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

Can ABCF2 protein expression predict the prognosis of uterine cancer?

Uterine cervical and endometrial cancers are common malignant solid neoplasms for which there are no useful prognostic markers. In this study, we evaluate the relationship between ATP-binding cassette superfamily F2 (ABCF2) expression and clinical factors including clinical stage, histologic type, grade and prognosis in uterine cervical and endometrial cancer. Two hundred and sixty seven cervical and 103 endometrial cancers were studied. ATP-binding cassette superfamily F2 cytoplasmic expression was detected by immunohistochemical staining and scored as positive or negative. Among cervical cancer cases, 149 (55.8%) expressed ABCF2. The overall survival was longer in ABCF2-negative than ABCF2-positive cases (P=0.0069). Statistically significant prognostic factors for survival were ABCF2 positivity (risk ratio (rr)=1.437), old age (rr=1.550) and advanced stage (rr=2.577). ATP-binding cassette superfamily F2 positivity was an independent prognostic factor by multivariate proportional hazard test (P=0.0002). Among endometrial cancer cases, 72 (69.9%) were cytoplasmic ABCF2 positive. However, there was no significant relationship between ABCF2 expression and age, clinical stage, histologic type, histologic grade, oestrogen receptor status or prognosis. ATP-binding cassette superfamily F2 expression may be a useful prognostic marker in cervical but not endometrial cancer. The role of ABCF2 protein may differ depending on the type of cancer

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