ABSTRACT
MiRNAs are edited or modified in multiple ways during their biogenesis pathways. It was reported that miRNA editing was deregulated in tumors, suggesting the potential value of miRNA editing in cancer classification. Here we extracted three types of miRNA features from 395 LUAD and control samples, including the abundances of original miRNAs, the abundances of edited miRNAs, and the editing levels of miRNA editing sites. Our results show that eight classification algorithms selected generally had better performances on combined features than on the abundances of miRNAs or editing features of miRNAs alone. One feature selection algorithm, i.e., the DFL algorithm, selected only three features, i.e., the frequencies of hsa-miR-135b-5p, hsa-miR-210-3p and hsa-mir-182_48u (an edited miRNA), from 316 training samples. Seven classification algorithms achieved 100% accuracies on these three features for 79 independent testing samples. These results indicate that the additional information of miRNA editing is useful in improving the classification of LUAD samples.
ABSTRACT
MOTIVATION: The data deluge of high-throughput sequencing (HTS) has posed great challenges to data storage and transfer. Many specific compression tools have been developed to solve this problem. However, most of the existing compressors are based on central processing unit (CPU) platform, which might be inefficient and expensive to handle large-scale HTS data. With the popularization of graphics processing units (GPUs), GPU-compatible sequencing data compressors become desirable to exploit the computing power of GPUs. RESULTS: We present a GPU-accelerated reference-free read compressor, namely CURC, for FASTQ files. Under a GPU-CPU heterogeneous parallel scheme, CURC implements highly efficient lossless compression of DNA stream based on the pseudogenome approach and CUDA library. CURC achieves 2-6-fold speedup of the compression with competitive compression rate, compared with other state-of-the-art reference-free read compressors. AVAILABILITY AND IMPLEMENTATION: CURC can be downloaded from https://github.com/BioinfoSZU/CURC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Subject(s)
Algorithms , Data Compression , Sequence Analysis, DNA , High-Throughput Nucleotide Sequencing , Gene LibraryABSTRACT
BACKGROUND: The potential advantages of laparoscopic gastrectomy (LG) compared with open gastrectomy (OG) for Siewert type II/III adenocarcinoma of the esophagogastric junction (AEG) have not been fully clarified. The aim of this meta-analysis was to evaluate the safety and efficacy of LG for Siewert type II/III AEG, compared with OG. METHODS: A comprehensive search was performed in various medical databases up to December 30, 2018. Seven non-randomized controlled trials comparing LG and OG for Siewert type II/III AEG were included. Outcomes evaluated including operation time, estimated blood loss, number of retrieved lymph nodes (LNs), post-operation complications, postoperative hospital stay, time to first flatus, time to ambulation, and overall survival (OS). RESULTS: Seven studies of 1915 patients were included for meta-analysis. The estimated blood loss [weighted mean difference (WMD) = - 77.49, 95%CI - 111.84 to - 43.15; P < 0.00001] was significantly less and the postoperative hospital stay (WMD = - 1.98, 95%CI - 2.14 to - 1.83; P < 0.00001) was significantly shorter in the LG group than in the OG group, while the operation time, number of retrieved LNs, time to first flatus, and time to ambulation showed no significant difference between LG and OG groups. The overall postoperative complications [odds ratio (OR) 0.78, 95%CI 0.60-1.02; P = 0.07] in LG group were less than those in OG group, although the difference was not significant between the two groups. CONCLUSION: LG can achieve short-term surgical outcomes comparable to OG, with respect to safety and efficiency in treatment of Siewert type II/III AEG.
Subject(s)
Esophagogastric Junction/surgery , Gastrectomy/methods , Laparoscopy/methods , Adenocarcinoma/surgery , Female , Humans , Male , Retrospective StudiesABSTRACT
BACKGROUND: Few studies have been designed to evaluate the short-term outcomes between robotic-assisted total gastrectomy (RATG) and laparoscopy-assisted total gastrectomy (LATG) for advanced gastric cancer (AGC). The purpose of this study was to assess the short-term outcomes of RATG compared with LATG for AGC. METHODS: We retrospectively evaluated 126 and 257 patients who underwent RATG or LATG, respectively. In addition, we performed propensity score matching (PSM) analysis between RATG and LATG for clinicopathological characteristics to reduce bias and compared short-term surgical outcomes. RESULTS: After PSM, the RATG group had a longer mean operation time (291.14 ± 59.18 vs. 270.34 ± 52.22 min, p = 0.003), less intraoperative bleeding (154.37 ± 89.68 vs. 183.77 ± 95.39 ml, p = 0.004) and more N2 tier RLNs (9.07 ± 5.34 vs. 7.56 ± 4.50, p = 0.016) than the LATG group. Additionally, the total RLNs of the RATG group were almost significantly different compared to that of the LATG group (34.90 ± 13.05 vs. 31.91 ± 12.46, p = 0.065). Moreover, no significant differences were found between the two groups in terms of the length of incision, proximal resection margin, distal resection margin, residual disease and postoperative hospital stay. There was no significant difference in the overall complication rate between the RATG and LATG groups after PSM (23.8% vs. 28.6%, p = 0.390). Grade II complications accounted for most of the complications in the two cohorts after PSM. The conversion rates were 4.55 and 8.54% in the RATG and LATG groups, respectively, with no significant difference (p = 0.145), and the ratio of splenectomy were 1.59 and 0.39% (p = 0.253). The mortality rates were 0.8 and 0.4% for the RATG and LATG groups, respectively (p = 1.000). CONCLUSION: This study demonstrates that RATG is comparable to LATG in terms of short-term surgical outcomes.
