0
selected
-
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.
-
3.
Instant Oatmeal Increases Satiety and Reduces Energy Intake Compared to a Ready-to-Eat Oat-Based Breakfast Cereal: A Randomized Crossover Trial.
Rebello, CJ, Johnson, WD, Martin, CK, Han, H, Chu, YF, Bordenave, N, van Klinken, BJ, O'Shea, M, Greenway, FL
Journal of the American College of Nutrition. 2016;(1):41-9
-
-
Free full text
-
Abstract
BACKGROUND Foods that enhance satiety can help consumers to resist environmental cues to eat and help adherence to calorie restriction. The objective of this study was to compare the effect of 2 oat-based breakfast cereals on appetite, satiety, and food intake. METHODS Forty-eight healthy individuals, 18 years of age or older, were enrolled in a randomized, crossover trial. Subjects consumed isocaloric servings of either oatmeal or an oat-based ready-to-eat breakfast cereal (RTEC) in random order at least a week apart. Visual analogue scales measuring appetite and satiety were completed before breakfast and throughout the morning. Lunch was served 4 hours after breakfast. The physicochemical properties of oat soluble fiber (β-glucan) were determined. Appetite and satiety responses were analyzed by area under the curve. Food intake and β-glucan properties were analyzed using t tests. RESULTS Oatmeal increased fullness (p = 0.001) and reduced hunger (p = 0.005), desire to eat (p = 0.001), and prospective intake (p = 0.006) more than the RTEC. Energy intake at lunch was lower after eating oatmeal compared to the RTEC (p = 0.012). Oatmeal had higher viscosity (p = 0.03), β-glucan content, molecular weight (p < 0.001), and radius of gyration (p < 0.001) than the RTEC. CONCLUSIONS Oatmeal suppresses appetite, increases satiety, and reduces energy intake compared to the RTEC. The physicochemical properties of β-glucan and sufficient hydration of oats are important factors affecting satiety and subsequent energy intake.
-
4.
Comparison of the pharmacokinetics and tolerability of HCP1004 (a fixed-dose combination of naproxen and esomeprazole strontium) and VIMOVO® (a marketed fixed-dose combination of naproxen and esomeprazole magnesium) in healthy volunteers.
Choi, Y, Han, H, Shin, D, Lim, KS, Yu, KS
Drug design, development and therapy. 2015;:4127-35
Abstract
BACKGROUND HCP1004 is a newly developed fixed-dose combination of naproxen (500 mg) and esomeprazole strontium (20 mg) that is used in the treatment of rheumatic diseases and can reduce the risk of nonsteroidal anti-inflammatory drug-associated ulcers. The aim of this study was to evaluate the pharmacokinetics (PK) and safety of HCP1004 compared to VIMOVO(®) (a marketed fixed-dose combination of naproxen and esomeprazole magnesium). SUBJECTS AND METHODS An open-label, randomized, two-treatment, two-sequence crossover, single-dose clinical study was conducted in 70 healthy volunteers. In each period, a reference (VIMOVO(®)) or test (HCP1004) drug was administered orally, and serial blood samples for PK analysis were collected up to 72 hours after dosing. To evaluate the PK profiles, the maximum plasma concentration (Cmax) and the area under the concentration-time curve from 0 to the last measurable time (AUC0-t) were estimated using a noncompartmental method. Safety profiles were evaluated throughout the study. RESULTS Sixty-six of the 70 subjects completed the study. The Cmax (mean ± standard deviation) and AUC0-t (mean ± standard deviation) for naproxen in HCP1004 were 61.67 ± 15.16 µg/mL and 1,206.52 ± 166.46 h · µg/mL, respectively; in VIMOVO(®); these values were 61.85 ± 14.54 µg/mL and 1,211.44 ± 170.01 h · µg/mL, respectively. The Cmax and AUC0-t for esomeprazole in HCP1004 were 658.21 ± 510.91 ng/mL and 1,109.11 ± 1,111.59 h · ng/mL, respectively; for VIMOVO(®), these values were 595.09 ± 364.23 ng/mL and 1,015.12 ± 952.98 h · ng/mL, respectively. The geometric mean ratios and 90% confidence intervals (CIs) (HCP1004 to VIMOVO(®)) of the Cmax and AUC0-t of naproxen were 0.99 (0.94-1.06) and 1.00 (0.98-1.01), respectively. For esomeprazole, the geometric mean ratios (90% CI) for the Cmax and AUC0-t were 0.99 (0.82-1.18) and 1.04 (0.91-1.18), respectively. The overall results of the safety assessment showed no clinically significant issues for either treatment. CONCLUSION The PK of HCP1004 500/20 mg was comparable to that of VIMOVO(®) 500/20 mg for both naproxen and esomeprazole after a single oral dose. Both drugs were well-tolerated without any safety issues.
-
5.
Effects of weight gain induced by controlled overfeeding on physical activity.
Apolzan, JW, Bray, GA, Smith, SR, de Jonge, L, Rood, J, Han, H, Redman, LM, Martin, CK
American journal of physiology. Endocrinology and metabolism. 2014;(11):E1030-7
Abstract
It is unclear whether physical activity changes following long-term overfeeding and in response to different dietary protein intakes. Twenty-five (16 males, 9 females) healthy adults (18-35 yr) with BMI ranging from 19 to 30 kg/m(2) enrolled in this inpatient study. In a parallel group design, participants were fed 140% of energy needs, with 5, 15, or 25% of energy from protein, for 56 days. Participants wore an RT3 accelerometer for at least 59 days throughout baseline and during overfeeding and completed 24-h whole room metabolic chamber assessments at baseline and on days 1, 14, and 56 of overfeeding and on day 57, when the baseline energy intake was consumed, to measure percent of time active and spontaneous physical activity (SPA; kcal/day). Changes in activity were also assessed by doubly labeled water (DLW). From accelerometry, vector magnitude (VM), a weight-independent measure of activity, and activity energy expenditure (AEE) increased with weight gain during overfeeding. AEE remained increased after adjusting for changes in body composition. Activity-related energy expenditure (AREE) from DLW and percent activity and SPA in the metabolic chamber increased with overfeeding, but SPA was no longer significant after adjusting for change in body composition. Change in VM and AEE were positively correlated with weight gain; however, change in activity was not affected by protein intake. Overfeeding produces an increase in physical activity and in energy expended in physical activity after adjusting for changes in body composition, suggesting that increased activity in response to weight gain might be one mechanism to support adaptive thermogenesis.