Both differential expression (DE) and differential co-expression (DC) analyses are appreciated as useful tools in understanding gene regulation related to complex diseases. The performance of ...integrating DE and DC, however, remains unexplored.
In this study, we proposed a novel analytical approach called DECODE (Differential Co-expression and Differential Expression) to integrate DC and DE analyses of gene expression data. DECODE allows one to study the combined features of DC and DE of each transcript between two conditions. By incorporating information of the dependency between DC and DE variables, two optimal thresholds for defining substantial change in expression and co-expression are systematically defined for each gene based on chi-square maximization. By using these thresholds, genes can be categorized into four groups with either high or low DC and DE characteristics. In this study, DECODE was applied to a large breast cancer microarray data set consisted of two thousand tumor samples. By identifying genes with high DE and high DC, we demonstrated that DECODE could improve the detection of some functional gene sets such as those related to immune system, metastasis, lipid and glucose metabolism. Further investigation on the identified genes and the associated functional pathways would provide an additional level of understanding of complex disease mechanism.
By complementing the recent DC and the traditional DE analyses, DECODE is a valuable methodology for investigating biological functions of genes exhibiting disease-associated DE and DC combined characteristics, which may not be easily revealed through DC or DE approach alone. DECODE is available at the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/decode/index.html .
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
To determine whether health-related physical fitness and body mass index (BMI) status differed before and after school closure from the COVID-19 pandemic in a population-based cohort of Hong Kong ...primary schoolchildren.
We examined the BMI z score, BMI status, and physical fitness z scores including (i) upper limb muscle strength, (ii) 1-minute sit-up test, (iii) sit-and-reach test, and (iv) endurance run tests, among 3 epochs: prepandemic (September 2018-August 2019), before school closure (September 2019-January 2020), and partial school reopening (September 2021-August 2022), using a repeated cross-sectional approach.
A total of 137 752 primary schoolchildren aged 6-12 years were recruited over 3 academic years. Obesity increased significantly from 25.9% in 2018/19 to 31.0% in 2021/22, while underweight increased slightly from 6.1% to 6.5%. All tested parameters were adversely affected by the pandemic. The negative trend over time was far more pronounced in all 4 physical fitness scores in the underweight group, although performance in handgrip strength had no significance between 2018/19 and 2021/22.
Schoolchildren who are both underweight and overweight/obese are vulnerable to adverse changes in physical fitness during the COVID-19 pandemic. To eliminate the negative health and fitness outcomes, it is urgent to develop strategies for assisting schoolchildren in achieving a healthy weight, especially in the postpandemic era.
Moderate sleep complaints are major gerontological issue affecting as many as 80% of older adults. More intriguing findings have indicated that moderate sleep complaints were associated with ...cognitive decline, functional deterioration, clinical depression, and even morbidity and mortality among older adults. The aim of this study is to evaluate the effects of an activity-based lifestyle intervention on moderate sleep complaint among community-dwelling older adults.
This sequential quantitative-qualitative mixed method study will randomly allocate 224 individuals to receive either the 16-week group-based moderate-intensity stepping exercise or 16-week health education. The exercise group receives three 60-min stepping exercises per week, whereas the education group receives weekly educative talks on health topics other than sleep. The primary outcomes are sleep quality as measured by the Pittsburgh Sleep Quality Index (PSQI) and sleep pattern as measured by the actiwatch. Physical fitness and mood status are measured as mediating variables by using the Rockport walking test and Profile of Mood States. The qualitative part will invite 30 individuals from the exercise group who have different sleep-related treatment responses to participate in individual interviews to explore their overall perception of using stepping exercise as a lifestyle intervention to improve sleep. Mixed effects model with intention-to-treat analysis will be used for quantitative data. Inductive thematic analysis with a prior coding framework will be used for the qualitative data.
By investigating the effects and the mediating mechanism of a moderate-intensity exercise program on moderate sleep complaints among older adults, this study will generate evidence of high scientific value and important public health implication. Understanding the sleep-promoting effects and acceptability of exercise informs how to apply lifestyle promotion as a public health practice to improve late-life moderate sleep complaints and forestall its progression to level of clinical severity.
Clinical Trial Registry Team, Center for Clinical Research and Biostatistics CUHK, CCRB00491 . Registered on 1 December 2015.
Summary Objective: To examine the effect of the glycemic index (GI) of a pre-exercise (PRE-ex) meal on plasma cytokine responses and endurance performance when carbohydrate-electrolyte (CHO-E) drink ...was consumed during exercise. Methods: Eight endurance-trained male runners (age: 28.6 ± 2.7 years; body mass: 61.9 ± 1.71 kg; V ˙ O 2 max : 58.5 ± 1.6 ml kg−1 min−1 ) completed three trials in a randomized order. The pre-exercise meal consisted of either high-GI (HGI) (GI = 83), low-GI (LGI) foods (GI = 36) or control (CON) (low energy sugar-free jelly) was given to the participant 2 h before a 21-km performance run on a level treadmill. During each trial, 2 ml kg−1 BM of 6.6% CHO-E solution was consumed immediately before exercise and every 2.5-km afterward. Blood samples were collected before (pre-meal), and 120 min after ingestion the meal (120 min), immediately (POST), and 60 min (POST-60 min) after exercise. Results: No difference was found in time to complete the 21-km run between LGI and HGI. The interleukin-6 (IL-6) level increased by more than 100 times immediately after exercise in the three trials and returned to the basal level only on LGI at POST-60 min. In contrast, interleukin-2 (IL-2) level showed a transitory decrease at POST on CON ( p < 0.001). Glucose concentrations did not recover to the pre-meal level by POST-60 min on HGI only. Cortisol concentrations increased throughout the exercise and were lower on LGI when compared with CON ( p < 0.05) at POST-60 min. Conclusions: HGI and LGI demonstrated similar performance when CHO-E solution was consumed during a 21-km run. However, pre-exercise LGI meal attenuated the increases in cortisol and quickened the recovery of the increased IL-6 value.
Regular intake of green tea (Camellia sinensis) lowers DNA damage in humans, but molecular mechanisms of genoprotection are not clear. Protection could be via direct antioxidant effects of tea ...catechins, but, paradoxically, catechins have pro‐oxidant activity in vitro, and it is hypothesized that mechanisms relate to redox‐sensitive cytoprotective adaptations. We investigated this hypothesis, focusing particularly on effects on the DNA repair enzyme human oxoguanine glycosylase 1 (hOGG1), and heme oxygenase‐1, a protein that has antioxidant and anti‐inflammatory effects. A randomized, placebo‐controlled, human supplementation study of crossover design was performed. Subjects (n = 16) took a single dose (200 mL of 1.5%, w/v) and 7‐days of (2 × 200 mL 1%, w/v per day) green tea (with water as control treatment). Lymphocytic DNA damage was ∼30% (p < 0.001) lower at 60 and 120 min after the single dose and in fasting samples collected after 7‐day tea supplementation. Lymphocytic hOGG1 activity was higher (p < 0.0001) at 60 and 120 min after tea ingestion. Significant increases (p < 0.0005) were seen in hOGG1 activity and heme oxygenase‐1 after 7 days. Results indicate that molecular triggering of redox‐sensitive cytoprotective adaptations and posttranslational changes affecting hOGG1 occur in vivo in response to both a single dose and regular intake of green tea, and contribute to the observed genoprotective effects of green tea.
Vitamin D deficiency (plasma 25-hydroxycholecalciferol (25(OH)D)<50 nmol/l) is highly prevalent, increases risk of non-communicable diseases (NCD) and associates with increased oxidative stress in ...obese subjects, the elderly and patients suffering from NCD. If confirmed as an independent driver of oxidative stress, nutritional and other public health strategies to improve vitamin D status would be strongly supported. We investigated vitamin D/oxidative stress links without the confounding effects of advanced age, obesity, smoking or pre-existing disease. Plasma 25(OH)D and biomarkers of oxidative stress and antioxidant status (plasma allantoin, oxidised LDL, ferric reducing antioxidant power (FRAP), ascorbic acid, urine 8-oxo-7,8-dihydro-2'-deoxyguanosine) were measured in fasting samples from 196 consenting, healthy adults aged 18–26 years. Correlation between 25(OH)D and each biomarker as well as biomarker differences across 25(OH)D quartiles and groups (<25/25–49/≥50 nmol/l) were investigated. Median 25(OH)D was 40 nmol/l; >70 % of participants were vitamin D deficient. No significant correlations and no biomarker differences across 25(OH)D quartiles or groups were seen except for total antioxidant status. A weak direct association (r 0·252, P<0·05) was observed between 25(OH)D and FRAP, and those in the lowest 25(OH)D quartile and group had significantly lower FRAP values. Results did not reveal a clear link between vitamin D status and oxidative stress biomarkers in the absence of advanced age, obesity and disease, though some evidence of depleted antioxidant status in those with vitamin D deficiency was seen. Poor antioxidant status may pre-date increased oxidative stress. Study of effects of correction of deficiency on antioxidant status and oxidative stress in vitamin D-deficient but otherwise healthy subjects is needed.
motivating older people with cognitive impairment to remain physically active is challenging.
this study aimed to examine the effects of a peer-supported exercise intervention on the cognitive ...function and health-related quality of life (HRQoL) of persons with mild cognitive impairment (MCI).
a two-arm randomised controlled trial.
community-dwelling persons with MCI were recruited from community centres for older adults in Hong Kong.
participants randomised to the intervention group received an 8-week group-based peer-supported multicomponent exercise intervention, while the waitlist control group received usual care. A battery of neuropsychological tests and the Short Form-36 were administered at baseline, immediately post-intervention and 3 months post-intervention.
two hundred and twenty-nine participants were randomised to the intervention (n = 116) or control (n = 113) group. Compared with the control group, participants in the intervention group showed significantly greater improvements in processing speed and attention measured by the Colour Trails Test 1 (β = 7.213, 95% confidence interval CI = 2.870-11.557, P = 0.001) and working memory measured by the Digit Span Backward Test (β = 0.540, 95% CI = 0.199-0.881, P = 0.002) immediately post-intervention. The effects were sustained at 3 months post-intervention. Similarly, significantly greater improvements in sequencing and mental flexibility measured by the Colour Trails Test 2 were observed in the intervention group 3 months post-intervention (β = 6.979, 95% CI = 3.375-10.584, P < 0.001). Changes in global cognition, short-term memory and HRQoL were not significant.
the peer-supported exercise intervention was effective at sustaining improvements in executive function, attention and working memory in persons with MCI.
Metabolic syndrome (MetS) is a clustering of cardiovascular risk factors, which is associated with diabetes mellitus and cardiovascular disease. Lifestyle interventions applied to people with MetS ...has considerable beneficial effects on disease preventive outcomes. This study aimed to examine the effects of 1-year of yoga exercise on the cardiovascular risk factors including central obesity, hypertension, dyslipidemia and hyperglycemia in middle-aged and older Hong Kong Chinese adults with MetS.
Adults diagnosed with MetS using National Cholesterol Education Program criteria (n = 182; mean ± SD age = 56 ± 9.1) were randomly assigned to a 1-year yoga intervention group or control group. Systolic and diastolic blood pressure, waist circumference, fasting plasma glucose, triglycerides, and high-density lipoprotein cholesterol were examined at baseline, midway, and on completion of the study. Physical activity level and caloric intake were assessed and included in the covariate analyses.
A reduction of the number of diagnostic components for MetS was found to be associated with the yoga intervention. Waist circumference was significantly improved after the 1-year yoga intervention. A trend towards a decrease in systolic blood pressure was observed following yoga intervention.
These results suggest that yoga exercise improves the cardiovascular risk factors including central obesity and blood pressure in middle-aged and older adults with MetS. These findings support the complementary beneficial role of yoga in managing MetS.
Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
Submitted 13 July 2008
; accepted in final form 26 July 2009
Pressure ulcer ...is a complex and significant health problem. Although the factors including pressure, shear, and ischemia have been identified in the etiology of pressure ulcer, the cellular and molecular mechanisms that contribute to the development of pressure ulcer are unclear. This study tested the hypothesis that the early-onset molecular regulation of pressure ulcer involves apoptosis in muscle tissue. Adult Sprague-Dawley rats were subjected to an in vivo protocol to mimic pressure-induced deep tissue injury. Static pressure was applied to the tibialis region of the right limb of the rats for 6 h each day on two consecutive days. The compression force was continuously monitored by a three-axial force transducer equipped in the compression indentor. The contralateral uncompressed limb served as intra-animal control. Tissues underneath the compressed region were collected for histological analysis, terminal dUTP nick-end labeling (TUNEL), cell death ELISA, immunocytochemical staining, and real-time RT-PCR gene expression analysis. The compressed muscle tissue generally demonstrated degenerative characteristics. TUNEL/dystrophin labeling showed a significant increase in the apoptotic muscle-related nuclei, and cell death ELISA demonstrated a threefold elevation of apoptotic DNA fragmentation in the compressed muscle tissue relative to control. Positive immunoreactivities of cleaved caspase-3, Bax, and Bcl-2 were evident in compressed muscle. The mRNA contents of Bax, caspase-3, caspase-8, and caspase-9 were found to be higher in the compressed muscle tissue than control. These results demonstrated that apoptosis is activated in muscle tissue following prolonged moderate compression. The data are consistent with the hypothesis that muscle apoptosis is involved in the underlying mechanism of pressure-induced deep tissue injury.
bed sore; muscle damage; caspase
Address for reprint requests and other correspondence: P. M. Siu, Dept. of Health Technology and Informatics, The Hong Kong Polytechnic Univ., Hung Hom, Kowloon, Hong Kong, China (e-mail: htpsiu{at}inet.polyu.edu.hk ).
Oxidation-induced damage to DNA can cause mutations, phenotypic changes and apoptosis. Agents that oppose such damage offer potential therapies for disease prevention. Vitamin D administration ...reportedly lowered DNA damage in type 2 diabetic mice, and higher DNA damage was reported in mononuclear cells of severely asthmatic patients who were vitamin D deficient. We hypothesised that lower vitamin D status associates with higher oxidation-induced DNA damage. Vitamin D deficiency (plasma 25(OH)D < 50 nmol/l) is highly prevalent worldwide, and association with DNA damage has high potential importance and impact in regard to the future health of vitamin D deficient young adults. In this study, oxidation-induced DNA damage in peripheral lymphocytes of 121 young (18-26 years) adults was measured using the formamidopyrimidine DNA glycosylase (FPG)-assisted comet assay. Plasma 25(OH)D was measured by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Correlational analysis was performed between 25(OH)D and DNA damage. Differences in DNA damage across tertiles of 25(OH)D were explored using analysis of variance. DNA damage in those with 25(OH)D <50 nmol and ≥50 nmol/l was compared using the unpaired t-test. Mean (SD) DNA damage (as %DNA in comet tail) and plasma 25(OH)D were, respectively, 18.58 (3.39)% and 44.7 (13.03) nmol/l. Most (82/121; 68%) of the subjects were deficient in vitamin D (25(OH)D <50nmol/l). No significant correlation was seen between 25(OH)D and DNA damage (r = -0.0824; P > 0.05). No significant difference was seen across 25(OH)D tertiles: mean (SD) %DNA in comet tail/25(OH)D nmol/l values in lowest, middle and highest tertiles were, respectively, 18.64 (3.30)/31.6 (4.4), 18.90 (3.98)/42.9 (3.5), 18.19 (2.84)/59.9 (8.5), nor across the binary divide: 18.73 (3.63)% in <50nmol/l group vs. 18.27 (2.84)% in the ≥50 nmol/l group. No association between vitamin D and oxidation-induced DNA damage was observed, but vitamin D deficiency was highly prevalent in the young adults studied, and we cannot rule out an ameliorative effect of correction of vitamin D deficiency on DNA damage.
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