A realistic assessment of methods for extracting gene/protein interactions from free text

Background: The automated extraction of gene and/or protein interactions from the literature is one of the most important targets of biomedical text mining research. In this paper we present a realistic evaluation of gene/protein interaction mining relevant to potential non-specialist users. Hence we have specifically avoided methods that are complex to install or require reimplementation, and we coupled our chosen extraction methods with a state-of-the-art biomedical named entity tagger. Results: Our results show: that performance across different evaluation corpora is extremely variable; that the use of tagged (as opposed to gold standard) gene and protein names has a significant impact on performance, with a drop in F-score of over 20 percentage points being commonplace; and that a simple keyword-based benchmark algorithm when coupled with a named entity tagger outperforms two of the tools most widely used to extract gene/protein interactions. Conclusion: In terms of availability, ease of use and performance, the potential non-specialist user community interested in automatically extracting gene and/or protein interactions from free text is poorly served by current tools and systems. The public release of extraction tools that are easy to install and use, and that achieve state-of-art levels of performance should be treated as a high priority by the biomedical text mining community

Space Weathering Products Found on the Surfaces of the Itokawa Dust Particles: A Summary of the Initial Analysis

Surfaces of airless bodies exposed to interplanetary space gradually have their structures, optical properties, chemical compositions, and mineralogy changed by solar wind implantation and sputtering, irradiation by galactic and solar cosmic rays, and micrometeorite bombardment. These alteration processes and the resultant optical changes are known as space weathering [1, 2, 3]. Our knowledge of space weathering has depended almost entirely on studies of the surface materials returned from the Moon and regolith breccia meteorites [1, 4, 5, 6] until the surface material of the asteroid Itokawa was returned to the Earth by the Hayabusa spacecraft [7]. Lunar soil studies show that space weathering darkens the albedo of lunar soil and regolith, reddens the slopes of their reflectance spectra, and attenuates the characteristic absorption bands of their reflectance spectra [1, 2, 3]. These changes are caused by vapor deposition of small (<40 nm) metallic Fe nanoparticles within the grain rims of lunar soils and agglutinates [5, 6, 8]. The initial analysis of the Itokawa dust particles revealed that 5 out of 10 particles have nanoparticle-bearing rims, whose structure varies depending on mineral species. Sulfur-bearing Fe-rich nanoparticles (npFe) exist in a thin (5-15 nm) surface layer (zone I) on olivine, low-Ca pyroxene, and plagioclase, suggestive of vapor deposition. Sulfur-free npFe exist deeper inside (<60 nm) ferromagnesian silicates (zone II). Their texture suggests formation by amorphization and in-situ reduction of Fe2+ in ferromagnesian silicates [7]. On the other hand, nanophase metallic iron (npFe0) in the lunar samples is embedded in amorphous silicate [5, 6, 8]. These textural differences indicate that the major formation mechanisms of the npFe0 are different between the Itokawa and the lunar samples. Here we report a summary of the initial analysis of space weathering of the Itokawa dust particles

Regulators of floral fragrance production and their target genes in petunia are not exclusively active in the epidermal cells of petals

In which cells of the flower volatile biosynthesis takes place is unclear. In rose and snapdragon, some enzymes of the volatile phenylpropanoid/benzenoid pathway have been shown to be present in the epidermal cells of petals. It is therefore generally believed that the production of these compounds occurs in these cells. However, whether the entire pathway is active in these cells and whether it is exclusively active in these cells remains to be proven. Cell-specific transcription factors activating these genes will determine in which cells they are expressed. In petunia, the transcription factor EMISSION OF BENZENOIDS II (EOBII) activates the ODORANT1 (ODO1) promoter and the promoter of the biosynthetic gene isoeugenol synthase (IGS). The regulator ODO1 in turn activates the promoter of the shikimate gene 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Here the identification of a new target gene of ODO1, encoding an ABC transporter localized on the plasma membrane, PhABCG1, which is co-expressed with ODO1, is described. PhABCG1 expression is up-regulated in petals overexpressing ODO1 through activation of the PhABCG1 promoter. Interestingly, the ODO1, PhABCG1, and IGS promoters were active in petunia protoplasts originating from both epidermal and mesophyll cell layers of the petal, suggesting that the volatile phenylpropanoid/benzenoid pathway in petunia is active in these different cell types. Since volatile release occurs from epidermal cells, trafficking of (volatile) compounds between cell layers must be involved, but the exact function of PhABCG1 remains to be resolved

Discourse structure and language technology

This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.An increasing number of researchers and practitioners in Natural Language Engineering face the prospect of having to work with entire texts, rather than individual sentences. While it is clear that text must have useful structure, its nature may be less clear, making it more difficult to exploit in applications. This survey of work on discourse structure thus provides a primer on the bases of which discourse is structured along with some of their formal properties. It then lays out the current state-of-the-art with respect to algorithms for recognizing these different structures, and how these algorithms are currently being used in Language Technology applications. After identifying resources that should prove useful in improving algorithm performance across a range of languages, we conclude by speculating on future discourse structure-enabled technology.Peer Reviewe

Epigenetic inactivation of TCF2 in ovarian cancer and various cancer cell lines

Transcription factor 2 gene (TCF2) encodes hepatocyte nuclear factor 1β (HNF1β), a transcription factor associated with development and metabolism. Mutation of TCF2 has been observed in renal cell cancer, and by screening aberrantly methylated genes, we have now identified TCF2 as a target for epigenetic inactivation in ovarian cancer. TCF2 was methylated in 53% of ovarian cancer cell lines and 26% of primary ovarian cancers, resulting in loss of the gene's expression. TCF2 expression was restored by treating cells with a methyltransferase inhibitor, 5-aza-2′deoxycitidine (5-aza-dC). In addition, chromatin immunoprecipitation showed deacetylation of histone H3 in methylated cells and, when combined with 5-aza-dC, the histone deacetylase inhibitor trichostatin A synergistically induced TCF2 expression. Epigenetic inactivation of TCF2 was also seen in colorectal, gastric and pancreatic cell lines, suggesting general involvement of epigenetic inactivation of TCF2 in tumorigenesis. Restoration of TCF2 expression induced expression of HNF4α, a transcriptional target of HNF1β, indicating that epigenetic silencing of TCF2 leads to alteration of the hepatocyte nuclear factor network in tumours. These results suggest that TCF2 is involved in the development of ovarian cancers and may represent a useful target for their detection and treatment