Structured digital tables on the Semantic Web: toward a structured digital literature

In parallel to the growth in bioscience databases, biomedical publications have increased exponentially in the past decade. However, the extraction of high-quality information from the corpus of scientific literature has been hampered by the lack of machine-interpretable content, despite text-mining advances. To address this, we propose creating a structured digital table as part of an overall effort in developing machine-readable, structured digital literature. In particular, we envision transforming publication tables into standardized triples using Semantic Web approaches. We identify three canonical types of tables (conveying information about properties, networks, and concept hierarchies) and show how more complex tables can be built from these basic types. We envision that authors would create tables initially using the structured triples for canonical types and then have them visually rendered for publication, and we present examples for converting representative tables into triples. Finally, we discuss how ‘stub' versions of structured digital tables could be a useful bridge for connecting together the literature with databases, allowing the former to more precisely document the later

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

<p>Abstract</p> <p>Background</p> <p>Short-read high-throughput DNA sequencing technologies provide new tools to answer biological questions. However, high cost and low throughput limit their widespread use, particularly in organisms with smaller genomes such as <it>S. cerevisiae</it>. Although ChIP-Seq in mammalian cell lines is replacing array-based ChIP-chip as the standard for transcription factor binding studies, ChIP-Seq in yeast is still underutilized compared to ChIP-chip. We developed a multiplex barcoding system that allows simultaneous sequencing and analysis of multiple samples using Illumina's platform. We applied this method to analyze the chromosomal distributions of three yeast DNA binding proteins (Ste12, Cse4 and RNA PolII) and a reference sample (input DNA) in a single experiment and demonstrate its utility for rapid and accurate results at reduced costs.</p> <p>Results</p> <p>We developed a barcoding ChIP-Seq method for the concurrent analysis of transcription factor binding sites in yeast. Our multiplex strategy generated high quality data that was indistinguishable from data obtained with non-barcoded libraries. None of the barcoded adapters induced differences relative to a non-barcoded adapter when applied to the same DNA sample. We used this method to map the binding sites for Cse4, Ste12 and Pol II throughout the yeast genome and we found 148 binding targets for Cse4, 823 targets for Ste12 and 2508 targets for PolII. Cse4 was strongly bound to all yeast centromeres as expected and the remaining non-centromeric targets correspond to highly expressed genes in rich media. The presence of Cse4 non-centromeric binding sites was not reported previously.</p> <p>Conclusion</p> <p>We designed a multiplex short-read DNA sequencing method to perform efficient ChIP-Seq in yeast and other small genome model organisms. This method produces accurate results with higher throughput and reduced cost. Given constant improvements in high-throughput sequencing technologies, increasing multiplexing will be possible to further decrease costs per sample and to accelerate the completion of large consortium projects such as modENCODE.</p

Francisella tularensis subsp. novicida isolated from a human in Arizona

<p>Abstract</p> <p>Background</p> <p><it>Francisella tularensis </it>is the etiologic agent of tularemia and is classified as a select agent by the Centers for Disease Control and Prevention. Currently four known subspecies of <it>F. tularensis </it>that differ in virulence and geographical distribution are recognized:<it>tularensis </it>(type A), <it>holarctica </it>(type B), <it>mediasiatica</it>, and <it>novicida</it>. Because of the Select Agent status and differences in virulence and geographical location, the molecular analysis of any clinical case of tularemia is of particular interest. We analyzed an unusual <it>Francisella </it>clinical isolate from a human infection in Arizona using multiple DNA-based approaches.</p> <p>Findings</p> <p>We report that the isolate is <it>F. tularensis </it>subsp. <it>novicida</it>, a subspecies that is rarely isolated.</p> <p>Conclusion</p> <p>The rarity of this <it>novicida </it>subspecies in clinical settings makes each case study important for our understanding of its role in disease and its genetic relationship with other <it>F. tularensis </it>subspecies.</p

Energy separation of single-particle and continuum states in a S=1/2 weakly-coupled chains antiferromagnet

Inelastic neutron scattering is used to study transverse-polarized magnetic excitations in the quasi-one-dimensional S=1/2 antiferromagnet BaCu_2Si_2O_7, where the saturation value for the N\'eel order parameter is $m_0=0.12 \mu_{\rm B}$ per spin. At low energies the spectrum is totally dominated by resolution-limited spin wave-like excitations. An excitation continuum sets in above a well-defined threshold frequency. Experimental results are discussed in the context of current theories for weakly-interacting quantum half-integer spin chains.Comment: 4 pages 4 figure

Genomic islands from five strains of Burkholderia pseudomallei

<p>Abstract</p> <p>Background</p> <p><it>Burkholderia pseudomallei </it>is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of <it>B. pseudomallei </it>are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species.</p> <p>Results</p> <p>We found that genomic islands (GIs) vary greatly among <it>B. pseudomallei </it>strains. We identified 71 distinct GIs from the genome sequences of five reference strains of <it>B. pseudomallei</it>: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3' end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA-mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described.</p> <p>Conclusion</p> <p>Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within <it>B. pseudomallei </it>and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of <it>B. pseudomallei</it>. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species.</p

Spin and Charge Structure Factor of the 2-d Hubbard Model

The spin and charge structure factors are calculated for the Hubbard model on the square lattice near half-filling using a spin-rotation invariant six-slave boson representation. The charge structure factor shows a broad maximum at the zone corner and is found to decrease monotonically with increasing interaction strength and electron density and increasing temperature. The spin structure factor develops with increasing interaction two incommensurate peaks at the zone boundary and along the zone diagonal. Comparison with results of Quantum Monte Carlo and variational calculations is carried out and the agreement is found to be good. The limitations of an RPA-type approach are pointed out.Comment: 18 pages, revtex, 13 postscript figures, submitted to Phys. Rev.

Tri-bimaximal mixing, discrete family symmetries, and a conjecture connecting the quark and lepton mixing matrices

Neutrino oscillation experiments (excluding the LSND experiment) suggest a tri-bimaximal form for the lepton mixing matrix. This form indicates that the mixing matrix is probably independent of the lepton masses, and suggests the action of an underlying discrete family symmetry. Using these hints, we conjecture that the contrasting forms of the quark and lepton mixing matrices may both be generated by such a discrete family symmetry. This idea is that the diagonalisation matrices out of which the physical mixing matrices are composed have large mixing angles, which cancel out due to a symmetry when the CKM matrix is computed, but do not do so in the MNS case. However, in the cases where the Higgs bosons are singlets under the symmetry, and the family symmetry commutes with SU(2)L, we prove a no-go theorem: no discrete unbroken family symmetry can produce the required mixing patterns. We then suggest avenues for future research.Comment: 14 pages, no figures, RevTeX4, references adde

Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response

Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in Caenorhabditis elegans that permits global identification of the binding sites for transcription factors using chromatin immunoprecipitation and deep sequencing. We describe and validate this strategy, and apply it to the transcription factor PHA-4, which plays critical roles in organ development and other cellular processes. We identified thousands of binding sites for PHA-4 during formation of the embryonic pharynx, and also found a role for this factor during the starvation response. Many binding sites were found to shift dramatically between embryos and starved larvae, from developmentally regulated genes to genes involved in metabolism. These results indicate distinct roles for this regulator in two different biological processes and demonstrate the versatility of transcription factors in mediating diverse biological roles.Molecular and Cellular Biolog

Yersinia pestis Evolution on a Small Timescale: Comparison of Whole Genome Sequences from North America

Yersinia pestis, the etiologic agent of plague, was responsible for several devastating epidemics throughout history and is currently of global importance to current public heath and biodefense efforts. Y. pestis is widespread in the Western United States. Because Y. pestis was first introduced to this region just over 100 years ago, there has been little time for genetic diversity to accumulate. Recent studies based upon single nucleotide polymorphisms have begun to quantify the genetic diversity of Y. pestis in North America.To examine the evolution of Y. pestis in North America, a gapped genome sequence of CA88-4125 was generated. Sequence comparison with another North American Y. pestis strain, CO92, identified seven regions of difference (six inversions, one rearrangement), differing IS element copy numbers, and several SNPs.The relatively large number of inverted/rearranged segments suggests that North American Y. pestis strains may be undergoing inversion fixation at high rates over a short time span, contributing to higher-than-expected diversity in this region. These findings will hopefully encourage the scientific community to sequence additional Y. pestis strains from North America and abroad, leading to a greater understanding of the evolutionary history of this pathogen

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured