A text-mining system for extracting metabolic reactions from full-text articles

Background: Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway—metabolic pathways—has been largely neglected. Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein–protein interactions. Results: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task. Conclusions: We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein–protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed

Defects and impurities in jarosite: A computer simulation study

Computer modelling techniques involving a rigid ion model have been used to investigate the defect structure and impurity site preferences in end-member K-jarosite. Calculated intrinsic vacancy energies show that the K2SO4 neutral cluster, with an energy per species of 1.34 eV, will be the most common defect in the pure phase. Defect reactions leading to vacancies on the Fe site have high energies, in excess of 4.0 eV per species, and are thus unlikely to occur in great numbers. However, the calculations show that divalent metal cations can be incorporated onto the Fe site via solution reactions with oxides leading to the formation of goethite. Calculated solution reactions are exothermic and thus predicted to be highly favourable. At K sites substitutions occur in the order Cd > Zn > Cu, but will be limited due to endothermic solution energies and structural considerations

Cosmological parameters from SDSS and WMAP

We measure cosmological parameters using the three-dimensional power spectrum P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in combination with WMAP and other data. Our results are consistent with a ``vanilla'' flat adiabatic Lambda-CDM model without tilt (n=1), running tilt, tensor modes or massive neutrinos. Adding SDSS information more than halves the WMAP-only error bars on some parameters, tightening 1 sigma constraints on the Hubble parameter from h~0.74+0.18-0.07 to h~0.70+0.04-0.03, on the matter density from Omega_m~0.25+/-0.10 to Omega_m~0.30+/-0.04 (1 sigma) and on neutrino masses from <11 eV to <0.6 eV (95%). SDSS helps even more when dropping prior assumptions about curvature, neutrinos, tensor modes and the equation of state. Our results are in substantial agreement with the joint analysis of WMAP and the 2dF Galaxy Redshift Survey, which is an impressive consistency check with independent redshift survey data and analysis techniques. In this paper, we place particular emphasis on clarifying the physical origin of the constraints, i.e., what we do and do not know when using different data sets and prior assumptions. For instance, dropping the assumption that space is perfectly flat, the WMAP-only constraint on the measured age of the Universe tightens from t0~16.3+2.3-1.8 Gyr to t0~14.1+1.0-0.9 Gyr by adding SDSS and SN Ia data. Including tensors, running tilt, neutrino mass and equation of state in the list of free parameters, many constraints are still quite weak, but future cosmological measurements from SDSS and other sources should allow these to be substantially tightened.Comment: Minor revisions to match accepted PRD version. SDSS data and ppt figures available at http://www.hep.upenn.edu/~max/sdsspars.htm

INNODIA Master Protocol for the evaluation of investigational medicinal products in children, adolescents and adults with newly diagnosed type 1 diabetes

Background The INNODIA consortium has established a pan-European infrastructure using validated centres to prospectively evaluate clinical data from individuals with newly diagnosed type 1 diabetes combined with centralised collection of clinical samples to determine rates of decline in beta-cell function and identify novel biomarkers, which could be used for future stratification of phase 2 clinical trials. Methods In this context, we have developed a Master Protocol, based on the “backbone” of the INNODIA natural history study, which we believe could improve the delivery of phase 2 studies exploring the use of single or combinations of Investigational Medicinal Products (IMPs), designed to prevent or reverse declines in beta-cell function in individuals with newly diagnosed type 1 diabetes. Although many IMPs have demonstrated potential efficacy in phase 2 studies, few subsequent phase 3 studies have confirmed these benefits. Currently, phase 2 drug development for this indication is limited by poor evaluation of drug dosage and lack of mechanistic data to understand variable responses to the IMPs. Identification of biomarkers which might permit more robust stratification of participants at baseline has been slow. Discussion The Master Protocol provides (1) standardised assessment of efficacy and safety, (2) comparable collection of mechanistic data, (3) the opportunity to include adaptive designs and the use of shared control groups in the evaluation of combination therapies, and (4) benefits of greater understanding of endpoint variation to ensure more robust sample size calculations and future baseline stratification using existing and novel biomarkers

Dissolution of jarosite [KFe3(SO4)2(OH)6] at pH 2 and 8: insights from batch experiments and computational modelling

Jarosite [KFe3(SO4)2(OH)6] is a mineral that is common in acidic, sulphate-rich environments, such as acid sulphate soils derived from pyrite-bearing sediments, weathering zones of sulphide ore deposits and acid mine or acid rock drainage (ARD/AMD) sites. The structure of jarosite is based on linear tetrahedral–octahedral–tetrahedral (T–O–T) sheets, made up from slightly distorted FeO6 octahedra and SO4 tetrahedra. Batch dissolution experiments carried out on synthetic jarosite at pH 2, to mimic environments affected by ARD/AMD, and at pH 8, to simulate ARD/AMD environments recently remediated with slaked lime (Ca(OH)2), suggest first order dissolution kinetics. Both dissolution reactions are incongruent, as revealed by non-ideal dissolution of the parent solids and, in the case of the pH 8 dissolution, because a secondary goethite precipitate forms on the surface of the dissolving jarosite grains. The pH 2 dissolution yields only aqueous K, Fe, and SO4. Aqueous, residual solid, and computational modelling of the jarosite structure and surfaces using the GULP and MARVIN codes, respectively, show for the first time that there is selective dissolution of the A- and T-sites, which contain K and SO4, respectively, relative to Fe, which is located deep within the T–O–T jarosite structure. These results have implications for the chemistry of ARD/AMD waters, and for understanding reaction pathways of ARD/AMD mineral dissolution

Raman and IR spectroscopic studies of alunite-supergroup compounds containing AI, Cr3+, Fe3+ and V3+ at the B site

Raman and IR spectroscopies, X-ray diffraction and chemical analysis have been used to characterize synthetic compounds of the alunite supergroup of formula AB3(SO4)2(OH)6, with A = Na+, K+, H3O+ and B = Al, Cr3+, Fe3+, V3+. For each A-site cation, the proportion of B-site vacancies decreases in the same order as the effective ionic radius of the B-site cations (Al > Cr > Fe > V). Raman and IR spectra of the compounds with B = Al and Fe3+ (alunite- and jarosite-group phases) show very close agreement with previously published spectra. The spectra for Cr- and V-based analogues show similarities to the alunite- and jarosite-group phases, and particularly the latter. The Raman and IR spectra are similar in the high-wavenumber ranges (around 3400–3500 cm–1), but are different in the intermediate and, particularly, the lower ranges, <700 cm–1, probably owing to the different responses of Raman and IR to SO4 and metal–O (M–O) group symmetries. The a parameter correlates well with {nu}1SO4, {nu}2SO4 and {nu}4SO4 Raman and {nu}4SO4 IR wavenumbers. There are differences in the OH-stretching regions, and shifts in the main {nu}SO4 and M–O peaks of the alunite-group phases, and Cr-, Fe- and V-based analogues with substitution of K, Na or H3O at the A site in the Raman and IR spectra. Raman and IR spectroscopies are therefore useful in distinguishing these compounds

Synthesis, characterization and thermochemistry of a Pb-jarosite

The enthalpy of formation from the elements of a well-characterized synthetic Pb-jarosite sample corresponding to the chemical formula (H3O)0.74Pb0.13Fe2.92(SO4)2(OH)5.76(H2O)0.24 was measured by high temperature oxide melt solution calorimetry. This value (View the MathML source = −3695.9 ± 9.7 kJ/mol) is the first direct measurement of the heat of formation for a lead-containing jarosite. Comparison to the thermochemical properties of hydronium jarosite and plumbojarosite end-members strongly suggests the existence of a negative enthalpy of mixing possibly related to the nonrandom distribution of Pb2+ ions within the jarosite structure. Based on these considerations, the following thermodynamic data are proposed as the recommended values for the enthalpy of formation from the elements of the ideal stoichiometric plumbojarosite Pb0.5Fe3(SO4)2(OH)6: View the MathML source = −3118.1 ± 4.6 kJ/mol, View the MathML source = −3603.6 ± 4.6 kJ/mol and S° = 376.6 ± 4.5 J/(mol K). These data should prove helpful for the calculation of phase diagrams of the Pb–Fe–SO4–H2O system and for estimating the solubility product of pure plumbojarosite. For illustration, the evolution of the estimated solubility product of ideal plumbojarosite as a function of temperature in the range 5–45 °C was computed (Log(Ksp) ranging from −24.3 to −26.2). An Eh–pH diagram is also presented

beta-AMYLASE4, a noncatalytic protein required for starch breakdown, acts upstream of three active beta-amylases in arabidopsis chloroplasts

This work investigated the roles of β-amylases in the breakdown of leaf starch. Of the nine β-amylase (BAM)–like proteins encoded in the Arabidopsis thaliana genome, at least four (BAM1, -2, -3, and -4) are chloroplastic. When expressed as recombinant proteins in Escherichia coli, BAM1, BAM2, and BAM3 had measurable β-amylase activity but BAM4 did not. BAM4 has multiple amino acid substitutions relative to characterized β-amylases, including one of the two catalytic residues. Modeling predicts major differences between the glucan binding site of BAM4 and those of active β-amylases. Thus, BAM4 probably lost its catalytic capacity during evolution. Total β-amylase activity was reduced in leaves of bam1 and bam3 mutants but not in bam2 and bam4 mutants. The bam3 mutant had elevated starch levels and lower nighttime maltose levels than the wild type, whereas bam1 did not. However, the bam1 bam3 double mutant had a more severe phenotype than bam3, suggesting functional overlap between the two proteins. Surprisingly, bam4 mutants had elevated starch levels. Introduction of the bam4 mutation into the bam3 and bam1 bam3 backgrounds further elevated the starch levels in both cases. These data suggest that BAM4 facilitates or regulates starch breakdown and operates independently of BAM1 and BAM3. Together, our findings are consistent with the proposal that β-amylase is a major enzyme of starch breakdown in leaves, but they reveal unexpected complexity in terms of the specialization of protein function

Epigenetic downregulation of human disabled homolog 2 switches TGF-beta from a tumor suppressor to a tumor promoter

The cytokine TGF-beta acts as a tumor suppressor in normal epithelial cells and during the early stages of tumorigenesis. During malignant progression, cancer cells can switch their response to TGF-beta and use this cytokine as a potent oncogenic factor; however, the mechanistic basis for this is poorly understood. Here we demonstrate that downregulation of disabled homolog 2 (DAB2) gene expression via promoter methylation frequently occurs in human squamous cell carcinomas (SCCs) and acts as an independent predictor of metastasis and poor prognosis. Retrospective microarray analysis in an independent data set indicated that low levels of DAB2 and high levels of TGFB2 expression correlate with poor prognosis. Immunohistochemistry, reexpression, genetic knockout, and RNAi silencing studies demonstrated that downregulation of DAB2 expression modulated the TGF-beta/Smad pathway. Simultaneously, DAB2 down-regulation abrogated TGF-beta tumor suppressor function, while enabling TGF-beta tumor-promoting activities. Downregulation of DAB2 blocked TGF-beta-mediated inhibition of cell proliferation and migration and enabled TGF-beta to promote cell motility, anchorage-independent growth, and tumor growth in vivo. Our data indicate that DAB2 acts as a tumor suppressor by dictating tumor cell TGF-beta responses, identify a biomarker for SCC progression, and suggest a means to stratify patients with advanced SCC who may benefit clinically from anti-TGF-beta therapies