Context-Free Path Queries on RDF Graphs

Navigational graph queries are an important class of queries that canextract implicit binary relations over the nodes of input graphs. Most of the navigational query languages used in the RDF community, e.g. property paths in W3C SPARQL 1.1 and nested regular expressions in nSPARQL, are based on the regular expressions. It is known that regular expressions have limited expressivity; for instance, some natural queries, like same generation-queries, are not expressible with regular expressions. To overcome this limitation, in this paper, we present cfSPARQL, an extension of SPARQL query language equipped with context-free grammars. The cfSPARQL language is strictly more expressive than property paths and nested expressions. The additional expressivity can be used for modelling graph similarities, graph summarization and ontology alignment. Despite the increasing expressivity, we show that cfSPARQL still enjoys a low computational complexity and can be evaluated efficiently.Comment: 25 page

Evidence for multiple roles for grainyheadlike 2 in the establishment and maintenance of human mucociliary airway epithelium

Most of the airways of the human lung are lined by an epithelium made up of ciliated and secretory luminal cells and undifferentiated basal progenitor cells. The integrity of this epithelium and its ability to act as a selective barrier are critical for normal lung function. In other epithelia, there is evidence that transcription factors of the evolutionarily conserved grainyheadlike (GRHL) family play key roles in coordinating multiple cellular processes required for epithelial morphogenesis, differentiation, remodeling, and repair. However, only a few target genes have been identified, and little is known about GRHL function in the adult lung. Here we focus on the role of GRHL2 in primary human bronchial epithelial cells, both as undifferentiated progenitors and as they differentiate in air-liquid interface culture into an organized mucociliary epithelium with transepithelial resistance. Using a dominant-negative protein or shRNA to inhibit GRHL2, we follow changes in epithelial phenotype and gene transcription using RNA sequencing or microarray analysis. We identify several hundreds of genes that are directly or indirectly regulated by GRHL2 in both undifferentiated cells and air-liquid interface cultures. Using ChIP sequencing to map sites of GRHL2 binding in the basal cells, we identify 7,687 potential primary targets and confirm that GRHL2 binding is strongly enriched near GRHL2-regulated genes. Taken together, the results support the hypothesis that GRHL2 plays a key role in regulating many physiological functions of human airway epithelium, including those involving cell morphogenesis, adhesion, and motility

Gravitational Waves from Collapsing Vacuum Domains

The breaking of an approximate discrete symmetry, the final stages of a first order phase transition, or a post-inflationary biased probability distribution for scalar fields are possible cosmological scenarios characterized by the presence of unstable domain wall networks. Combining analytical and numerical techniques, we show that the non-spherical collapse of these domains can be a powerful source of gravitational waves. We compute their contribution to the stochastic background of gravitational radiation and explore their observability by present and future gravitational wave detectors.Comment: Revised version to appear in Physical Review Letters. Changes have been made which improve the presentation of the results. Figure 3 was modified, but conclusions remain the sam

The Universe Was Reionized Twice

We show the universe was reionized twice, first at z~15-16 and second at z~6. Such an outcome appears inevitable, when normalizing to two well determined observational measurements, namely, the epoch of the final cosmological reionization at z~6 and the density fluctuations at z~6, which in turn are tight ly constrained by Lyman alpha forest observations at z~3. These two observations most importantly fix the product of star formation efficiency and ionizing photon escape fraction from galaxies at high redshift. To the extent that the relative star formation efficiencies in gaseous minihalos with H2 cooling and large halos with atomic cooling at high redshift are still unknown, the primary source for the first reionization could be Pop III stars either in minihalos or in large halos. We show that gas in minihalos can be cooled efficiently by H2 molecules and star formation can continue to take place largely unimpeded throughout the first reionization period, thanks to two new mechanisms for generating a high X-ray background during the Pop III era, put forth here. Moreover, an important process for producing a large number of H2 molecules in relic HII regions of Pop III galaxies, first pointed out by Ricotti, Gnedin, & Shull, is quantified here. It is shown that the Lyman-Werner background may never build up during the Pop III era. The long cosmological reionization and reheating history is complex. We discuss a wide range of implications and possible tests for this new reionization picture. In particular, Thomson scattering optical depth is increased to 0.10 +- 0.03, compared to 0.027 for the case of only one rapid reionization at z=6. Upcoming Microwave Anisotropy Probe observation of the polarization of the cosmic microwave background should be able to distinguish between these two scenarios.Comment: submitted to ApJ, 69 pages, substantial revision made and conclusions strengthene

Mutants in the Mouse NuRD/Mi2 Component P66α Are Embryonic Lethal

The NuRD/Mi2 chromatin complex is involved in histone modifications and contains a large number of subunits, including the p66 protein. There are two mouse and human p66 paralogs, p66alpha and p66beta. The functions of these genes are not clear, in part because there are no mutants available, except in invertebrate model systems.We made loss of function mutants in the mouse p66alpha gene (mp66alpha, official name Gatad2a, MGI:2384585). We found that mp66alpha is essential for development, as mutant embryos die around day 10 of embryogenesis. The gene is not required for normal blastocyst development or for implantation. The phenotype of mutant embryos and the pattern of gene expression in mutants are consistent with a role of mp66alpha in gene silencing.mp66alpha is an essential gene, required for early mouse development. The lethal phenotype supports a role in execution of methylated DNA silencing

FUSE Deuterium Observations: A Strong Case For Galactic Infall

Measurements of deuterium in the local interstellar medium have revealed large variations in D/H along different lines of sight. Moreover, recent {\it Far Ultraviolet Spectroscopic Explorer} (FUSE) measurements find D/H to be anticorrelated with several indicators of dust formation and survival, suggesting that interstellar deuterium suffers significant depletion onto dust grains. This in turn implies that the total deuterium abundance in the local Galactic disk could be as high as $\sim 84$ of the primordial D abundance. It was proposed that the infall/accretion of pristine gas is needed to explain such a high deuterium abundance. However, we point out that the infall needed to maintain a high present-day D/H is, within the preferred models, in tension with observations that gas represents only some $\sim 20$ of Galactic baryons, with the balance in stars. We study this tension in the context of a wide class of Galactic evolution models for baryonic processing through stars, which show that deuterium destruction is strongly and cleanly correlated with the drop in the gas fraction. We find that FUSE deuterium observations and Galactic gas fraction estimates can be reconciled in some models; these demand a significant infall rate of pristine material that almost completely balances the rate of star formation. These successful models also require that the average fraction of gas that is returned by dying stars is less than 40% of the initial stellar mass. Cosmological implications of dust depletion of D in high-redshift systems are discussed.Comment: 22 pages, 6 figures. Matches version to appear in JCAP; presentation revised and improved following referee comments; conclusions unchange

A physiologically based kinetic model for elucidating the in vivo distribution of administered mesenchymal stem cells

Although mesenchymal stem cells (MSCs) present a promising tool in cell therapy for the treatment of various diseases, the in vivo distribution of administered MSCs has still been poorly understood, which hampers the precise prediction and evaluation of their therapeutic efficacy. Here, we developed the first model to characterize the physiological kinetics of administered MSCs based on direct visualization of cell spatiotemporal disposition by intravital microscopy and assessment of cell quantity using flow cytometry. This physiologically based kinetic model was validated with multiple external datasets, indicating potential inter-route and inter-species predictive capability. Our results suggest that the targeting efficiency of MSCs is determined by the lung retention and interaction between MSCs and target organs, including cell arrest, depletion and release. By adapting specific parameters, this model can be easily applied to abnormal conditions or other types of circulating cells for designing treatment protocols and guiding future experiments

Spatiotemporal dynamics of ultrarelativistic beam-plasma instabilities

An electron or electron-positron beam streaming through a plasma is notoriously prone to micro-instabilities. For a dilute ultrarelativistic infinite beam, the dominant instability is a mixed mode between longitudinal two-stream and transverse filamentation modes, with a phase velocity oblique to the beam velocity. A spatiotemporal theory describing the linear growth of this oblique mixed instability is proposed, which predicts that spatiotemporal effects generally prevail for finite-length beams, leading to a significantly slower instability evolution than in the usually assumed purely temporal regime. These results are accurately supported by particle-in-cell (PIC) simulations. Furthermore, we show that the self-focusing dynamics caused by the plasma wakefields driven by finite-width beams can compete with the oblique instability. Analyzed through PIC simulations, the interplay of these two processes in realistic systems bears important implications for upcoming accelerator experiments on ultrarelativistic beam-plasma interactions

Web Queries as a Source for Syndromic Surveillance

In the field of syndromic surveillance, various sources are exploited for outbreak detection, monitoring and prediction. This paper describes a study on queries submitted to a medical web site, with influenza as a case study. The hypothesis of the work was that queries on influenza and influenza-like illness would provide a basis for the estimation of the timing of the peak and the intensity of the yearly influenza outbreaks that would be as good as the existing laboratory and sentinel surveillance. We calculated the occurrence of various queries related to influenza from search logs submitted to a Swedish medical web site for two influenza seasons. These figures were subsequently used to generate two models, one to estimate the number of laboratory verified influenza cases and one to estimate the proportion of patients with influenza-like illness reported by selected General Practitioners in Sweden. We applied an approach designed for highly correlated data, partial least squares regression. In our work, we found that certain web queries on influenza follow the same pattern as that obtained by the two other surveillance systems for influenza epidemics, and that they have equal power for the estimation of the influenza burden in society. Web queries give a unique access to ill individuals who are not (yet) seeking care. This paper shows the potential of web queries as an accurate, cheap and labour extensive source for syndromic surveillance