A Technique for the Analysis of Unbalanced Data

The regression methods with dummy variables have been shown to be effective in preventing confusion in the analysis of linear models. In particular, this model simplifies interpretation of parameters and clarifies hypothesis statements. All existing methods have been shown as special cases of the general linear hypothesis in regression setting. Three regression on dummy variables methods are examined critically to bring out the salient features of each method. The choice of a method should be based on the way definitions of the parameters are desired. The linear models are considered in a regression model setting. This has been done by defining appropriate dummy variables in a regression model which often is desirable, if not mandatory, when dealing with unbalanced data involving two or more factors.     

Association,Symmetry and Diagonal Models for Occupational Mobility and Other Similar Square Contingency Tables Having Ordered Categorical Variables

This paper examines various association, symmetry and “diagonal band” class models for both the British and Danish social mobility data. Composite models are also fitted to these data and the variety of models considered ensures that for most square tables, parsimonious models within the class of models examined in this study can always be found that will adequately describe such tables. The models considered in this study, which have been described in various forms by Goodman (1984), Upton (1985) and Tomizawa (1986) can suit most square tables having ordered classificatory variables. A model selection procedure is also examined.     

Are the recommended allowances for dietary antioxidants adequate?

Recommended dietary allowances are standards for maintaining health. Claims that intakes substantially above the allowances may provide protection from xenobiotics and prevent diseases, including cancer, are examined critically for five nutrients that have antioxidant potential. Major criticism is directed at the failure of epidemiologists to recognize that for many of these nutrients, metabolic differences among individuals preclude a direct relationship between dietary intake and plasma or tissue concentration. Also, the fact that no differences in disease incidence have been described within various species of animals that have markedly different metabolic patterns for some of these nutrients has not been considered. It is concluded that the experimental and epidemiological evidence to data that increased intakes of certain nutrients will have beneficial effects on human health are tenuous.     

Studies of mitochondrial respiration in muscle cells in situ: Use and misuse of experimental evidence in mathematical modelling

Applications of permeabilized cell and skinned fiber techniques in combination with methods of mathematical modelling for studies of mitochondrial function in the cell are critically evaluated. Mathematical models may be useful tools for explaining biological phenomena, but only if they are selected by fitting the computing results with real experimental data. Confocal microscopy has been used in experiments with permeabilized cardiomyocytes and myocardial fibers to determine the maximal diffusion distance from medium to the core of cells, which is shown not to exceed 8-10 microm. This is a principal index for correctly explaining high apparent Km for exogenous ADP (200-300 microM) in regulation of mitochondrial respiration in oxidative muscle cells in situ. The best fitting of the results of in silico studies may be achieved by using of the compartmentalized energy transfer model. From these results, it may be concluded that in cardiac muscle cells the mitochondria and ATPases are organized into intracellular energetic units (ICEUs) separated from the bulk phase of cytoplasm by some barriers which limit the diffusion of adenine nucleotides. In contrast, alternative models based on the concept of the cell as homogenous system do not explain the observed experimental phenomena and have led to misleading conclusions. The various sources of experimental and conceptual errors are analyzed.     

Neurodevelopmental animal models of schizophrenia: effects on prepulse inhibition

Epidemiological studies have shown increased incidence of schizophrenia in patients subjected to different forms of pre- or perinatal stress. However, as the onset of schizophrenic illness does not usually occur until adolescence or early adulthood, it is not yet fully understood how disruption of early brain development may ultimately lead to malfunction years later. In order to elucidate a possible role for neurodevelopmental factors in the pathogenesis of schizophrenia and to highlight potential new treatments, animal models are needed. Prepulse inhibition (PPI) is a model of sensorimotor gating mechanisms in the brain. It is disrupted in schizophrenia patients and the disruption can be reversed with atypical antipsychotics. It has been widely used in animal studies to explore central mechanisms possibly involved in schizophrenia. There has been a recent surge of behavioural and neurochemical animal studies on neurodevelopmental models, particularly on the effects of postweaning isolation, maternal separation and neonatal lesions of the hippocampus. In these models, long lasting alterations in behaviour and/or molecular changes in specific brain regions are observed, comparable to those seen in schizophrenia. The aim of this article is to critically review the available literature on such neurodevelopmental animal models with special focus on the effects on PPI and brain regions that are putatively involved in regulation of PPI.     

Translational physiology: porcine models of human coronary artery disease: implications for preclinical trials of therapeutic angiogenesis.

"Therapeutic angiogenesis" describes an emerging field of cardiovascular medicine whereby new blood vessels are induced to grow to supply oxygen and nutrients to ischemic cardiac or skeletal muscle. Various methods of producing therapeutic angiogenesis have been employed, including mechanical means, gene therapy, and the use of growth factors, among others. The use of appropriate large-animal models is essential if these therapies are to be critically evaluated in a preclinical setting before their use in humans, yet little has been written comparing the various available models. Over the past decade, swine have been increasingly used in studies of chronic ischemia because of their numerous similarities to humans, including minimal preexisting coronary collaterals as well as similar coronary anatomy and physiology. Consequently, this review describes the most commonly used swine models of chronic myocardial ischemia with special attention to regional myocardial blood flow and function and critically evaluates the strengths and weaknesses of each model in terms of utility for preclinical trials of angiogenic therapies.     

G protein-coupled receptors as therapeutic targets for multiple sclerosis

G protein-coupled receptors (GPCRs) mediate most of our physiological responses to hormones, neurotransmitters and environmental stimulants. They are considered as the most successful therapeutic targets for a broad spectrum of diseases. Multiple sclerosis (MS) is an inflammatory disease that is characterized by immune-mediated demyelination and degeneration of the central nervous system (CNS). It is the leading cause of non-traumatic disability in young adults. Great progress has been made over the past few decades in understanding the pathogenesis of MS. Numerous data from animal and clinical studies indicate that many GPCRs are critically involved in various aspects of MS pathogenesis, including antigen presentation, cytokine production, T-cell differentiation, T-cell proliferation, T-cell invasion, etc. In this review, we summarize the recent findings regarding the expression or functional changes of GPCRs in MS patients or animal models, and the influences of GPCRs on disease severity upon genetic or pharmacological manipulations. Hopefully some of these findings will lead to the development of novel therapies for MS in the near future.     

Perpendicular distance models for line transect sampling

Perpendicular distance line transect models are examined to assess whether any single model can provide a general procedure for analysing line transect data. Of the two-parameter models considered, the hazard-rate model appears promising, whereas the exponential power series and exponential quadratic models do not. Of the nonparametric models, the Fourier series is the best developed, and is favoured by many researchers as a general model. However, for a given data set, the Fourier series estimate may be highly dependent on the number of terms selected, and so the model is not a clear improvement over the hazard-rate model. A similar variable-term model, using Hermite polynomials, is considered, and is shown to be less dependent on the number of terms selected. There has been some debate about whether the derivative of the density function of perpendicular distances evaluated at 0 should be 0, so that the function has a "shoulder." The problem is examined in detail, and it is argued that reliable estimation is not possible from line transect data unless a shoulder exists. Many data sets appear to exhibit no shoulder; possible reasons are examined.     

Importance of being Nernst: Synaptic activity and functional relevance in stem cell-derived neurons

Functional synaptogenesis and network emergence are signature endpoints of neurogenesis. These behaviors provide higher-order confirmation that biochemical and cellular processes necessary for neurotransmitter release, post-synaptic detection and network propagation of neuronal activity have been properly expressed and coordinated among cells. The development of synaptic neurotransmission can therefore be considered a defining property of neurons. Although dissociated primary neuron cultures readily form functioning synapses and network behaviors in vitro, continuously cultured neurogenic cell lines have historically failed to meet these criteria. Therefore, in vitro-derived neuron models that develop synaptic transmission are critically needed for a wide array of studies, including molecular neuroscience, developmental neurogenesis, disease research and neurotoxicology. Over the last decade, neurons derived from various stem cell lines have shown varying ability to develop into functionally mature neurons. In this review, we will discuss the neurogenic potential of various stem cells populations, addressing strengths and weaknesses of each, with particular attention to the emergence of functional behaviors. We will propose methods to functionally characterize new stem cell-derived neuron (SCN) platforms to improve their reliability as physiological relevant models. Finally, we will review how synaptically active SCNs can be applied to accelerate research in a variety of areas. Ultimately, emphasizing the critical importance of synaptic activity and network responses as a marker of neuronal maturation is anticipated to result in in vitro findings that better translate to efficacious clinical treatments.     

Silicon: A neglected micronutrient essential for bone health

Bone matrix is predominantly made up of collagen, and in vitro and in animal models studies have shown that silicon is linked to glycosaminoglycans and plays an important role in the formation of cross-links between collagen and proteoglycans, determining the beneficial effects on strength, composition, and mechanical properties of bone. However, there are still no precise indications regarding a possible role of silicon on bone health in humans. Given this background, the aim of this narrative review was to consider the effectiveness of silicon dietary intake and silicon dietary supplementation (alone or with other micronutrients), in order to suggest a daily dosage of Si supplementation, on bone mineral density in humans. This review included eight eligible studies: four regarding dietary intake and four considering supplementation with silicon alone or with other nutrients. Despite the number of studies considered being low, the number of subjects studied is high (10012) and the results are interesting. Although to date the available scientific evidences are not considered valid enough to allow to establish an adequate level of Silicon intake, based on extrapolations from the data obtained with studies on animal and human models, it has been suggested that an adequate intake in order to promote beneficial effects for bone could be considered to be around 25 mg silicon/day. As for silicon dietary supplements, it has been shown that the combined treatment with orthosilicic acid (6 mg), calcium, and vitamin D has a potentially beneficial effect on femoral BMD compared to only use of calcium and vitamin D.     

Quantification of the power of Hardy-Weinberg equilibrium testing to detect genotyping error

Deviation from Hardy-Weinberg equilibrium has become an accepted test for genotyping error. While it is generally considered that testing departures from Hardy-Weinberg equilibrium to detect genotyping error is not sensitive, little has been done to quantify this sensitivity. Therefore, we have examined various models of genotyping error, including error caused by neighboring SNPs that degrade the performance of genotyping assays. We then calculated the power of chi-square goodness-of-fit tests for deviation from Hardy-Weinberg equilibrium to detect such error. We have also examined the affects of neighboring SNPs on risk estimates in the setting of case-control association studies. We modeled the power of departure from Hardy-Weinberg equilibrium as a test to detect genotyping error and quantified the effect of genotyping error on disease risk estimates. Generally, genotyping error does not generate sufficient deviation from Hardy-Weinberg equilibrium to be detected. As expected, genotyping error due to neighboring SNPs attenuates risk estimates, often drastically. For the moment, the most widely accepted method of detecting genotyping error is to confirm genotypes by sequencing and/or genotyping via a separate method. While these methods are fairly reliable, they are also costly and time consuming.     

Vacuolar Lucifer Yellow Uptake in Plants: Endocytosis or Anion Transport; A Critical Opinion

Because of its membrane-impermeant-properties Lucifer Yellow-CH (LY) is regarded by animal cell biologists as an ideal tracer for fluid-phase endocytosis. When presented to plant cells or protoplasts this fluoroprobe accumulates in the vacuole. On the other hand there are many cases where LY does not enter the vacuole when loaded into the plant cytosol. These, superficially divergent, results have previously been explained in terms of endocytosis whereby access to the vacuole is considered to occur through vesicle transport. This interpretation has now been challenged in three recent papers where the benzoic acid derivative, probenecid, has been shown to prevent vacuolar LY accumulation in plants. Since probenecid is a well-known inhibitor of organic anion transport in animal cells it has been argued that anion carriers capable of transporting LY might also exist at the plasma membrane and tonoplast of plant cells. Unfortunately probenecid has rarely, if ever, been used in plant transport studies. The fact that it is a weak acid, whose inhibitory effects are observed at concentrations of around 1 mM suggests that caution should prevail when interpreting results obtained with probenecid. The purpose of this article is therefore to highlight the current controversy surrounding LY uptake by plants and to critically evaluate the recent probenecid data.     

Mitochondrial functional alterations in relation to pathophysiology of Huntington’s disease

Huntington’s disease (HD) is an autosomal dominant neurodegenerative disease which is characterized by psychiatric symptoms, involuntary choreiform movements and dementia with maximum degeneration occurring in striatum and cerebral cortex. Several studies implicate mitochondrial dysfunction to the selective neurodegeneration happening in this disorder. Calcium buffering imbalance and oxidative stress in the mitochondria, critically impaired movement across axons and abnormal fission or fusion of this organelle in the cells are some of the salient features that results in the loss of mitochondrial electron transport chain (ETC) complex function in HD. Although several models involving mutant huntingtin, excitotoxins and mitochondrial complex-II inhibitors have been used to explore the disease, it is not clear how disturbances in mitochondrial functioning is associated with such selective neurodegeneration, or in the expression of huntingtonian phenotypes in animals or man. We have carefully assessed various mitochondrial abnormalities observed in human patient samples, postmortem HD brains, cellular, vertebrate and invertebrate models of the disease, to conclude that ETC dysfunction is an integral part of the disease and justify a causal role of mitochondrial ETC dysfunction for the genesis of this disorder     

The expanding role of fish models in understanding non-alcoholic fatty liver disease

Non-alcoholic fatty liver disease (NAFLD) is a condition in which excessive fat accumulates in the liver of an individual who has not consumed excessive alcohol. Non-alcoholic steatohepatitis (NASH), a severe form of NAFLD, can progress to hepatic cirrhosis and/or hepatocellular carcinoma (HCC). NAFLD is considered to be a hepatic manifestation of metabolic syndrome, and its incidence has risen worldwide in lockstep with the increased global prevalence of obesity. Over the last decade, rodent studies have yielded an impressive list of molecules associated with NAFLD and NASH pathogenesis. However, the identification of currently unknown metabolic factors using mammalian model organisms is inefficient and expensive compared with studies using fish models such as zebrafish (Danio rerio) and medaka (Oryzias latipes). Substantial advances in unraveling the molecular pathogenesis of NAFLD have recently been achieved through unbiased forward genetic screens using small fish models. Furthermore, these easily manipulated organisms have been used to great advantage to evaluate the therapeutic effectiveness of various chemical compounds for the treatment of NAFLD. In this Review, we summarize aspects of NAFLD (specifically focusing on NASH) pathogenesis that have been previously revealed by rodent models, and discuss how small fish are increasingly being used to uncover factors that contribute to normal hepatic lipid metabolism. We describe the various types of fish models in use for this purpose, including those generated by mutation, transgenesis, or dietary or chemical treatment, and contrast them with rodent models. The use of small fish in identifying novel potential therapeutic agents for the treatment of NAFLD and NASH is also addressed.     

Inference on Risk Rates Based on Mortality Data Under Censoring and Competing Risks Using Parametric Models

In this paper we consider the competing risks model where the risks may not be independent. We assume both fixed and random censoring. The random censoring mechanism could have either a parametric or a non-parametric form. The life distributions and the parametric censoring distribution considered are exponential or Weibull. The expressions for the asymptotic confidence intervals for various parameters of interest under different models, using the estimated Fisher information matrix and parametric bootstrap techniques have been derived. Monte Carlo simulation studies for some of these cases have been carried out.     

Identification of structures for ion channel kinetic models

Markov models of ion channel dynamics have evolved as experimental advances have improved our understanding of channel function. Past studies have examined limited sets of various topologies for Markov models of channel dynamics. We present a systematic method for identification of all possible Markov model topologies using experimental data for two types of native voltage-gated ion channel currents: mouse atrial sodium currents and human left ventricular fast transient outward potassium currents. Successful models identified with this approach have certain characteristics in common, suggesting that aspects of the model topology are determined by the experimental data. Incorporating these channel models into cell and tissue simulations to assess model performance within protocols that were not used for training provided validation and further narrowing of the number of acceptable models. The success of this approach suggests a channel model creation pipeline may be feasible where the structure of the model is not specified a priori.     

Carotenoids and cardiovascular disease: what research gaps remain?

PURPOSE OF REVIEW: Dietary and blood carotenoids, including alpha-carotene, beta-carotene, lycopene, lutein/zeaxanthin, and beta-cryptoxanthin, have been examined in a number of epidemiological studies in recent years for the risk of cardiovascular disease. This review assimilated the existing and recent literature on carotenoids and cardiovascular disease and considered what research gaps may remain. RECENT FINDINGS: Numerous large cohort studies have been published in largely American men and women that have examined dietary intake or blood levels of total or individual carotenoids with the risk of various cardiovascular endpoints. Overall, early, promising results have grown increasingly inconsistent over time. More recently, studies examining lycopene and lutein/zeaxanthin have offered more promising data on a possible, but not yet established, inverse association with the risk of cardiovascular disease. Recent epidemiological data on beta-cryptoxanthin and cardiovascular disease are lacking. Primary and secondary prevention trials have extensively examined beta-carotene, but not other carotenoids, for the risk of cardiovascular disease as either the primary or secondary endpoint with largely null results. More recent studies have focused on individual carotenoids in relation to cardiovascular disease and require a more careful evaluation of potential mechanisms of effect. SUMMARY: The promise of early epidemiological studies on carotenoids and cardiovascular disease paved the way to largely disappointing results from several large prevention trials of beta-carotene. Emerging recent evidence of potential cardioprotective effects for lycopene and other carotenoids besides beta-carotene in the diet and blood suggest that there is more to be learned in the story of carotenoids and both atherosclerotic progression and clinically manifested cardiovascular disease.     

Finite element assessment of block-augmented total knee arthroplasty

Loosening and migration of tibial prostheses have been identified as causes of early total knee replacement (TKR) failure. The problem is made more complex when defects occur in the proximal tibia compromising fixation and alignment. Clinical studies using metal augments have shown these to be an alternative to other means of defect treatment. Finite element (FE) analysis can be used to identify regions that may be prone to loosening and migration. In the current work, 3D FE models of TKR uncontained type-2 defects treated with block augments have been constructed and analysed. It has been shown that a metal augment is the most suitable. The use of bone cement (PMMA) to fill proximal defects is not considered suitable as stresses carried by the cement block exceed those of the fatigue limit of bone cement. It has been shown that the stresses in the proximal cancellous bone of block-augmented models are significantly below levels likely to cause damage due to overloading. Furthermore, the use of stem extensions has been shown to reduce the cancellous bone stresses in the proximal region thus increasing the likelihood of bone resorption. Given this, it is recommended that stem extensions are not required unless necessary to mitigate some other problem.     

Selenium and asthma

Se is a potent nutritional antioxidant important for various aspects of human health. Because asthma has been demonstrated to involve increased oxidative stress, levels of Se intake have been hypothesized to play an important role in the pathogenesis of asthma. However, significant associations between Se status and prevalence or severity of asthma have not been consistently demonstrated in human studies. This highlights both the complex etiology of human asthma and the inherent problems with correlative nutritional studies. In this review, the different findings in human studies are discussed along with results from limited intervention studies. Mouse models of asthma have provided more definitive results suggesting that the benefits of Se supplementation may depend on an individual’s initial Se status. This likely involves T helper cell differentiation and the mechanistic studies that have provided important insight into the effects of Se levels on immune cell function are summarized. Importantly, the benefits and adverse effects of Se supplementation must both be considered in using this nutritional supplement for treating asthma. With this in mind new approaches are discussed that may provide more safe and effective means for using Se supplementation for asthma or other disorders involving inflammation or immunity.