A Step-Wise Multiple Testing for Linear Regression Models with Application to the Study of Resting Energy Expenditure

Statistics in Biosciences - Motivated by the mechanistic model of the resting energy expenditure, we present a new multiple hypothesis testing approach to evaluate organ/tissue-specific resting...     

Linear Mixed-Effects Models to Describe Individual Tree Crown Width for China-Fir in Fujian Province,Southeast China

A multiple linear model was developed for individual tree crown width of Cunninghamia lanceolata (Lamb.) Hook in Fujian province, southeast China. Data were obtained from 55 sample plots of pure China-fir plantation stands. An Ordinary Linear Least Squares (OLS) regression was used to establish the crown width model. To adjust for correlations between observations from the same sample plots, we developed one level linear mixed-effects (LME) models based on the multiple linear model, which take into account the random effects of plots. The best random effects combinations for the LME models were determined by the Akaike’s information criterion, the Bayesian information criterion and the -2logarithm likelihood. Heteroscedasticity was reduced by three residual variance functions: the power function, the exponential function and the constant plus power function. The spatial correlation was modeled by three correlation structures: the first-order autoregressive structure [AR(1)], a combination of first-order autoregressive and moving average structures [ARMA(1,1)], and the compound symmetry structure (CS). Then, the LME model was compared to the multiple linear model using the absolute mean residual (AMR), the root mean square error (RMSE), and the adjusted coefficient of determination (adj-R ²). For individual tree crown width models, the one level LME model showed the best performance. An independent dataset was used to test the performance of the models and to demonstrate the advantage of calibrating LME models.     

Prediction of Random Effects in Linear and Generalized Linear Models under Model Misspecification

Summary Statistical models that include random effects are commonly used to analyze longitudinal and correlated data, often with the assumption that the random effects follow a Gaussian distribution. Via theoretical and numerical calculations and simulation, we investigate the impact of misspecification of this distribution on both how well the predicted values recover the true underlying distribution and the accuracy of prediction of the realized values of the random effects. We show that, although the predicted values can vary with the assumed distribution, the prediction accuracy, as measured by mean square error, is little affected for mild‐to‐moderate violations of the assumptions. Thus, standard approaches, readily available in statistical software, will often suffice. The results are illustrated using data from the Heart and Estrogen/Progestin Replacement Study using models to predict future blood pressure values.     

A Single Oral Administration of Theaflavins Increases Energy Expenditure and the Expression of Metabolic Genes

Theaflavins are polyphenols found in black tea, whose physiological activities are not well understood. This study on mice evaluated the influence of a single oral administration of theaflavins on energy metabolism by monitoring the initial metabolic changess in skeletal muscle and brown adipose tissue (BAT). Oxygen consumption (VO₂) and energy expenditure (EE) were increased significantly in mice treated with theaflavin rich fraction (TF) compared with the group administered vehicle alone. There was no difference in locomotor activity. Fasting mice were euthanized under anesthesia before and 2 and 5, 20-hr after treatment with TF or vehicle. The mRNA levels of uncoupling protein-1 (UCP-1) and peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α) in BAT were increased significantly 2-hr after administration ofTF. The levels of UCP-3 and PGC-1α in the gastrocnemius muscle were increased significantly 2 and 5-hr after administration of TF. The concentration of phosphorylated AMP-activated protein kinase (AMPK) 1α was also increased significantly in the gastrocnemius 2 and 5-hr after treatment with TF. These results indicate that TF significantly enhances systemic energy expenditure, as evidenced by an increase in expression of metabolic genes.     

Mathematical Models for Sleep-Wake Dynamics: Comparison of the Two-Process Model and a Mutual Inhibition Neuronal Model

Sleep is essential for the maintenance of the brain and the body, yet many features of sleep are poorly understood and mathematical models are an important tool for probing proposed biological mechanisms. The most well-known mathematical model of sleep regulation, the two-process model, models the sleep-wake cycle by two oscillators: a circadian oscillator and a homeostatic oscillator. An alternative, more recent, model considers the mutual inhibition of sleep promoting neurons and the ascending arousal system regulated by homeostatic and circadian processes. Here we show there are fundamental similarities between these two models. The implications are illustrated with two important sleep-wake phenomena. Firstly, we show that in the two-process model, transitions between different numbers of daily sleep episodes can be classified as grazing bifurcations. This provides the theoretical underpinning for numerical results showing that the sleep patterns of many mammals can be explained by the mutual inhibition model. Secondly, we show that when sleep deprivation disrupts the sleep-wake cycle, ostensibly different measures of sleepiness in the two models are closely related. The demonstration of the mathematical similarities of the two models is valuable because not only does it allow some features of the two-process model to be interpreted physiologically but it also means that knowledge gained from study of the two-process model can be used to inform understanding of the behaviour of the mutual inhibition model. This is important because the mutual inhibition model and its extensions are increasingly being used as a tool to understand a diverse range of sleep-wake phenomena such as the design of optimal shift-patterns, yet the values it uses for parameters associated with the circadian and homeostatic processes are very different from those that have been experimentally measured in the context of the two-process model.     

A Conserved Role for Syndecan Family Members in the Regulation of Whole-Body Energy Metabolism

Syndecans are a family of type-I transmembrane proteins that are involved in cell-matrix adhesion, migration, neuronal development, and inflammation. Previous quantitative genetic studies pinpointed Drosophila Syndecan (dSdc) as a positional candidate gene affecting variation in fat storage between two Drosophila melanogaster strains. Here, we first used quantitative complementation tests with dSdc mutants to confirm that natural variation in this gene affects variability in Drosophila fat storage. Next, we examined the effects of a viable dSdc mutant on Drosophila whole-body energy metabolism and associated traits. We observed that young flies homozygous for the dSdc mutation had reduced fat storage and slept longer than homozygous wild-type flies. They also displayed significantly reduced metabolic rate, lower expression of spargel (the Drosophila homologue of PGC-1), and reduced mitochondrial respiration. Compared to control flies, dSdc mutants had lower expression of brain insulin-like peptides, were less fecund, more sensitive to starvation, and had reduced life span. Finally, we tested for association between single nucleotide polymorphisms (SNPs) in the human SDC4 gene and variation in body composition, metabolism, glucose homeostasis, and sleep traits in a cohort of healthy early pubertal children. We found that SNP rs4599 was significantly associated with resting energy expenditure (P = 0.001 after Bonferroni correction) and nominally associated with fasting glucose levels (P = 0.01) and sleep duration (P = 0.044). On average, children homozygous for the minor allele had lower levels of glucose, higher resting energy expenditure, and slept shorter than children homozygous for the common allele. We also observed that SNP rs1981429 was nominally associated with lean tissue mass (P = 0.035) and intra-abdominal fat (P = 0.049), and SNP rs2267871 with insulin sensitivity (P = 0.037). Collectively, our results in Drosophila and humans argue that syndecan family members play a key role in the regulation of body metabolism.     

Contribution of Different Mechanisms to Compensation for Energy Restriction in the Mouse

Objective: Restriction of energy intake produces weight loss, but the rate of loss is seldom sustained. This is presumed to be a consequence of compensatory reductions in energy expenditure, although the exact contributions of different components to the energy budget remain uncertain. We examined the compensatory responses of mice to a 20% dietary restriction. Research Methods and Procedures: We measured body mass, body fatness, body temperature, and the components of daily energy expenditure for 50 MF1 mice. Forty mice were then placed on a restricted diet at 80% of their ad libitum intake for 50 days. The remaining 10 mice continued to feed ad libitum. Ten days before the end of the restriction period, the same measurements were taken. Results: There were no significant differences between the control and restricted groups in any parameters before restriction. During the restriction period, body mass increased in both the control and restricted groups, but at a slower rate in the restricted mice. The control group increased in both fat and fat free mass; however, although the restricted group increased fat to the same extent as the controls, fat free mass increased to a lesser extent. The contributions of the different components of the expended energy to compensate for the reduced energy intake were energy deposition, 2.2%; resting metabolic rate, 22.3%; and activity, 75.5%. Discussion: Mice were able to compensate almost completely for the restricted energy intake that was achieved by altering the amount of energy required for each component of the energy budget except digestive efficiency.     

The General Linear Model as a Framework for Models in Configural Frequency Analysis

The present paper discusses models of Configural Frequency Analysis (CFA). For most models of CFA maximum likelihood estimators are given. For all of these models least squares estimators are also given. These estimators are equivalent to each other if quasiparametric conditions prevail. Using the second approach, the general linear model can be used to systematize CFA models. Numerical examples are given, using both artificial and psychiatric data.     

The Contribution of Different Organs to Grain Weight in Upland and Swamp Rice

The contribution of dry matter was significantly greater inthe ears of Dima than that of Kindinga. The flag-leaf lamina,flag-leaf sheath and peduncle, lower leaves and stem of Kindingamade greater contribution of dry matter in the grain at harvestthan those of Dima. On the average of the two varieties 23 percent. of the dry matter in the grain at harvest originated fromphotosynthesis in the ears; 60 per cent. came from photosynthesisin the flag-leaf lamina and sheath and peduncle and 17 per cent.from parts of the shoot below the flag leaf.     

Overview of Mathematical Approaches Used to Model Bacterial Chemotaxis I: The Single Cell

Mathematical modeling of bacterial chemotaxis systems has been influential and insightful in helping to understand experimental observations. We provide here a comprehensive overview of the range of mathematical approaches used for modeling, within a single bacterium, chemotactic processes caused by changes to external gradients in its environment. Specific areas of the bacterial system which have been studied and modeled are discussed in detail, including the modeling of adaptation in response to attractant gradients, the intracellular phosphorylation cascade, membrane receptor clustering, and spatial modeling of intracellular protein signal transduction. The importance of producing robust models that address adaptation, gain, and sensitivity are also discussed. This review highlights that while mathematical modeling has aided in understanding bacterial chemotaxis on the individual cell scale and guiding experimental design, no single model succeeds in robustly describing all of the basic elements of the cell. We conclude by discussing the importance of this and the future of modeling in this area.     

Classical Molecular Dynamics Simulation of Kappa Squared Factor in Resonance Energy Transfer for Linear Dipole Models

Molecular dynamics simulations of linear models interacting through a dipolar Kihara intermolecular potential are presented. Molecular orientation correlations are used to calculate the orientational factor kappa squared in the resonance energy transfer (RET) as a function of the intermolecular separation. The distance, R 0 (2/3), at which the simulated systems show an isotropic behavior is calculated and an analysis of the dependence of R 0 (2/3) on microscopic properties (molecular aspect ratio and dipole moment) as well on thermodynamics (temperature and density) is presented. An explanation of the use of metallic cations as probes in RET is given and some relations of our models with biological molecules are pointed out.     

Daily Energy Expenditure and the Cost of Activity in Mammals

Among 17 species of mammals, field metabolic rates exclusiveof thermoregulatory and productive costs (designated FMR*) averaged2.65 x standard metabolism (SMR). Daily activity costswere calculatedby subtraction from FMR* of the daily energy expenditure associatedwith SMR and assimilation of nutrients. Total expenditure foractivity was of a similar magnitude to that for daily standardmetabolism. Calculations indicate that expenditures by mammalsfor locomotion probably account for less than half of dailyactivity costs. Expenditures by mammals engaged in other kindsof activities are also reviewed. During their daily activityperiods, terrestrial mammals expend energy at a rate of about4.1 x SMR. The utility of energetic increments for activityin time-energy budgets, thermal energy budgets, and analysesof the economics of foraging are discussed.     

HEPNet: A Knowledge Base Model of Human Energy Pool Network for Predicting the Energy Availability Status of an Individual

HEPNet is an electronic representation of metabolic reactions occurring within human cellular organization focusing on inflow and outflow of the energy currency ATP, GTP and other energy associated moieties. The backbone of HEPNet consists of primary bio-molecules such as carbohydrates, proteins and fats which ultimately constitute the chief source for the synthesis and obliteration of energy currencies in a cell. A series of biochemical pathways and reactions constituting the catabolism and anabolism of various metabolites are portrayed through cellular compartmentalization. The depicted pathways function synchronously toward an overarching goal of producing ATP and other energy associated moieties to bring into play a variety of cellular functions. HEPNet is manually curated with raw data from experiments and is also connected to KEGG and Reactome databases. This model has been validated by simulating it with physiological states like fasting, starvation, exercise and disease conditions like glycaemia, uremia and dihydrolipoamide dehydrogenase deficiency (DLDD). The results clearly indicate that ATP is the master regulator under different metabolic conditions and physiological states. The results also highlight that energy currencies play a minor role. However, the moiety creatine phosphate has a unique character, since it is a ready-made source of phosphoryl groups for the rapid synthesis of ATP from ADP. HEPNet provides a framework for further expanding the network diverse age groups of both the sexes, followed by the understanding of energetics in more complex metabolic pathways that are related to human disorders.     

The Contribution of p53 in the Dynamics of Cell Cycle Response to DNA Damage Interpreted by a Mathematical Model

Despite numerous studies on the tumor suppressor p53, a complete picture of its role in cell arrest and killing in G1, S and G2M phases after drug treatment is lacking. We tackled the analysis of the complexity of cell cycle effects combining the time-course measures with different techniques with the aid of a computer program simulating cell cycle progression. This mixed experimental-simulation approach enabled us to decode the dynamics of the cytostatic and cytotoxic responses to cisplatin and doxorubicin treatments in a p53-proficient colon carcinoma cell line (HCT-116) and in its p53-deficient counterpart. We achieved a separate evaluation of the activity of each cell cycle control and we connected these results with measures of p53 level in G1, S and G2M. We confirmed the action of p53 in all cell cycle phases, but also the presence of strong p53-independent cytostatic and cytotoxic activities exerted by both drugs. In G1 phase, p53 was responsible for a medium/long term block, distinct from the short-term block, which was p53-independent. The delay in traversing S phase was reduced by the presence of p53. In G2M phase, despite a strong p53-independent block, there was a weaker but more persistent p53-dependent block. At cytotoxic concentrations, p53-dependent and p53-independent cell death was observed. The former was poorly phase-specific, occurred earlier and exploited the apoptotic mechanism more than p53-independent death.Computer simulation produced a framework where previous partial and sometimes apparently contradictory observations of the p53-mediated effects could be reconciled and explained.     

Exploring Metrics to Express Energy Expenditure of Physical Activity in Youth

Background

Several approaches have been used to express energy expenditure in youth, but no consensus exists as to which best normalizes data for the wide range of ages and body sizes across a range of physical activities. This study examined several common metrics for expressing energy expenditure to determine whether one metric can be used for all healthy children. Such a metric could improve our ability to further advance the Compendium of Physical Activities for Youth.

Methods

A secondary analysis of oxygen uptake (VO₂) data obtained from five sites was completed, that included 947 children ages 5 to 18 years, who engaged in 14 different activities. Resting metabolic rate (RMR) was computed based on Schofield Equations [Hum Nutr Clin Nut. 39(Suppl 1), 1985]. Absolute oxygen uptake (ml.min^-1), oxygen uptake per kilogram body mass (VO₂ in ml.kg^-1.min^-1), net oxygen uptake (VO₂ – resting metabolic rate), allometric scaled oxygen uptake (VO₂ in ml.kg^-0.75.min^-1) and YOUTH-MET (VO₂.[resting VO₂] ^-1) were calculated. These metrics were regressed with age, sex, height, and body mass.

Results

Net and allometric-scaled VO₂, and YOUTH-MET were least associated with age, sex and physical characteristics. For moderate-to-vigorous intensity activities, allometric scaling was least related to age and sex. For sedentary and low-intensity activities, YOUTH-MET was least related to age and sex.

Conclusions

No energy expenditure metric completely eliminated the influence of age, physical characteristics, and sex. The Adult MET consistently overestimated EE. YOUTH-MET was better for expressing energy expenditure for sedentary and light activities, whereas allometric scaling was better for moderate and vigorous intensity activities. From a practical perspective, The YOUTH-MET may be the more feasible metric for improving of the Compendium of Physical Activities for Youth.     

A Single Oral Administration of Acetic Acid Increased Energy Expenditure in C57BL/6J Mice

We have reported that acetic acid (AcOH) intake suppresses body fat mass and up-regulates the genes involved in fatty acid oxidation, but it is not clear whether the suppression of body fat mass by AcOH administration is due to an increase in energy expenditure (EE). In this study, we investigated to determine whether a single oral administration of AcOH would increase EE in C57BL/6J mice treated with 1.5% AcOH. The AcOH treatment group had significantly higher oxygen consumption (VO₂), EE, and fat oxidation (FAT) than the water treatment group. These results suggest that a single administration of AcOH increases EE, resulting in suppression of body fat mass.