BACKGROUND Identifying key variables such as disorders within the clinical narratives in electronic health records has wide-ranging applications within clinical practice and biomedical research. Previous research has demonstrated reduced performance of disorder named entity recognition (NER) and normalization (or grounding) in clinical narratives than in biomedical publications. In this work, w...

Rev3, the catalytic subunit of DNA polymerase ζ, is essential for translesion synthesis of cytotoxic DNA photolesions, whereas the Rev1 protein plays a noncatalytic role in translesion synthesis. Here, we reveal that mammalian Rev3(-/-) and Rev1(-/-) cell lines additionally display a nucleotide excision repair (NER) defect, specifically during S phase. This defect is correlated with the normal ...

The molecular basis of resistance to nucleotide excision repair (NER) of certain bulky DNA lesions is poorly understood. To address this issue, we have studied NER in human HeLa cell extracts of two topologically distinct lesions, one derived from benzo[a]pyrene (10R-(+)-cis-anti-B[a]P-N(2)-dG), and one from the food mutagen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (C8-dG-PhIP), embedded...

BACKGROUND Nucleotide excision repair (NER) removes many types of DNA lesions including those induced by UV radiation and platinum-based therapy. Resistance to platinum-based therapy correlates with high expression of ERCC1, a major element of the NER machinery. The interaction between ERCC1 and XPA is essential for a successful NER function. Therefore, one way to regulate NER is by inhibiting ...

More than 20 polypeptides are required for the process of nucleotide excision repair (NER) in both human and yeast cells. This pathway of excision repair has most often been viewed as an ordered multi-step process involving steps of damage recognition, incision/excision and finally repair DNA synthesis. Here we present evidence for the existence of a complex of human NER proteins pre-assembled ...

This paper addresses the problem of named entity recognition (NER) in travel-related search queries. NER is an important step toward a richer understanding of user-generated inputs in information retrieval systems. NER in queries is challenging due to minimal context and few structural clues. NER in restricted-domain queries is useful in vertical search applications, for example following query...

Named Entity Recognition (NER) from speech usually involves two sequential steps: transcribing the speech using Automatic Speech Recognition (ASR) and annotating the outputs of the ASR process using NER techniques. Recognizing named entities in automatic transcripts is difficult due to the presence of transcription errors and the absence of some important NER clues, such as capitalization and p...

Named Entity Recognition or Extraction (NER) is an important task for automated text processing for industries and academia engaged in the field of language processing, intelligence gathering and Bioinformatics. In this paper we discuss the general problem of Named Entity Recognition, more specifically the challenges in NER in languages that do not have language resources e.g. large annotated c...

To restore full genomic integrity in a eukaryotic cell, DNA repair processes have to be coordinated with the resetting of nucleosomal organization. We have established a cell-free system using Drosophila embryo extracts to investigate the mechanism linking de novo nucleosome formation to nucleotide excision repair (NER). Closed-circular DNA containing a uniquely placed cisplatin-DNA adduct was ...

This paper explores the use of unlabeled data in a knowledge-poor approach to German NER. German is especially interesting for NER since not only names but all nouns are capitalized. Therefore, large and reliable lexical resources are necessary to develop and adapt systems for NER. Motivated by a model of word form observance, distinguishing three levels of different granularity, a method for t...