1.
iT3SE-PX: Identification of Bacterial Type III Secreted Effectors Using PSSM Profiles and XGBoost Feature Selection.
Ding, C, Han, H, Li, Q, Yang, X, Liu, T
Computational and mathematical methods in medicine. 2021;:6690299
Abstract
Identification of bacterial type III secreted effectors (T3SEs) has become a popular research topic in the field of bioinformatics due to its crucial role in understanding host-pathogen interaction and developing better therapeutic targets against the pathogens. However, the recognition of all effector proteins by using traditional experimental approaches is often time-consuming and laborious. Therefore, development of computational methods to accurately predict putative novel effectors is important in reducing the number of biological experiments for validation. In this study, we proposed a method, called iT3SE-PX, to identify T3SEs solely based on protein sequences. First, three kinds of features were extracted from the position-specific scoring matrix (PSSM) profiles to help train a machine learning (ML) model. Then, the extreme gradient boosting (XGBoost) algorithm was performed to rank these features based on their classification ability. Finally, the optimal features were selected as inputs to a support vector machine (SVM) classifier to predict T3SEs. Based on the two benchmark datasets, we conducted a 100-time randomized 5-fold cross validation (CV) and an independent test, respectively. The experimental results demonstrated that the proposed method achieved superior performance compared to most of the existing methods and could serve as a useful tool for identifying putative T3SEs, given only the sequence information.
2.
Biportal endoscopic versus microscopic lumbar decompressive laminectomy in patients with spinal stenosis: a randomized controlled trial.
Park, SM, Park, J, Jang, HS, Heo, YW, Han, H, Kim, HJ, Chang, BS, Lee, CK, Yeom, JS
The spine journal : official journal of the North American Spine Society. 2020;(2):156-165
Abstract
BACKGROUND CONTEXT Biportal endoscopic decompressive laminectomy is a widely performed procedure and shows acceptable clinical outcomes. However, the evidence regarding the advantages of biportal endoscopic surgery is weak, a randomized controlled trial is therefore warranted. PURPOSE To compare the clinical efficacies of biportal endoscopic and microscopic decompressive laminectomy in patients with lumbar spinal stenosis. STUDY DESIGN Randomized controlled trial. PATIENT SAMPLE Sixty-four participants suffering from low back and leg pain with single-level lumbar spinal stenosis who required decompressive laminectomy. OUTCOME MEASURES Outcomes were assessed with the use of patient-reported outcome measures, visual analog scale (VAS) score for low back and lower extremity radiating pain, Oswestry disability index (ODI), European Quality of Life-5 Dimensions (EQ-5D) score, and painDETECT for neuropathic pain. Surgery-related outcomes including operation time, length of hospital stay, postoperative drainage, and serum creatine phosphokinase were evaluated. Perioperative (<30 days) and late (1-12 months) complications were also noted. METHODS All participants were randomly assigned in a 1:1 ratio to undergo biportal endoscopic or microscopic decompressive laminectomy. The primary outcome was the ODI score at 12 months after surgery based on a modified intention-to-treat strategy. The secondary outcomes included VAS score for low back and lower extremity radiating pain, ODI scores, EQ-5D score, and painDETECT score. There were no sources of funding and no conflicts of interest associated with this study. RESULTS There was no significant difference between groups in the mean ODI score at 12 months after surgery (30 in the microscopy vs. 29 in the biportal endoscopy group, p=.635). There were also no significant differences in low back and lower extremity pain VAS scores, ODI, EQ-5D scores, and painDETECT scores at the 3-, 6-, or 12-month follow-up. Operation time, length of hospital stay, serum creatine phosphokinase, and perioperative complications, such as durotomies and symptomatic hematoma, showed no significant differences between the groups; however, one participant underwent additional revision surgery 9 months after the index surgery in the microscopy group. CONCLUSIONS Despite the study design limitation of relatively short duration of follow-up, this trial suggests that biportal endoscopic decompressive laminectomy is an alternative to and offers similar clinical outcomes as microscopic open surgery in patients with symptomatic lumbar spinal stenosis.