BACKGROUND Named entity recognition (NER) is an important task in clinical natural language processing (NLP) research. Machine learning (ML) based NER methods have shown good performance in recognizing entities in clinical text. Algorithms and features are two important factors that largely affect the performance of ML-based NER systems. Conditional Random Fields (CRFs), a sequential labelling ...

Repair of oxidative DNA damage, particularly Base Excision Repair (BER), impairment is often associated with Alzheimer's disease pathology. Here, we aimed at investigating the complete Nucleotide Excision Repair (NER), a DNA repair pathway involved in the removal of bulky DNA adducts, status in an Alzheimer-like cell line. The level of DNA damage was quantified using mass spectrometry, NER gene...

Nucleotide excision repair (NER) is a major cellular defense mechanism against DNA damage. We have investigated the role of Mms19 in NER in the yeast Saccharomyces cerevisiae. NER was deficient in the mms19 deletion mutant cell extracts, which was complemented by the NER/transcription factor TFIIH, but not by purified Mms19 protein. In mms19 mutant cells, protein levels of the core TFIIH compon...

To investigate the role of nucleotide excision repair (NER) in the cellular processing of carcinogenic DNA photoproducts induced by defined, environmentally relevant portions of the solar wavelength spectrum, we have determined the mutagenic specificity of simulated sunlight (310-1100 nm), UVA (350-400 nm), and UVB (290-320 nm), as well as of the "nonsolar" model mutagen 254-nm UVC, at the aden...

PM01183 is a novel marine-derived covalent DNA binder in clinical development. PM01183 is structurally similar to trabectedin (yondelis, ecteinascidin-743) except for the C subunit, and this modification is accompanied by different pharmacokinetics in cancer patients. We here characterize the interaction of PM01183 with the nucleotide excision repair (NER) pathway in comparison with trabectedin...

There is a wealth of information about financial systems that is embedded in document collections. In this paper, we focus on a specialized text extraction task for this domain. The objective is to extract mentions of names of financial institutions, or FI names, from financial prospectus documents, and to identify the corresponding real world entities, e.g., by matching against a corpus of suc...

This paper describes about information extraction system, which is an extension of the system developed by team Hitachi for "Disease/Disorder Template filling” task organized by ShARe/CLEF eHealth Evolution Lab 2014. In this extension module we focus on extraction of numerical attributes and values from discharge summary records and associating correct relation between attributes and values. We...

Domain-specific named entity recognition (NER) on Computer Science (CS) scholarly articles is an information extraction task that arguably more challenging for the various annotation aims can hamper and has been less studied than NER in general domain. Given significant progress made NER, we anticipate domain-specific will receive increasing attention years to come. Currently, CS – focus of thi...