SUMMARY POSBIOTM-NER is a trainable biomedical named-entity recognition system. POSBIOTM-NER can be automatically trained and adapted to new datasets without performance degradation, using CRF (conditional random field) machine learning techniques and automatic linguistic feature analysis. Currently, we have trained our system on three different datasets. GENIA-NER was trained based on GENIA Co...

Nerolidol (Ner), a major component of many plant essential oils, is known for its various biological properties. However, the low solubility of Ner in water and its susceptibility to degradation limit its application. The aim of our study was to improve the solubility and photostability of Ner through its encapsulation in different cyclodextrins (CDs). The formation constants of cis-, trans-Ner...

In this study, we present a brief overview of Named Entity Recognition (NER) system, various approaches followed for NER systems and finally NER systems for Urdu language. Urdu language raises several challenges to Natural Language Processing (NLP) largely due to its rich morphology. Research against NER systems in Urdu language is at infancy stage therefore the focus of this study is on challe...

Nucleotide excision repair (NER) removes UV-induced DNA damage and other bulky DNA lesions, thereby maintaining genomic integrity. Dr Qingyi Wei's group demonstrated over the last decade that NER fidelity and single-nucleotide polymorphisms (SNPs) in NER genes constitute melanoma risk biomarkers. In this issue, Li et al. provide evidence that SNPs in NER genes may also predict melanoma survival.

Nucleotide excision repair (NER) is a highly conserved genome repair pathway acting on helix distorting DNA lesions. NER is divided into two subpathways: global genome NER (GG-NER), which is responsible for repair throughout genomes, and transcription-coupled NER (TC-NER), which acts on lesions that impede transcription. The extent of the Trypanosoma brucei genome that is transcribed is highly ...

Named entity recognition (NER) in information extraction (IE) systems is usually based on large gazetteers — datasets of well-known and classified entities. NER is also often performed by independent look-up piece of code, which is considered as a bottleneck of many NER systems. In this paper, we present two approaches for building tree gazetteers for NER; i.e. lookup by token and by character.

Named Entity Recognition (NER) poses new challenges in real-world documents in which there are entities with different roles according to their purpose or meaning. Retrieving all the possible entities in scenarios in which only a subset of them based on their role is needed, produces noise on the overall precision. This work proposes a NER model that relies on role classification models that su...

Impaired gap filling and sealing of chromosomal DNA in nucleotide excision repair (NER) leads to genome instability. XRCC1-DNA ligase IIIalpha (XRCC1-Lig3) plays a central role in the repair of DNA single-strand breaks but has never been implicated in NER. Here we show that XRCC1-Lig3 is indispensable for ligation of NER-induced breaks and repair of UV lesions in quiescent cells. Furthermore, o...

Exposure to aristolochic acid (AA), a component of Aristolochia plants used in herbal remedies, is associated with chronic kidney disease and urothelial carcinomas of the upper urinary tract. Following metabolic activation, AA reacts with dA and dG residues in DNA to form aristolactam (AL)-DNA adducts. These mutagenic lesions generate a unique TP53 mutation spectrum, dominated by A:T to T:A tra...