Monolithic simulation of convection-coupled phase-change - verification and reproducibility

Phase interfaces in melting and solidification processes are strongly affected by the presence of convection in the liquid. One way of modeling their transient evolution is to couple an incompressible flow model to an energy balance in enthalpy formulation. Two strong nonlinearities arise, which account for the viscosity variation between phases and the latent heat of fusion at the phase interface. The resulting coupled system of PDE's can be solved by a single-domain semi-phase-field, variable viscosity, finite element method with monolithic system coupling and global Newton linearization. A robust computational model for realistic phase-change regimes furthermore requires a flexible implementation based on sophisticated mesh adaptivity. In this article, we present first steps towards implementing such a computational model into a simulation tool which we call Phaseflow. Phaseflow utilizes the finite element software FEniCS, which includes a dual-weighted residual method for goal-oriented adaptive mesh refinement. Phaseflow is an open-source, dimension-independent implementation that, upon an appropriate parameter choice, reduces to classical benchmark situations including the lid-driven cavity and the Stefan problem. We present and discuss numerical results for these, an octadecane PCM convection-coupled melting benchmark, and a preliminary 3D convection-coupled melting example, demonstrating the flexible implementation. Though being preliminary, the latter is, to our knowledge, the first published 3D result for this method. In our work, we especially emphasize reproducibility and provide an easy-to-use portable software container using Docker.Comment: 20 pages, 8 figure

Evidence for Intrinsic Redshifts in Normal Spiral Galaxies

The Tully-Fisher Relationship (TFR) is utilized to identify anomalous redshifts in normal spiral galaxies. Three redshift anomalies are identified in this analysis: (1) Several clusters of galaxies are examined in which late type spirals have significant excess redshifts relative to early type spirals in the same clusters, (2) Galaxies of morphology similar to ScI galaxies are found to have a systematic excess redshift relative to the redshifts expected if the Hubble Constant is 72 km s-1 Mpc-1, (3) individual galaxies, pairs, and groups are identified which strongly deviate from the predictions of a smooth Hubble flow. These redshift deviations are significantly larger than can be explained by peculiar motions and TFR errors. It is concluded that the redshift anomalies identified in this analysis are consistent with previous claims for large non-cosmological (intrinsic) redshifts.Comment: Accepted for publication at Astrophysics&Space Science. 36 pages including 8 tables and 7 figure

An Aromatic Inventory of the Local Volume

Using infrared photometry from the Spitzer Space Telescope, we perform the first inventory of aromatic feature emission (AFE, but also commonly referred to as PAH emission) for a statistically complete sample of star-forming galaxies in the local volume. The photometric methodology involved is calibrated and demonstrated to recover the aromatic fraction of the IRAC 8 micron flux with a standard deviation of 6% for a training set of 40 SINGS galaxies (ranging from stellar to dust dominated) with both suitable mid-infrared Spitzer IRS spectra and equivalent photometry. A potential factor of two improvement could be realized with suitable 5.5 and 10 micron photometry, such as what may be provided in the future by JWST. The resulting technique is then applied to mid-infrared photometry for the 258 galaxies from the Local Volume Legacy (LVL) survey, a large sample dominated in number by low-luminosity dwarf galaxies for which obtaining comparable mid-infrared spectroscopy is not feasible. We find the total LVL luminosity due to five strong aromatic features in the 8 micron complex to be 2.47E10 solar luminosities with a mean volume density of 8.8E6 solar luminosities per cubic Megaparsec. Twenty-four of the LVL galaxies, corresponding to a luminosity cut at M = -18.22 in the B band, account for 90% of the aromatic luminosity. Using oxygen abundances compiled from the literature for 129 of the 258 LVL galaxies, we find a correlation between metallicity and the aromatic to total infrared emission ratio but not the aromatic to total 8 micron dust emission ratio. A possible explanation is that metallicity plays a role in the abundance of aromatic molecules relative to the total dust content, but other factors such as star formation and/or the local radiation field affect the excitation of those molecules.Comment: ApJ in press; 29 pages, 14 figures, 3 tables; emulateapj forma

Massive stars exploding in a He-rich circumstellar medium. I. Type Ibn (SN 2006jc-like) events

We present new spectroscopic and photometric data of the type Ibn supernovae 2006jc, 2000er and 2002ao. We discuss the general properties of this recently proposed supernova family, which also includes SN 1999cq. The early-time monitoring of SN 2000er traces the evolution of this class of objects during the first few days after the shock breakout. An overall similarity in the photometric and spectroscopic evolution is found among the members of this group, which would be unexpected if the energy in these core-collapse events was dominated by the interaction between supernova ejecta and circumstellar medium. Type Ibn supernovae appear to be rather normal type Ib/c supernova explosions which occur within a He-rich circumstellar environment. SNe Ibn are therefore likely produced by the explosion of Wolf-Rayet progenitors still embedded in the He-rich material lost by the star in recent mass-loss episodes, which resemble known luminous blue variable eruptions. The evolved Wolf-Rayet star could either result from the evolution of a very massive star or be the more evolved member of a massive binary system. We also suggest that there are a number of arguments in favour of a type Ibn classification for the historical SN 1885A (S-Andromedae), previously considered as an anomalous type Ia event with some resemblance to SN 1991bg.Comment: 17 pages including 12 figures and 4 tables. Slightly revised version, conclusions unchanged, 1 figure added. Accepted for publication in MNRA

An immunohistochemical perspective of PPARβ and one of its putative targets PDK1 in normal ovaries, benign and malignant ovarian tumours

Peroxisome proliferator-activated receptor β (PPARβ) is a member of the nuclear hormone receptor family and is a ligand-activated transcription factor with few known molecular targets including 3-phosphoinositide-dependent protein kinase 1(PDK1). In view of the association of PPARβ and PDK1 with cancer, we have examined the expression of PPARβ and PDK1 in normal ovaries and different histological grades of ovarian tumours. Normal ovaries, benign, borderline, grades 1, 2 and 3 ovarian tumours of serous, muciuous, endometrioid, clear cell and mixed subtypes were analysed by immunohistochemistry for PPARβ and PDK1 expression. All normal ovarian tissues, benign, borderline and grade 1 tumours showed PPARβ staining localised in the epithelium and stroma. Staining was predominantly nuclear, but some degree of cytoplasmic staining was also evident. Approximately 20% of grades 2 and 3 tumours lacked PPARβ staining, whereas the rest displayed some degree of nuclear and cytoplasmic staining of the scattered epithelium and stroma. The extent of epithelial and stromal PPARβ staining was significantly different among the normal and the histological grades of tumours (χ2=59.25, d.f.=25, P<0.001; χ2=64.48, d.f.=25, P<0.001). Significantly different staining of PPARβ was observed in the epithelium and stroma of benign and borderline tumours compared with grades 1, 2 and 3 tumours (χ2=11.28, d.f.=4, P<0.05; χ2=16.15, d.f.=4, P<0.005). In contrast, PDK1 immunostaining was absent in 9 out of 10 normal ovaries. Weak staining for PDK1 was observed in one normal ovary and 40% of benign ovarian tumours. All borderline and malignant ovarian tumours showed positive cytoplasmic and membrane PDK1 staining. Staining of PDK1 was confined to the epithelium and the blood vessels, and no apparent staining of the stroma was evident. Significantly different PDK1 staining was observed between the benign/borderline and malignant ovarian tumours (χ2=22.45, d.f.=5, P<0.001). In some borderline and high-grade tumours, staining of the reactive stroma was also evident. Our results suggest that unlike the colon, the endometrial, head and neck carcinomas, overexpression of PPARβ does not occur in ovarian tumours. However, overexpression of PDK1 was evident in borderline and low- to high-grade ovarian tumours and is consistent with its known role in tumorigenesis

Screening of protein kinase inhibitors identifies PKC inhibitors as inhibitors of osteoclastic acid secretion and bone resorption

<p>Abstract</p> <p>Background</p> <p>Bone resorption is initiated by osteoclastic acidification of the resorption lacunae. This process is mediated by secretion of protons through the V-ATPase and chloride through the chloride antiporter ClC-7. To shed light on the intracellular signalling controlling extracellular acidification, we screened a protein kinase inhibitor library in human osteoclasts.</p> <p>Methods</p> <p>Human osteoclasts were generated from CD14+ monocytes. The effect of different kinase inhibitors on lysosomal acidification in human osteoclasts was investigated using acridine orange for different incubation times (45 minutes, 4 and 24 hours). The inhibitors were tested in an acid influx assay using microsomes isolated from human osteoclasts. Bone resorption by human osteoclasts on bone slices was measured by calcium release. Cell viability was measured using AlamarBlue.</p> <p>Results</p> <p>Of the 51 compounds investigated only few inhibitors were positive in both acidification and resorption assays. Rottlerin, GF109203X, Hypericin and Ro31-8220 inhibited acid influx in microsomes and bone resorption, while Sphingosine and Palmitoyl-DL-carnitine-Cl showed low levels of inhibition. Rottlerin inhibited lysosomal acidification in human osteoclasts potently.</p> <p>Conclusions</p> <p>In conclusion, a group of inhibitors all indicated to inhibit PKC reduced acidification in human osteoclasts, and thereby bone resorption, indicating that acid secretion by osteoclasts may be specifically regulated by PKC in osteoclasts.</p

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Mathematical Model of Plasmid-Mediated Resistance to Ceftiofur in Commensal Enteric Escherichia coli of Cattle

Antimicrobial use in food animals may contribute to antimicrobial resistance in bacteria of animals and humans. Commensal bacteria of animal intestine may serve as a reservoir of resistance-genes. To understand the dynamics of plasmid-mediated resistance to cephalosporin ceftiofur in enteric commensals of cattle, we developed a deterministic mathematical model of the dynamics of ceftiofur-sensitive and resistant commensal enteric Escherichia coli (E. coli) in the absence of and during parenteral therapy with ceftiofur. The most common treatment scenarios including those using a sustained-release drug formulation were simulated; the model outputs were in agreement with the available experimental data. The model indicated that a low but stable fraction of resistant enteric E. coli could persist in the absence of immediate ceftiofur pressure, being sustained by horizontal and vertical transfers of plasmids carrying resistance-genes, and ingestion of resistant E. coli. During parenteral therapy with ceftiofur, resistant enteric E. coli expanded in absolute number and relative frequency. This expansion was most influenced by parameters of antimicrobial action of ceftiofur against E. coli. After treatment (>5 weeks from start of therapy) the fraction of ceftiofur-resistant cells among enteric E. coli, similar to that in the absence of treatment, was most influenced by the parameters of ecology of enteric E. coli, such as the frequency of transfer of plasmids carrying resistance-genes, the rate of replacement of enteric E. coli by ingested E. coli, and the frequency of ceftiofur resistance in the latter