specific methylation (methylated in normal tissue (n=1); methylated only in RCC cell lines (n=9) and not methylated in RCC cell lines (n=12)). Re-expression of CXCL16 reduced growth of an RCC cell line in vitro. In a summary, a functional epigenomic analysis of four RCC cell lines using microarrays representing 11 000 human genes yielded both known and novel candidate TSGs epigenetically inactivated in RCC, suggesting that this is valid strategy for the identification of novel TSGs and biomarkers