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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.
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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.
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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
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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.
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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.
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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.
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Change in food cravings, food preferences, and appetite during a low-carbohydrate and low-fat diet.
Martin, CK, Rosenbaum, D, Han, H, Geiselman, PJ, Wyatt, HR, Hill, JO, Brill, C, Bailer, B, Miller, BV, Stein, R, et al
Obesity (Silver Spring, Md.). 2011;(10):1963-70
Abstract
The study objective was to evaluate the effect of prescribing a low-carbohydrate diet (LCD) and a low-fat diet (LFD) on food cravings, food preferences, and appetite. Obese adults were randomly assigned to a LCD (n = 134) or a LFD (n = 136) for 2 years. Cravings for specific types of foods (sweets, high-fats, fast-food fats, and carbohydrates/starches); preferences for high-sugar, high-carbohydrate, and low-carbohydrate/high-protein foods; and appetite were measured during the trial and evaluated during this secondary analysis of trial data. Differences between the LCD and LFD on change in outcome variables were examined with mixed linear models. Compared to the LFD, the LCD had significantly larger decreases in cravings for carbohydrates/starches and preferences for high-carbohydrate and high-sugar foods. The LCD group reported being less bothered by hunger compared to the LFD group. Compared to the LCD group, the LFD group had significantly larger decreases in cravings for high-fat foods and preference for low-carbohydrate/high-protein foods. Men had larger decreases in appetite ratings compared to women. Prescription of diets that promoted restriction of specific types of foods resulted in decreased cravings and preferences for the foods that were targeted for restriction. The results also indicate that the LCD group was less bothered by hunger compared to the LFD group and that men had larger reductions in appetite compared to women.
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An environmental intervention to prevent excess weight gain in African-American students: a pilot study.
Newton, RL, Han, H, Anton, SD, Martin, CK, Stewart, TM, Lewis, L, Champagne, CM, Sothern, M, Ryan, D, Williamson, DA
American journal of health promotion : AJHP. 2010;(5):340-3
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Abstract
PURPOSE To examine the influence of an environmental intervention to prevent excess weight gain in African-American children. DESIGN Single-group repeated measures. SETTING The intervention was delivered to a school composed of African-American children. PARTICIPANTS Approximately 45% (N = 77) of enrolled second through sixth grade students. INTERVENTION The 18-month intervention was designed to alter the school environment to prevent excess weight gain by making healthier eating choices and physical activity opportunities more available. MEASURES Body mass index percentile was the primary outcome variable. Body mass index z score was also calculated, and percent body fat, using bioelectrical impedance, was also measured. Total caloric intake (kilocalories) and percent kilocalories from fat, carbohydrate, and protein were measured by digital photography. Minutes of physical activity and sedentary behavior were selfreported. ANALYSIS Mixed-models analysis was used with covarying baseline values. RESULTS Boys maintained, whereas girls increased, percent body fat over 18 months (p = .027). All children decreased percent of kilocalories consumed from total and saturated fat and increased carbohydrate intake and self-reported physical activity during the intervention (p < .025). Body mass index z score, sedentary behavior, and total caloric intake were unchanged. CONCLUSION The program may have resulted in maintenance of percent body fat in boys. The percent body fat in girls steadily increased, despite similar behavioral changes as boys. School-based interventions targeting African-American children should investigate strategies that can be effective across gender.
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Measurement of dietary restraint: validity tests of four questionnaires.
Williamson, DA, Martin, CK, York-Crowe, E, Anton, SD, Redman, LM, Han, H, Ravussin, E
Appetite. 2007;(2):183-92
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Abstract
This study tested the validity of four measures of dietary restraint: Dutch Eating Behavior Questionnaire, Eating Inventory (EI), Revised Restraint Scale (RS), and the Current Dieting Questionnaire. Dietary restraint has been implicated as a determinant of overeating and binge eating. Conflicting findings have been attributed to different methods for measuring dietary restraint. The validity of four self-report measures of dietary restraint and dieting behavior was tested using: (1) factor analysis, (2) changes in dietary restraint in a randomized controlled trial of different methods to achieve calorie restriction, and (3) correlation of changes in dietary restraint with an objective measure of energy balance, calculated from the changes in fat mass and fat-free mass over a six-month dietary intervention. Scores from all four questionnaires, measured at baseline, formed a dietary restraint factor, but the RS also loaded on a binge eating factor. Based on change scores, the EI Restraint Scale was the only measure that correlated significantly with energy balance expressed as a percentage of energy required for weight maintenance. These findings suggest that, of the four questionnaires tested, the EI Restraint Scale was the most valid measure of the intent to diet and actual caloric restriction.
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Selective interactions of cationic porphyrins with G-quadruplex structures.
Han, H, Langley, DR, Rangan, A, Hurley, LH
Journal of the American Chemical Society. 2001;(37):8902-13
Abstract
G-quadruplex DNA presents a potential target for the design and development of novel anticancer drugs. Because G-quadruplex DNA exhibits structural polymorphism, different G-quadruplex typologies may be associated with different cellular processes. Therefore, to achieve therapeutic selectivity using G-quadruplexes as targets for drug design, it will be necessary to differentiate between different types of G-quadruplexes using G-quadruplex-interactive agents. In this study, we compare the interactions of three cationic porphyrins, TMPyP2, TMPyP3, and TMPyP4, with parallel and antiparallel types of G-quadruplexes using gel mobility shift experiments and a helicase assay. Gel mobility shift experiments indicate that TMPyP3 specifically promotes the formation of parallel G-quadruplex structures. A G-quadruplex helicase unwinding assay reveals that the three porphyrins vary dramatically in their abilities to prevent the unwinding of both the parallel tetrameric G-quadruplex and the antiparallel hairpin dimer G-quadruplex DNA by yeast Sgs1 helicase (Sgs1p). For the parallel G-quadruplex, TMPyP3 has the strongest inhibitory effect on Sgs1p, followed by TMPyP4, but the reverse is true for the antiparallel G-quadruplex. TMPyP2 does not appear to have any effect on the helicase-catalyzed unwinding of either type of G-quadruplex. Photocleavage experiments were carried out to investigate the binding modes of all three porphyrins with parallel G-quadruplexes. The results reveal that TMPyP3 and TMPyP4 appear to bind to parallel G-quadruplex structures through external stacking at the ends rather than through intercalation between the G-tetrads. Since intercalation between G-tetrads has been previously proposed as an alternative binding mode for TMPyP4 to G-quadruplexes, this mode of binding, versus that determined by a photocleavage assay described here (external stacking), was subjected to molecular dynamics calculations to identify the relative stabilities of the complexes and the factors that contribute to these differences. The DeltaG(o) for the external binding mode was found to be driven by DeltaH(o) with a small unfavorable TDeltaS(o) term. The DeltaG(o) for the intercalation binding model was driven by a large TDeltaS(o) term and complemented by a small DeltaH(o) term. One of the main stabilizing components of the external binding model is the energy of solvation, which favors the external model over the intercalation model by -67.94 kcal/mol. Finally, we propose that intercalative binding, although less favored than external binding, may occur, but because of the nature of the intercalative binding, it is invisible to the photocleavage assay. This study provides the first experimental insight into how selectivity might be achieved for different G-quadruplexes by using structural variants within a single group of G-quadruplex-interactive drugs.