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

Galactic Evolution along the Hubble Sequence

A generalization of the multiphase chemical evolution model applied to a wide set of theoretical galaxies is shown. This set of models has been computed by using the so-called Universal Rotation Curve from Persic, Salucci & Steel to calculate the radial mass distributions of each theoretical galaxy. By assuming that the molecular cloud and star formation efficiencies depend on the morphological type of each galaxy, we construct a bi-parametric grid of models whose results are valid in principle for any spiral galaxy, of given maximum rotation velocity or total mass, and morphological type.Comment: Proceedings of the Euroconference "The Evolution of Galaxies. III..." (Kiel 2002

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

Reconstructing native American migrations from whole-genome and whole-exome data.

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern American ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations

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

Kinematics and physical properties of Southern interacting galaxies: the minor merger AM 2306-721

We present an observational study about the effects of the interactions in the kinematics, stellar population and abundances of the components of the galaxy pair AM2306-721. Rotation curves for the main and companion galaxies were obtained, showing a deprojected velocity amplitude of 175 km/s and 185 km/s, respectively. The interaction between the main and companion galaxies was modeled using numerical N-body/hydrodynamical simulations, with the result indicating that the current stage of the merger would be about 250 Myr after perigalacticum. The spatial variation in the distribution of the stellar population components in both galaxies was analysed by fitting combinations of stellar population models of different age groups. The central region of main galaxy is dominated by an old (5-10 Gyr) population, while significant contributions from a young (200 Myr) and intermediate (1 Gyr) components are found in the disk, being enhanced in the direction of the tidal features. The stellar population of the companion galaxy is overall much younger, being dominated by components with 1 Gyr or less, quite widely spread over the whole disk. Spatial profiles of the oxygen abundance were obtained from the a grid of photoionization models using the R23 line ratio. The disk of the main galaxy shows a clear radial gradient, while the companion galaxy presents an oxygen abundance relatively homogeneous across the disk. The absence of an abundance gradient in the secondary galaxy is interpreted in terms of mixing by gas flows from the outer parts to the center of the galaxy due to the gravitational interaction with the more massive primary.Comment: 13 pages, 12 figures, accepted for publication on MNRA

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

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

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

A grid of chemical evolution models as a tool to interpret spiral and irregular galaxies data

We present a generalization of the multiphase chemical evolution model applied to a wide set of theoretical galaxies with different masses and evolutionary rates. This generalized set of models has been computed using the so-called Universal Rotation Curve from Persic et al (1996) to calculate the radial mass distribution of 44 theoretical protogalaxies. This distribution is a fundamental input which, besides its own effect on the galaxy evolution, defines the characteristic collapse time-scale or gas infall rate onto the disc.We have adopted 10 sets of values, between 0 and 1, for the molecular cloud and star formation efficiencies, as corresponding to their probability nature, for each one of the radial distributions of total mass. Thus, we have constructed a bi-parametric grid of models, depending on those efficiency sets and on the rotation velocity, whose results are valid in principle for any spiral or irregular galaxy. The model results provide the time evolution of different regions of the disc and the halo along galactocentric distance, measured by the gas (atomic and molecular) and stellar masses, the star formation rate and chemical abundances of 14 elements, for a total of 440 models. This grid may be used to estimate the evolution of a given galaxy for which only present time information -- such as radial distributions of elemental abundances, gas densities and/or star formation, which are the usual observational constraints of chemical evolution models -- is available.Comment: 27 pag., 20 fig, to be published in MNRA