Molecular characterization of dysplasia-initiated colorectal cancer with assessing matched tumor and dysplasia samples

Purpose@#Ulcerative colitis (UC) is known to have an association with the increased risk of colorectal cancer (CRC), and UC-associated CRC does not follow the typical progress pattern of adenoma-carcinoma. The aim of this study is to investigate molecular characteristics of UC-associated CRC and further our understanding of the association between UC and CRC. @*Methods@#From 5 patients with UC-associated CRC, matched normal, dysplasia, and tumor specimens were obtained from formalin-fixed paraffin-embedded (FFPE) samples for analysis. Genomic DNA was extracted and whole exome sequencing was conducted to identify somatic variations in dysplasia and tumor samples. Statistical analysis was performed to identify somatic variations with significantly higher frequencies in dysplasia-initiated tumors, and their relevant functions were investigated. @*Results@#Total of 104 tumor mutation genes were identified with higher mutation frequencies in dysplasia-initiated tumors. Four of the 5 dysplasia-initiated tumors (80.0%) have TP53 mutations with frequent stop-gain mutations that were originated from matched dysplasia. APC and KRAS are known to be frequently mutated in general CRC, while none of the 5 patients have APC or KRAS mutation in their dysplasia and tumor samples. Glycoproteins including mucins were also frequently mutated in dysplasia-initiated tumors. @*Conclusion@#UC-associated CRC tumors have distinct mutational characteristics compared to typical adenoma-carcinoma tumors and may have different cancer-driving molecular mechanisms that are initiated from earlier dysplasia status.

Comparison of differences in microbial compositions between negative controls and subject samples with varying analysis configurations

PURPOSE: Identifying microbial communities with 16S ribosomal RNA (rRNA) gene sequencing is a popular approach in microbiome studies, and various software tools and data resources have been developed for microbial analysis. Our aim in this study is investigating various available software tools and reference sequence databases to compare their performance in differentiating subject samples and negative controls. METHODS: We collected 4 negative control samples using various acquisition protocols, and 2 respiratory samples were acquired from a healthy subject also with different acquisition protocols. Quantitative methods were used to compare the results of taxonomy compositions of these 6 samples by varying the configuration of analysis software tools and reference databases. RESULTS: The results of taxonomy assignments showed relatively little difference, regardless of pipeline configurations and reference databases. Nevertheless, the effect on the discrepancy was larger using different software configurations than using different reference databases. In recognizing different samples, the 4 negative controls were clearly separable from the 2 subject samples. Additionally, there is a tendency to differentiate samples from different acquisition protocols. CONCLUSION: Our results suggest little difference in microbial compositions between different software tools and reference databases, but certain configurations can improve the separability of samples. Changing software tools shows a greater impact on results than changing reference databases; thus, it is necessary to utilize appropriate configurations based on the objectives of studies.

Effects of a Well-dying Program on Nursing Students / 한국호스피스완화의료학회지

PURPOSE: We examined the effects of a well-dying program on nursing students in terms of death preparation, death recognition and perception of well-dying perception. METHODS: The design of this study was quasi-experimental and non-synchronized with a non-equivalent control group. The study was conducted with nursing students: 32 in the experimental group and 36 in the control group. The well-dying program was consisted of five sessions: introduction, thinking about meaning of death, organizing things to do before dying, looking back on my life, and leaving a trail of my life. Descriptive analysis, t-test, chi2 test and ANCOVA were used with SPSS 18.0 program to analyze the data. RESULTS: After attending the program, a difference was observed in death preparation of the experimental group (t=2.61, P=0.014). The death recognition (F=154.15, P<0.001) score of the experimental group was significantly higher than the control group. There was no significant difference between the groups in perception of well-dying (F=0.11, P=0.747). CONCLUSIONS: The well-dying program helped nursing students build positive death recognition. Therefore, this study is expected to contribute to development of a death education program for nursing students.

Toward the Automatic Generation of the Entry Level CDA Documents / 대한의료정보학회지

OBJECTIVE: CDA (Clinical Document Architecture) is a markup standard for clinical document exchange. In order to increase the semantic interoperability of documents exchange, the clinical statements in the narrative blocks should be encoded with code values. Natural language processing (NLP) is required in order to transform the narrative blocks into the coded elements in the level 3 CDA documents. In this paper, we evaluate the accuracy of text mapping methods which are based on NLP. METHODS: We analyzed about one thousand discharge summaries to know their characteristics and focused the syntactic patterns of the diagnostic sections in the discharge summaries. According to the patterns, different rules were applied for matching code values of Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT). RESULTS: The accuracy of matching was evaluated using five-hundred discharge summaries. The precision was as follows: 86.5% for diagnosis, 61.8% for chief complaint, 62.7%, for problem list, and 64.8% for discharge medication. CONCLUSION: The text processing method based on the pattern analysis of a clinical statement can be effectively used for generating CDA entries.