Finding Related Publications: Extending the Set of Terms Used to Assess Article Similarity.

Recommendation of related articles is an important feature of the PubMed. The PubMed Related Citations (PRC) algorithm is the engine that enables this feature, and it leverages information on 22 million citations. We analyzed the performance of the PRC algorithm on 4584 annotated articles from the 2005 Text REtrieval Conference (TREC) Genomics Track data. Our analysis indicated that the PRC highest weighted term was not always consistent with the critical term that was most directly related to the topic of the article. We implemented term expansion and found that it was a promising and easy-to-implement approach to improve the performance of the PRC algorithm for the TREC 2005 Genomics data and for the TREC 2014 Clinical Decision Support Track data. For term expansion, we trained a Skip-gram model using the Word2Vec package. This extended PRC algorithm resulted in higher average precision for a large subset of articles. A combination of both algorithms may lead to improved performance in related article recommendations

The Impact of Automatic Pre-annotation in Clinical Note Data Element Extraction - the CLEAN Tool

Objective. Annotation is expensive but essential for clinical note review and clinical natural language processing (cNLP). However, the extent to which computer-generated pre-annotation is beneficial to human annotation is still an open question. Our study introduces CLEAN (CLinical note rEview and ANnotation), a pre-annotation-based cNLP annotation system to improve clinical note annotation of data elements, and comprehensively compares CLEAN with the widely-used annotation system Brat Rapid Annotation Tool (BRAT). Materials and Methods. CLEAN includes an ensemble pipeline (CLEAN-EP) with a newly developed annotation tool (CLEAN-AT). A domain expert and a novice user/annotator participated in a comparative usability test by tagging 87 data elements related to Congestive Heart Failure (CHF) and Kawasaki Disease (KD) cohorts in 84 public notes. Results. CLEAN achieved higher note-level F1-score (0.896) over BRAT (0.820), with significant difference in correctness (P-value < 0.001), and the mostly related factor being system/software (P-value < 0.001). No significant difference (P-value 0.188) in annotation time was observed between CLEAN (7.262 minutes/note) and BRAT (8.286 minutes/note). The difference was mostly associated with note length (P-value < 0.001) and system/software (P-value 0.013). The expert reported CLEAN to be useful/satisfactory, while the novice reported slight improvements. Discussion. CLEAN improves the correctness of annotation and increases usefulness/satisfaction with the same level of efficiency. Limitations include untested impact of pre-annotation correctness rate, small sample size, small user size, and restrictedly validated gold standard. Conclusion. CLEAN with pre-annotation can be beneficial for an expert to deal with complex annotation tasks involving numerous and diverse target data elements

Application of social vulnerability indicators to climate change for the southwest coastal areas of Taiwan

The impact of climate change on the coastal zones of Taiwan not only affects the marine environment, ecology, and human communities whose economies rely heavily on marine activities, but also the sustainable development of national economics. The southwest coast is known as the area most vulnerable to climate change; therefore, this study aims to develop indicators to assess social vulnerability in this area of Taiwan using the three dimensions of susceptibility, resistance, and resilience. The modified Delphi method was used to develop nine criteria and 26 indexes in the evaluation, and the analytic hierarchy process method was employed to evaluate the weight of each indicator based on the perspectives of experts collected through questionnaire surveys. The results provide important information pertaining to the vulnerability of the most susceptive regions, the lowest-resistance areas, and the least resilient townships on the southwest coast. The most socially vulnerable areas are plotted based on the present analysis. Experts can consider the vulnerability map provided here when developing adaptation policies. It should be kept in mind that improving the capacities of resistance and resilience is more important than reducing susceptibility in Taiwan

The risk for bacterial endocarditis in cirrhotic patients: a population-based 3-year follow-up study

[[abstract]]Background We noted only rare reports of cirrhotic patients with bacterial endocarditis (BE). There is insufficient data on the risk of BE in liver cirrhosis. This is the first national population-based study evaluating the risk of BE in cirrhotic patients. Methods We used the National Health Insurance Database, which is derived from the Taiwan National Health Insurance Program. The study cohort comprised 40 803 patients with cirrhosis and the comparison cohort consisted of 40 841 randomly selected subjects with a similar age and sex distribution. Results Of the total 81 644 patients, 192 (0.24%) experienced BE during the 3-year follow-up period, 121 patients from the study cohort (0.30% of the cirrhotic patients) and 71 patients from the comparison group (0.17% of non-cirrhotic patients) (p＜0.001). After adjusting for patient age, sex, and comorbid disorders, the Cox regression analysis showed that cirrhotic patients had a high risk of BE compared to non-cirrhotic patients during the 3-year follow-up period (hazard ratio 2.04, 95% confidence interval 1.61–2.44, p＜0.001). Conclusion We conclude that liver cirrhosis is a risk factor for the occurrence of BE.[[notice]]補正完畢[[incitationindex]]SCI[[booktype]]紙

Improvement of Statistical Typhoon Rainfall Forecasting with ANN-Based Southwest Monsoon Enhancement

Typhoon Morakot 2009, with significant southwest monsoon flow, produced a record-breaking rainfall of 2361 mm in 48 hours. This study hopes to improve a statistical typhoon rainfall forecasting method used over the mountain region of Taiwan via an artificial neural network based southwest monsoon enhancement (ANNSME) model. Rainfall data collected at two mountain weather stations, ALiShan and YuShan, are analyzed to establish the relation to the southwest monsoon moisture flux which is calculated at a designated sea area southwest of Taiwan. The results show that the moisture flux, with southwest monsoon flow, transported water vapor during the landfall periods of Typhoons Mindulle, Bilis, Fungwong, Kalmaegi, Haitaing and Morakot. Based on the moisture flux, a linear regression is used to identify an effective value of moisture flux as the threshold flux which can enhance mountain rainfall in southwestern Taiwan. In particular, a feedforward neural network (FNN) is applied to estimate the residuals from the linear model to the differences between simulated rainfalls by a typhoon rainfall climatology model (TRCM) and observations. Consequently, the ANNSME model integrates the effective moisture flux, linear rainfall model and the FNN for residuals. Even with very limited training cases, our results indicate that the ANNSME model is robust and suitable for improvement of TRCM rainfall prediction. The improved prediction of the total rainfall and of the multiple rainfall peaks is important for emergency operation

The Use of the ROS Scavenger Cysteine as a Surface Ligand of Metal Nanoclusters and Its Bactericidal Elimination Effect

The bactericidal effects of fluorescent metal nanoclusters have impeded their bacterial bioimaging applications due to the reactive oxygen species (ROS) generation that is induced by the nanoclusters in bacteria to cause bacterial death. Herein, an ROS scavenger of cysteine was exploited as a surface ligand to prepare cysteine-conjugated gold nanoclusters (Cys–AuNCs) and cysteine-conjugated silver nanoclusters (Cys–AgNCs) using a facile hydrothermal approach. The structural and optical characterizations demonstrated successful syntheses of Cys–AuNCs and Cys–AgNCs. With the same weight concentration, the bactericidal effect increased in the order of Cys–AuNCs, Cys–AgNCs, and silver nanoparticles (AgNPs), according to the results of the bacterial growth curves. Furthermore, based on the results of the standard colony-counting method, the Cys–AuNCs revealed the best biocompatibility compared to those of the Cys–AgNCs and AgNPs in Escherichia coli (E. coli). The superior biocompatibility of the Cys–AuNCs can be attributed to the use of the ligand of cysteine as an ROS scavenger to reduce ROS in E. coli. Electron paramagnetic resonance (EPR) analyses indicated that the use of the ROS scavenger cysteine as the surface ligand of the Cys–AuNCs eliminated the ROS production induced by the Cys–AuNCs in E. coli. The biocompatible Cys–AuNCs were also confirmed as a fluorescent probe using confocal microscopy. Highly biocompatible Cys–AuNCs could be a potential fluorescent probe in the application of bacterial bioimaging

Thrombomodulin Regulates Keratinocyte Differentiation and Promotes Wound Healing

The membrane glycoprotein thrombomodulin (TM) has been implicated in keratinocyte differentiation and wound healing, but its specific function remains undetermined. The epidermis-specific TM knockout mice were generated to investigate the function of TM in these biological processes. Primary cultured keratinocytes obtained from TMlox/lox; K5-Cre mice, in which TM expression was abrogated, underwent abnormal differentiation in response to calcium induction. Poor epidermal differentiation, as evidenced by downregulation of the terminal differentiation markers loricrin and filaggrin, was observed in TMlox/lox; K5-Cre mice. Silencing TM expression in human epithelial cells impaired calcium-induced extracellular signal–regulated kinase pathway activation and subsequent keratinocyte differentiation. Compared with wild-type mice, the cell spreading area and wound closure rate were lower in keratinocytes from TMlox/lox; K5-Cre mice. In addition, the lower density of neovascularization and smaller area of hyperproliferative epithelium contributed to slower wound healing in TMlox/lox; K5-Cre mice than in wild-type mice. Local administration of recombinant TM (rTM) accelerated healing rates in the TM-null skin. These data suggest that TM has a critical role in skin differentiation and wound healing. Furthermore, rTM may hold therapeutic potential for the treatment of nonhealing chronic wounds

A novel derivative of betulinic acid, SYK023, suppresses lung cancer growth and malignancy

Herein, we evaluated the anti-cancer effect and molecular mechanisms of a novel betulinic acid (BA) derivative, SYK023, by using two mouse models of lung cancer driven by KrasG12D or EGFRL858R. We found that SYK023 inhibits lung tumor proliferation, without side effects in vivo or cytotoxicity in primary lung cells in vitro. SYK023 triggered endoplasmic reticulum (ER) stress. Blockage of ER stress in SYK023-treated cells inhibited SYK023-induced apoptosis. In addition, we found that the expression of cell cycle-related genes, including cyclin A2, B1, D3, CDC25a, and CDC25b decreased but, while those of p15INK4b, p16INK4a, and p21CIP1 increased following SYK023 treatment. Finally, low doses of SYK023 significantly decreased lung cancer metastasis in vitro and in vivo. Expression of several genes related to cell migration, including synaptopodin, were downregulated by SYK023, thereby impairing F-actin polymerization and metastasis. Therefore, SYK023 may be a potentially therapeutic treatment for metastatic lung cancer