Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens

<p>Abstract</p> <p>Background</p> <p>The Enteropathogen Resource Integration Center (ERIC; <url>http://www.ericbrc.org</url>) has a goal of providing bioinformatics support for the scientific community researching enteropathogenic bacteria such as <it>Escherichia coli </it>and <it>Salmonella </it>spp. Rapid and accurate identification of experimental conclusions from the scientific literature is critical to support research in this field. Natural Language Processing (NLP), and in particular Information Extraction (IE) technology, can be a significant aid to this process.</p> <p>Description</p> <p>We have trained a powerful, state-of-the-art IE technology on a corpus of abstracts from the microbial literature in PubMed to automatically identify and categorize biologically relevant entities and predicative relations. These relations include: Genes/Gene Products and their Roles; Gene Mutations and the resulting Phenotypes; and Organisms and their associated Pathogenicity. Evaluations on blind datasets show an F-measure average of greater than 90% for entities (genes, operons, etc.) and over 70% for relations (gene/gene product to role, etc). This IE capability, combined with text indexing and relational database technologies, constitute the core of our recently deployed text mining application.</p> <p>Conclusion</p> <p>Our Text Mining application is available online on the ERIC website <url>http://www.ericbrc.org/portal/eric/articles</url>. The information retrieval interface displays a list of recently published enteropathogen literature abstracts, and also provides a search interface to execute custom queries by keyword, date range, etc. Upon selection, processed abstracts and the entities and relations extracted from them are retrieved from a relational database and marked up to highlight the entities and relations. The abstract also provides links from extracted genes and gene products to the ERIC Annotations database, thus providing access to comprehensive genomic annotations and adding value to both the text-mining and annotations systems.</p

Search for sterile neutrino mixing in the MINOS long-baseline experiment

A search for depletion of the combined flux of active neutrino species over a 735 km baseline is reported using neutral-current interaction data recorded by the MINOS detectors in the NuMI neutrino beam. Such a depletion is not expected according to conventional interpretations of neutrino oscillation data involving the three known neutrino flavors. A depletion would be a signature of oscillations or decay to postulated noninteracting sterile neutrinos, scenarios not ruled out by existing data. From an exposure of 3.18×1020 protons on target in which neutrinos of energies between ~500¿¿MeV and 120 GeV are produced predominantly as ¿µ, the visible energy spectrum of candidate neutral-current reactions in the MINOS far detector is reconstructed. Comparison of this spectrum to that inferred from a similarly selected near-detector sample shows that of the portion of the ¿µ flux observed to disappear in charged-current interaction data, the fraction that could be converting to a sterile state is less than 52% at 90% confidence level (C.L.). The hypothesis that active neutrinos mix with a single sterile neutrino via oscillations is tested by fitting the data to various models. In the particular four-neutrino models considered, the mixing angles ¿24 and ¿34 are constrained to be less than 11° and 56° at 90% C.L., respectively. The possibility that active neutrinos may decay to sterile neutrinos is also investigated. Pure neutrino decay without oscillations is ruled out at 5.4 standard deviations. For the scenario in which active neutrinos decay into sterile states concurrently with neutrino oscillations, a lower limit is established for the neutrino decay lifetime t3/m3&gt;2.1×10-12¿¿s/eV at 90% C.L

First observations of separated atmospheric nu_mu and bar{nu-mu} events in the MINOS detector

The complete 5.4 kton MINOS far detector has been taking data since the beginning of August 2003 at a depth of 2070 meters water-equivalent in the Soudan mine, Minnesota. This paper presents the first MINOS observations of nuµ and [overline nu ]µ charged-current atmospheric neutrino interactions based on an exposure of 418 days. The ratio of upward- to downward-going events in the data is compared to the Monte Carlo expectation in the absence of neutrino oscillations, giving Rup/downdata/Rup/downMC=0.62-0.14+0.19(stat.)±0.02(sys.). An extended maximum likelihood analysis of the observed L/E distributions excludes the null hypothesis of no neutrino oscillations at the 98% confidence level. Using the curvature of the observed muons in the 1.3 T MINOS magnetic field nuµ and [overline nu ]µ interactions are separated. The ratio of [overline nu ]µ to nuµ events in the data is compared to the Monte Carlo expectation assuming neutrinos and antineutrinos oscillate in the same manner, giving R[overline nu ][sub mu]/nu[sub mu]data/R[overline nu ][sub mu]/nu[sub mu]MC=0.96-0.27+0.38(stat.)±0.15(sys.), where the errors are the statistical and systematic uncertainties. Although the statistics are limited, this is the first direct observation of atmospheric neutrino interactions separately for nuµ and [overline nu ]µ

Search for Kaluza-Klein Graviton Emission in ppˉp\bar{p} Collisions at s=1.8\sqrt{s}=1.8 TeV using the Missing Energy Signature

We report on a search for direct Kaluza-Klein graviton production in a data sample of 84 ${pb}^{-1}$ of \ppb collisions at $\sqrt{s}$ = 1.8 TeV, recorded by the Collider Detector at Fermilab. We investigate the final state of large missing transverse energy and one or two high energy jets. We compare the data with the predictions from a $3+1+n$-dimensional Kaluza-Klein scenario in which gravity becomes strong at the TeV scale. At 95% confidence level (C.L.) for $n$=2, 4, and 6 we exclude an effective Planck scale below 1.0, 0.77, and 0.71 TeV, respectively.Comment: Submitted to PRL, 7 pages 4 figures/Revision includes 5 figure

Measurement of the average time-integrated mixing probability of b-flavored hadrons produced at the Tevatron

We have measured the number of like-sign (LS) and opposite-sign (OS) lepton pairs arising from double semileptonic decays of $b$ and $\bar{b}$-hadrons, pair-produced at the Fermilab Tevatron collider. The data samples were collected with the Collider Detector at Fermilab (CDF) during the 1992-1995 collider run by triggering on the existence of $\mu \mu$ and $e \mu$ candidates in an event. The observed ratio of LS to OS dileptons leads to a measurement of the average time-integrated mixing probability of all produced $b$-flavored hadrons which decay weakly, $\bar{\chi} = 0.152 \pm 0.007$ (stat.) $\pm 0.011$ (syst.), that is significantly larger than the world average $\bar{\chi} = 0.118 \pm 0.005$.Comment: 47 pages, 10 figures, 15 tables Submitted to Phys. Rev.

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes

Measurement of single π0 production by coherent neutral-current ν Fe interactions in the MINOS Near Detector

Forward single π0 production by coherent neutral-current interactions, νA→νAπ0, is investigated using a 2.8×1020 protons-on-target exposure of the MINOS Near Detector. For single-shower topologies, the event distribution in production angle exhibits a clear excess above the estimated background at very forward angles for visible energy in the range 1-8 GeV. Cross sections are obtained for the detector medium comprised of 80% iron and 20% carbon nuclei with =48, the highest- target used to date in the study of this coherent reaction. The total cross section for coherent neutral-current single π0 production initiated by the νμ flux of the NuMI low-energy beam with mean (mode) Eν of 4.9 GeV (3.0 GeV), is 77.6±5.0(stat)-16.8+15.0(syst)×10-40 cm2 pernucleus. The results are in good agreement with predictions of the Berger-Sehgal model

Measurements of atmospheric neutrinos and antineutrinos in the MINOS far detector

This paper reports measurements of atmospheric neutrino and antineutrino interactions in the MINOS Far Detector, based on 2553 live-days (37.9 kton-years) of data. A total of 2072 candidate events are observed. These are separated into 905 contained-vertex muons and 466 neutrino-induced rock-muons, both produced by charged-current v_µ and v¯_µ interactions, and 701 contained-vertex showers, composed mainly of charged-current v_e and v¯_e interactions and neutral-current interactions. The curvature of muon tracks in the magnetic field of the MINOS Far Detector is used to select separate samples of v_µ and v¯_µ events. The observed ration of v¯_µ to v_µ events is compared with the Monte Carlo (MC) simulation, giving a double ration of (R^(data)_(v¯/v))/(R^(MC)_(v¯/v)) = 1.03 ± 0.08(stat) ± 0.08(syst). The v_µ and v¯_µ data are separated into bins of L/E resolution, based on the reconstructed energy and direction of each event, and a maximum likelihood fit to the observed L/E distributions is used to determine the atmospheric neutrino oscillation parameters. This fit returns 90% confidence limits of |Δm^2| = (1.9 ± 0.4) x 10^(-3) eV^2 and sin^(2)2θ > 0.86. The fit is extended to incorporate separate v_µ and v¯_µ oscillation parameters, returning 90% confidence limits of |Δm^2|-|Δm¯^2| = 0.6^(2.4)_(-0.8) x 10^(-3) eV^2 on the difference between the squared-mass splittings for neutrinos and antineutrinos

Search for Sterile Neutrinos Mixing with Muon Neutrinos in MINOS

We report results of a search for oscillations involving a light sterile neutrino over distances of 1.04 and 735 km in a νμ-dominated beam with a peak energy of 3 GeV. The data, from an exposure of 10.56 × 10^20 protons on target, are analyzed using a phenomenological model with one sterile neutrino. We constrain the mixing parameters θ24 and Δm41^2 and set limits on parameters of the four-dimensional Pontecorvo-Maki- Nakagawa-Sakata matrix, |Uμ4|2 and |Uτ4|2, under the assumption that mixing between νe and νs is negligible (|Ue4|^2 = 0). No evidence for νμ → νs transitions is found and we set a world-leading limit on θ24 for values of Δm41^2 ≲ 1 eV^2

Search for flavor-changing nonstandard neutrino interactions using nu(e) appearance in MINOS

We report new constraints on flavor-changing nonstandard neutrino interactions from the MINOS long-baseline experiment using νe and ¯νe appearance candidate events from predominantly νμ and ¯νμ beams. We used a statistical selection algorithm to separate νe candidates from background events, enabling an analysis of the combined MINOS neutrino and antineutrino data. We observe no deviations from standard neutrino mixing, and thus place constraints on the nonstandard interaction matter effect, |ϵeτ|, and phase, (δCP+δeτ), using a 30-bin likelihood fit