Biomedical event extraction based on GRU integrating attention mechanism.

BACKGROUND: Biomedical event extraction is a crucial task in biomedical text mining. As the primary forum for international evaluation of different biomedical event extraction technologies, BioNLP Shared Task represents a trend in biomedical text mining toward fine-grained information extraction (IE). The fourth series of BioNLP Shared Task in 2016 (BioNLP-ST'16) proposed three tasks, in which the Bacteria Biotope event extraction (BB) task has been put forward in the earlier BioNLP-ST. Deep learning methods provide an effective way to automatically extract more complex features and achieve notable results in various natural language processing tasks. RESULTS: The experimental results show that the presented approach can achieve an F-score of 57.42% in the test set, which outperforms previous state-of-the-art official submissions to BioNLP-ST 2016. CONCLUSIONS: In this paper, we propose a novel Gated Recurrent Unit Networks framework integrating attention mechanism for extracting biomedical events between biotope and bacteria from biomedical literature, utilizing the corpus from the BioNLP'16 Shared Task on Bacteria Biotope task. The experimental results demonstrate the potential and effectiveness of the proposed framework.

Environmental vanadium distribution, mobility and bioaccumulation in different land-use districts in Panzhihua Region, SW China.

In order to characterize environmental vanadium distribution, mobility, and bioaccumulation, a total of 55 soil samples and 36 plant samples were collected in four typical land-use districts in Panzhihua region, Southwestern China. Soil samples were analyzed with the modified Community Bureau of Reference (BCR) sequential extraction procedure, and the content of vanadium in soil and plant was determined by ICP-AES. The total content of vanadium was 208.1-938.4 mg kg(-1) in smelting area, 111.6-591.2 mg kg(-1) in mining area, 94.0-183.6 mg kg(-1) in urban park, and 71.7-227.2 mg kg(-1) in agricultural area, respectively, while the bio-available content of vanadium was characterized that the polluted areas (mining area 18.8-83.6 mg kg(-1), smelting area 41.7-132.1 mg kg(-1)) and the unpolluted area (agricultural area 9.8-26.4 mg kg(-1), urban park 9.9-25.2 mg kg(-1)). In addition, the contamination degree of vanadium in soil was smelting area > mining area > agricultural area ≈ urban park. Moreover, the fraction of vanadium in each sequential extraction characterized that residual fraction > oxidizable fraction > reducible fraction > acid soluble fraction. The bioaccumulation of vanadium from soil to plant was weak to intermediate absorption. Therefore, some countermeasures such as soil monitoring and remediation should be to take in the sooner future, especially in mining and smelting area.