PQL: A Declarative Query Language over Dynamic Biological Schemata

We introduce the PQL query language (PQL) used in the GeneSeek genetic data integration project. PQL incorporates many features of query languages for semi-structured data. To this we add the ability to express metadata constraints like intended semantics and database curation approach. These constraints guide the dynamic generation of potential query plans. This allows a single query to remain relevant even in the presence of source and mediated schemas that are continually evolving, as is often the case in data integration

Absence of Magnetism in Hcp Iron-Nickel at 11 K

Synchrotron Mössbauer spectroscopy (SMS) was performed on an hcp-phase alloy of composition Fe92Ni8 at a pressure of 21 GPa and a temperature of 11 K. Density functional theoretical calculations predict antiferromagnetism in both hcp Fe and hcp Fe-Ni. For hcp Fe, these calculations predict no hyperfine magnetic field, consistent with previous experiments. For hcp Fe-Ni, however, substantial hyperfine magnetic fields are predicted, but these were not observed in the SMS spectra. Two possible explanations are suggested. First, small but significant errors in the generalized gradient approximation density functional may lead to an erroneous prediction of magnetic order or of erroneous hyperfine magnetic fields in antiferromagnetic hcp Fe-Ni. Alternately, quantum fluctuations with periods much shorter than the lifetime of the nuclear excited state would prohibit the detection of moments by SMS

Post-spinel transformations and equation of state in ZnGa2O4: Determination at high-pressure by in situ x-ray diffraction

Room temperature angle-dispersive x-ray diffraction measurements on spinel ZnGa2O4 up to 56 GPa show evidence of two structural phase transformations. At 31.2 GPa, ZnGa2O4 undergoes a transition from the cubic spinel structure to a tetragonal spinel structure similar to that of ZnMn2O4. At 55 GPa, a second transition to the orthorhombic marokite structure (CaMn2O4-type) takes place. The equation of state of cubic spinel ZnGa2O4 is determined: V0 = 580.1(9) A3, B0 = 233(8) GPa, B0'= 8.3(4), and B0''= -0.1145 GPa-1 (implied value); showing that ZnGa2O4 is one of the less compressible spinels studied to date. For the tetragonal structure an equation of state is also determined: V0 = 257.8(9) A3, B0 = 257(11) GPa, B0'= 7.5(6), and B0''= -0.0764 GPa-1 (implied value). The reported structural sequence coincides with that found in NiMn2O4 and MgMn2O4.Comment: 20 pages, 4 figures, 2 Table

Structural, electronic, and magnetic characteristics of Np_2Co_(17)

A previously unknown neptunium-transition-metal binary compound Np_2Co_(17) has been synthesized and characterized by means of powder x-ray diffraction, ^(237)Np Mössbauer spectroscopy, superconducting-quantum-interference-device magnetometry, and x-ray magnetic circular dichroism (XMCD). The compound crystallizes in a Th_2Ni_(17)-type hexagonal structure with room-temperature lattice parameters α=8.3107(1) Å and c=8.1058(1) Å. Magnetization curves indicate the occurrence of ferromagnetic order below T_C>350 K. Mössbauer spectra suggest a Np^(3+) oxidation state and give an ordered moment of μ_(Np)=1.57(4) μ_B and μ_(Np)=1.63(4) μ_B for the Np atoms located, respectively, at the 2b and 2d crystallographic positions of the P6_3/mmc space group. Combining these values with a sum-rule analysis of the XMCD spectra measured at the neptunium M_(4,5) absorption edges, one obtains the spin and orbital contributions to the site-averaged Np moment [μ_S=−1.88(9) μ_B, μ_L=3.48(9) μ_B]. The ratio between the expectation value of the magnetic-dipole moment and the spin magnetic moment (m_(md)/μS=+1.36) is positive as predicted for localized 5f electrons and lies between the values calculated in intermediate-coupling (IC) and jj approximations. The expectation value of the angular part of the spin-orbit-interaction operator is in excellent agreement with the IC estimate. The ordered moment averaged over the four inequivalent Co sites, as obtained from the saturation value of the magnetization, is μ_(Co)≃1.6 μ_B. The experimental results are discussed against the predictions of first-principles electronic-structure calculations based on the spin-polarized local-spin-density approximation plus the Hubbard interaction

ReNoun: Fact Extraction for Nominal Attributes

Search engines are increasingly relying on large knowledge bases of facts to provide direct answers to users' queries. However, the construction of these knowledge bases is largely manual and does not scale to the long and heavy tail of facts. Open information extraction tries to address this challenge, but typically assumes that facts are expressed with verb phrases, and therefore has had difficulty extracting facts for noun‐based relations. We describe ReNoun, an open information extraction system that complements previous efforts by focusing on nominal attributes and on the long tail. ReNoun's approach is based on leveraging a large ontology of noun attributes mined from a text corpus and from user queries. ReNoun creates a seed set of training data by using specialized patterns and requiring that the facts mention an attribute in the ontology. ReNoun then generalizes from this seed set to produce a much larger set of extractions that are then scored. We describe experiments that show that we extract facts with high precision and for attributes that cannot be extracted with verb‐based techniques

Reversion of FMR1 Methylation and Silencing by Editing the Triplet Repeats in Fragile X iPSC-Derived Neurons

SummaryFragile X syndrome (FXS) is the most common form of inherited intellectual disability, resulting from a CGG repeat expansion in the fragile X mental retardation 1 (FMR1) gene. Here, we report a strategy for CGG repeat correction using CRISPR/Cas9 for targeted deletion in both embryonic stem cells and induced pluripotent stem cells derived from FXS patients. Following gene correction in FXS induced pluripotent stem cells, FMR1 expression was restored and sustained in neural precursor cells and mature neurons. Strikingly, after removal of the CGG repeats, the upstream CpG island of the FMR1 promoter showed extensive demethylation, an open chromatin state, and transcription initiation. These results suggest a silencing maintenance mechanism for the FMR1 promoter that is dependent on the existence of the CGG repeat expansion. Our strategy for deletion of trinucleotide repeats provides further insights into the molecular mechanisms of FXS and future therapies of trinucleotide repeat disorders

Global modelling of the early Martian climate under a denser CO2 atmosphere: Water cycle and ice evolution

We discuss 3D global simulations of the early Martian climate that we have performed assuming a faint young Sun and denser CO2 atmosphere. We include a self-consistent representation of the water cycle, with atmosphere-surface interactions, atmospheric transport, and the radiative effects of CO2 and H2O gas and clouds taken into account. We find that for atmospheric pressures greater than a fraction of a bar, the adiabatic cooling effect causes temperatures in the southern highland valley network regions to fall significantly below the global average. Long-term climate evolution simulations indicate that in these circumstances, water ice is transported to the highlands from low-lying regions for a wide range of orbital obliquities, regardless of the extent of the Tharsis bulge. In addition, an extended water ice cap forms on the southern pole, approximately corresponding to the location of the Noachian/Hesperian era Dorsa Argentea Formation. Even for a multiple-bar CO2 atmosphere, conditions are too cold to allow long-term surface liquid water. Limited melting occurs on warm summer days in some locations, but only for surface albedo and thermal inertia conditions that may be unrealistic for water ice. Nonetheless, meteorite impacts and volcanism could potentially cause intense episodic melting under such conditions. Because ice migration to higher altitudes is a robust mechanism for recharging highland water sources after such events, we suggest that this globally sub-zero, `icy highlands' scenario for the late Noachian climate may be sufficient to explain most of the fluvial geology without the need to invoke additional long-term warming mechanisms or an early warm, wet Mars.Comment: Minor revisions to text, one new table, figs. 1,3 11 and 18 redon

SemLAV: Local-As-View Mediation for SPARQL Queries

International audienceThe Local-As-View(LAV) integration approach aims at querying heterogeneous data in dynamic environments. In LAV, data sources are described as views over a global schema which is used to pose queries. Query processing requires to generate and execute query rewritings, but for SPARQL queries, the LAV query rewritings may not be generated or executed in a reasonable time. In this paper, we present SemLAV, an alternative technique to process SPARQL queries over a LAV integration system without generating rewritings. SemLAV executes the query against a partial instance of the global schema which is built on-the-fly with data from the relevant views. The paper presents an experimental study for SemLAV, and compares its performance with traditional LAV-based query processing techniques. The results suggest that SemLAV scales up to SPARQL queries even over a large number of views, while it significantly outperforms traditional solutions