BIOADI: a machine learning approach to identifying abbreviations and definitions in biological literature

BACKGROUND: To automatically process large quantities of biological literature for knowledge discovery and information curation, text mining tools are becoming essential. Abbreviation recognition is related to NER and can be considered as a pair recognition task of a terminology and its corresponding abbreviation from free text. The successful identification of abbreviation and its corresponding definition is not only a prerequisite to index terms of text databases to produce articles of related interests, but also a building block to improve existing gene mention tagging and gene normalization tools. RESULTS: Our approach to abbreviation recognition (AR) is based on machine-learning, which exploits a novel set of rich features to learn rules from training data. Tested on the AB3P corpus, our system demonstrated a F-score of 89.90% with 95.86% precision at 84.64% recall, higher than the result achieved by the existing best AR performance system. We also annotated a new corpus of 1200 PubMed abstracts which was derived from BioCreative II gene normalization corpus. On our annotated corpus, our system achieved a F-score of 86.20% with 93.52% precision at 79.95% recall, which also outperforms all tested systems. CONCLUSION: By applying our system to extract all short form-long form pairs from all available PubMed abstracts, we have constructed BIOADI. Mining BIOADI reveals many interesting trends of bio-medical research. Besides, we also provide an off-line AR software in the download section on http://bioagent.iis.sinica.edu.tw/BIOADI/

KINEMATIC ANALYSIS OF THE SUPPORTING LEG BETWEEN DIFFERENT WEIGHT DIVISIONS IN THE ROUNDHOUSE KICK OF TAEKWONDO

The purpose of this study was to compare kinematic differences in the supporting leg between two weight divisions in the Taekwondo Roundhouse Kick. Collegiate Taekwondo athletes participated in the study and differences in maximum joint angles and ranges of motion on the supporting leg during executing the Roundhouse Kick were examined. The results showed significantly larger (

Burkitt's Lymphoma Mimicking a Primary Gynecologic Tumor

SummaryObjectiveBurkitt's lymphoma (BL) occurs mostly in children; bilateral ovarian involvement mimicking a gynecologic malignancy in adults is extremely rare. Here, we report a patient with BL mimicking a gynecologic tumorCase ReportA 50-year-old Taiwanese woman presented with the complaint of persistent lower abdominal distension with dull pain, easy satiety, and progressively increasing abdominal girth for 2 weeks. Amenorrhea was also noted for about 2 months, and her review of systems was negative for the common “B” symptoms associated with lymphoma. At our hospital, imaging studies revealed a huge pelvic mass (10.8 ×8.7 cm), suggesting a large subserous myoma or an ovarian tumor. Under the impression of pelvic mass, she underwent exploratory laparotomy. Primary ovarian sex-cord malignancy with cecum involvement was impressed by the primitive intraoperative frozen section report. Subsequently, an optimal cytoreductive operation with right hemicolectomy was performed. However, final histopathologic report was an extranodal multifocal BL.ConclusionAlthough extranodal BL in ovaries is a rare condition, it should be noted in the differential diagnosis of pelvic gynecologic malignancies

Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization

Abstract Background Previously, gene normalization (GN) systems are mostly focused on disambiguation using contextual information. An effective gene mention tagger is deemed unnecessary because the subsequent steps will filter out false positives and high recall is sufficient. However, unlike similar tasks in the past BioCreative challenges, the BioCreative III GN task is particularly challenging because it is not species-specific. Required to process full-length articles, an ineffective gene mention tagger may produce a huge number of ambiguous false positives that overwhelm subsequent filtering steps while still missing many true positives. Results We present our GN system participated in the BioCreative III GN task. Our system applies a typical 2-stage approach to GN but features a soft tagging gene mention tagger that generates a set of overlapping gene mention variants with a nearly perfect recall. The overlapping gene mention variants increase the chance of precise match in the dictionary and alleviate the need of disambiguation. Our GN system achieved a precision of 0.9 (F-score 0.63) on the BioCreative III GN test corpus with the silver annotation of 507 articles. Its TAP-k scores are competitive to the best results among all participants. Conclusions We show that despite the lack of clever disambiguation in our gene normalization system, effective soft tagging of gene mention variants can indeed contribute to performance in cross-species and full-text gene normalization.</p

Ontology-based HBIM for historic buildings with traditional woodwork in Taiwan

In recent years, the use of Historic Building Information Modeling (HBIM) has grown prevalent and thus provided a research opportunity. Differing from newly constructed buildings, structural components of historic buildings come with unique physical configurations and have amassed impressive amount of restoration data, all of which must be taken into consideration when incorporating Building Information Modeling. In terms of modelling, it is critical to determine the appropriate level of detail (LoD), level of information (LoI), especially the comprehensiveness and expandability of the database. International Committee for Documentation/Conceptual Reference Model (CIDOC CRM) is a widely accepted standard for ontology model. This study aims to integrate the HBIM and CIDOC CRM to construct a framework and comprehensive operational procedure for the modeling of traditional Minan architecture and a database with complete semantics archiving the background and restoration data. Autodesk A360 is ideal for collaborative. However, there are limitations when it comes to developing advanced models for data management or query; interactive experience; meeting model applications derived from future scenarios. Therefore, the study also offers a 3D modeling platform constructed using Unity, as well as a comparison of the platforms built with Unity, three.js and Autodesk A360 as a reference for users

Effect of bis(hydroxymethyl) alkanoate curcuminoid derivative MTH-3 on cell cycle arrest, apoptotic and autophagic pathway in triple-negative breast adenocarcinoma MDA-MB-231 cells: An in vitro study

Curcumin has been shown to exert potential antitumor activity in vitro and in vivo involved in multiple signaling pathways. However, the application of curcumin is still limited because of its poor hydrophilicity and low bio-availability. In the present study, we investigated the therapeutic effects of a novel and water soluble bis(hydroxymethyl) alkanoate curcuminoid derivative, MTH-3, on human breast adenocarcinoma MDA-MB-231 cells. This study investigated the effect of MTH-3 on cell viability, cell cycle and induction of autophagy and apoptosis in MDA-MB-231 cells. After 24-h treatment with MTH-3, a concentration-dependent decrease in MDA-MB-231 cell viability was observed, and the IC50 value was 5.37±1.22 μM. MTH-3 significantly triggered G2/M phase arrest and apoptosis in MDA-MB-231 cells. Within a 24-h treatment, MTH-3 decreased the CDK1 activity by decreasing CDK1 and cyclin B1 protein levels. MTH-3-induced apoptosis was further confirmed by morphological assessment and Annexin V/PI staining assay. Induction of apoptosis caused by MTH-3 was accompanied by an apparent increase of DR3, DR5 and FADD and, as well as a marked decrease of Bcl-2 and Bcl-xL protein expression. MTH-3 also decreased the protein levels of Ero1, PDI, PERK and calnexin, as well as increased the expression of IRE1α, CHOP and Bip that consequently led to ER stress and MDA-MB-231 cell apoptosis. In addition, MTH-3-treated cells were involved in the autophagic process and cleavage of LC3B was observed. MTH-3 enhanced the protein levels of LC3B, Atg5, Atg7, Atg12, p62 and Beclin-1 in MDA-MB-231 cells. Finally, DNA microarray was carried out to investigate the level changes of gene expression modulated by MTH-3 in MDA-MB-231 cells. Taken together, our results suggest that MTH-3 might be a novel therapeutic agent for the treatment of triple-negative breast cancer in the near future

Effects of income and residential area on survival of patients with head and neck cancers following radiotherapy: working age individuals in Taiwan

Objectives The five-year survival rate of head and neck cancer (HNC) after radiotherapy (RT) varies widely from 35% to 89%. Many studies have addressed the effect of socioeconomic status and urban dwelling on the survival of HNC, but a limited number of studies have focused on the survival rate of HNC patients after RT. Materials and methods During the period of 2000–2013, 40,985 working age individuals (20  medium income group > low income group and northern > central > southern > eastern Taiwan. Patients with moderate income levels had a 36.9% higher risk of mortality as compared with patients with high income levels (hazard ratio (HR) = 1.369; p < 0.001). Patients with low income levels had a 51.4% greater risk of mortality than patients with high income levels (HR = 1.514, p < 0.001). Conclusion In Taiwan, income and residential area significantly affected the survival rate of HNC patients receiving RT. The highest income level group had the best survival rate, regardless of the geographic area. The difference in survival between the low and high income groups was still pronounced in more deprived areas