Gimli: open source and high-performance biomedical name recognition.
Campos D, Matos S, Oliveira JL.
BMC Bioinformatics. 2013 Feb 15;14:54. doi:10.1186/1471-2105-14-54.
PMID: #23413997# Free
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TrigNER: automatically optimized biomedical event trigger recognition on scientific documents. Campos D, Bui QC, Matos S, Oliveira JL.
Source Code Biol Med. 2014 Jan 8;9(1):1. doi:10.1186/1751-0473-9-1.
PMID: #24401704# Free
recognition of named entities (NER)
The recognition of named entities (NER) is an elementary task in biomedical text mining.
A number of NER solutions have been proposed in recent years, taking advantage of available annotated corpora, terminological resources and machine-learning techniques.
Currently, the best performing solutions combine the outputs from selected annotation solutions measured against a single corpus. However, little effort has been spent on a systematic analysis of (...)
seen in up to 50% of psoriasis patients, more common in patients with psoriatic arthropathy
histopath -> psoriasiform onychitis with spongiform pustulation, negative fungal special stains (see photos)
differential -> onychomycosis, eczematous onychitis, Reiter syndrome
melanoma excision with residual pigmentation : only melanophages present, melanoma markers negative https://twitter.com/DermpathMGH/status/751453426890993664
nasolabial cyst Nasolabial cysts are located in the soft tissue just lateral to the nose at the lateral aspect of the maxillary alveolar process. They are thought to arise from the nasolacrimal duct. Non-ciliated pseudostratified columnar epithelium with interspersed mucous cells forms the epithelial lining. These features may be lost through squamous metaplasia. Apocrine metaplasia of the cyst lining has also been (...)
nasopalatine duct cyst The nasopalatine duct cyst is located within the nasopalatine canal that runs from nose to the oral cavity through the midline of the anterior bony palate, just posterior to the central incisor teeth. The cyst arises from epithelial remnants of the nasopalatine duct, and its lining may be pseudostratified columnar ciliated epithelium, stratified squamous epithelium, columnar or cuboidal epithelium and combinations of these. As surgical treatment comprises emptying (...)
Exon 19 deletions
Definition: EGFR-Del19 are exon 19 deletions.
Comparing overall survival between first generation EGFR-TKIs and chemotherapy in lung cancer patients with Del19/L858R.
Deng W, Lei Y, Liu S, Yang J, Tu H, Yan H, Wu Y.
Chin J Cancer Res. 2016 Jun;28(3):339-47.
Ibrutinib selectively and irreversibly targets EGFR (L858R, Del19) mutant but is moderately resistant to EGFR (T790M) mutant NSCLC (...)
tumor budding in colorectal cancer
Definition: Tumor budding is a well-established adverse prognostic factor in colorectal cancer.
Recommendations for Reporting Tumor Budding in CRC based on the International Tumor Budding Consensus Conference 2016 at ESPIAP Cologne2016 https://twitter.com/pathologia/status/781235895932510209
tumor budding in colorectal carcinoma (CRC) Tumor budding is a well-established adverse prognostic factor in colorectal cancer.
IL-34; Interleukin-34 WKPD
Interleukin 34 (IL-34) is a protein belonging to a group of cytokines called interleukins. It was originally identified in humans, by large scale screening of secreted proteins; chimpanzee, murine, rat and chicken interleukin 34 orthologs have also been found.
IL-34 increases growth or survival of immune cells known as monocytes; it elicits its activity by binding the Colony stimulating factor 1 receptor.
Messenger RNA (mRNA) expression of human IL-34 is (...)