A New Distribution-Free Approach to Constructing the Confidence Region for Multiple Parameters

Construction of confidence intervals or regions is an important part of statistical inference. The usual approach to constructing a confidence interval for a single parameter or confidence region for two or more parameters requires that the distribution of estimated parameters is known or can be assumed. In reality, the sampling distributions of parameters of biological importance are often unknown or difficult to be characterized. Distribution-free nonparametric resampling methods such as bootstrapping and permutation have been widely used to construct the confidence interval for a single parameter. There are also several parametric (ellipse) and nonparametric (convex hull peeling, bagplot and HPDregionplot) methods available for constructing confidence regions for two or more parameters. However, these methods have some key deficiencies including biased estimation of the true coverage rate, failure to account for the shape of the distribution inherent in the data and difficulty to implement. The purpose of this paper is to develop a new distribution-free method for constructing the confidence region that is based only on a few basic geometrical principles and accounts for the actual shape of the distribution inherent in the real data. The new method is implemented in an R package, distfree.cr/R. The statistical properties of the new method are evaluated and compared with those of the other methods through Monte Carlo simulation. Our new method outperforms the other methods regardless of whether the samples are taken from normal or non-normal bivariate distributions. In addition, the superiority of our method is consistent across different sample sizes and different levels of correlation between the two variables. We also analyze three biological data sets to illustrate the use of our new method for genomics and other biological researches.     

Fitting Survival Data to a Piecewise Linear Hazard Rate in the Presence of Covariates

This paper extends the work of KODLIN (1967), who proposed a method for analyzing patient survival data wherein the hazard rate was linearly related to the survival time. The present paper extends Kodlin's model to permit maximum likelihood estimation of the parameters so that covariate effects are included and the slope and intercept parameters are allowed to change over fixed intervals of the time domain of study. An illustration of the method using multiple myeloma data is given and the results are compared with those of Kodlin's model, the Feigl-Zelen, Zippin-Armitage model, the exponential model, and Cox's proportional hazards model.     

Recent advances in the genetics underlying wheat grain protein content and grain protein deviation in hexaploid wheat

Wheat is one of the most important global crops and selection for better performance has been ongoing since ancient times. As a quantitative trait controlled by the interplay of several genomic loci and under the strong influence of the environment, grain protein content (GPC) is of major interest in breeding programs. Here, we review the most recent contributions to the genetics underlying wheat GPC and grain protein deviation (GPD, representing the relationship between grain protein content and yield), together with the performance of genomic prediction models characterizing these traits. A total of 364 significant loci related to GPC and GPD are positioned on the hexaploid wheat genome, highlighting genomic regions where significant independent QTL overlap, with special focus on two regions located on chromosomes 3A and 5A. Some of the corresponding homoeologous sequences co-locate with significant independent QTL reported on the B and D subgenomes. Overlapping independent QTL from different studies are indicative of genomic regions exhibiting stability across environments and genotypes, with promising candidates for improving grain quality.     

Comparing the likelihood ratios of two binary diagnostic tests in the presence of partial verification

The comparison of the efficiency of two binary diagnostic tests requires one to know the disease status for all patients in the sample, by applying a gold standard. In two-phase studies the gold standard is not applied to all patients in a sample, and the problem of partial verification of the disease arises. At present, one of the approaches most used for comparing two binary diagnostic tests are the likelihood ratios. In this study, the maximum likelihood estimators of likelihood ratios are obtained. The tests of hypothesis to compare the likelihood ratios of two binary diagnostic tests when both are applied to the same random sample in the presence of verification bias are deduced, and simulation experiments are performed in order to investigate the asymptotic behaviour of the tests of hypothesis. The results obtained have been applied to the study of Alzheimer's disease.     

Checking homogeneity of motifs' distribution in heterogenous sequences.

Studying the distribution of a motif along sequences may help in the understanding of its biological function, or to detect regions of interest. A statistical model is needed to assess the significance of the observed distribution. We propose a heterogenous compound Poisson process to model the possibility of overlap between occurrences and some heterogeneity of the sequence known a priori. The estimation procedure of the parameters is described and tests of homogenous sub-models are proposed. We also consider the detection of rich regions using either cumulated distances or moving intervals, via a homogenization technique. Illustrations of the method are given with applications to bacterial genomes.     

The impact of genetic parental distance on developmental stability and fitness in Drosophila buzzatii

Measures of genetic parental distances (GPD) based on microsatellite loci (D (2) and IR), have been suggested to be better correlated with fitness than individual heterozygosity (H), as they contain information about past events of inbreeding or admixture. We investigated if GPD increased with increasing genetic divergence between parental populations in Drosophila buzzatii and if the measures indicate past events of admixture. Further we evaluated the relationship between GPD, fitness and fluctuating asymmetry (FA) of size and shape. We investigated three populations of Drosophila buzzati, from Argentina, Europe and Australia. From these populations two intraspecific hybridisation lines were made; one between the Argentinean and European populations, which have been separated 200 years and one between the populations from Argentina and Australia, which have been separated 80 years. By doing this we obtained hybrid progeny having different levels of GPD. We found that D (2) and H can be used as indicators of admixture when comparing hybrid individuals with their parentals. IR was not informative. Our results does not exclude the presence of genetic fitness correlations (GFC) over individuals with a broad fitness range from populations in equilibrium, but we doubt the presence of GFC using GPD measures in admixed populations. Shape FA could be a relevant measure for fitness, however, only when comparing populations, not at individual level.     

Interaction between pancreatic β cell and electromagnetic fields: A systematic study toward finding the natural frequency spectrum of β cell system

Interaction between biological systems and environmental electric or magnetic fields has gained attention during the past few decades. Although there are a lot of studies that have been conducted for investigating such interaction, the reported results are considerably inconsistent. Besides the complexity of biological systems, the important reason for such inconsistent results may arise due to different excitation protocols that have been applied in different experiments. In order to investigate carefully the way that external electric or magnetic fields interact with a biological system, the parameters of excitation, such as intensity or frequency, should be selected purposefully due to the influence of these parameters on the system response. In this study, pancreatic β cell, the main player of blood glucose regulating system, is considered and the study is focused on finding the natural frequency spectrum of the system using modeling approach. Natural frequencies of a system are important characteristics of the system when external excitation is applied. The result of this study can help researchers to select proper frequency parameter for electrical excitation of β cell system. The results show that there are two distinct frequency ranges for natural frequency of β cell system, which consist of extremely low (or near zero) and 100–750 kHz frequency ranges. There are experimental works on β cell exposure to electromagnetic fields that support such finding.     

Segmented and "equivalent" representation of the cable equation

The linear cable theory has been applied to a modular structure consisting of n repeating units each composed of two subunits with different values of resistance and capacitance. For n going to infinity, i.e., for infinite cables, we have derived analytically the Laplace transform of the solution by making use of a difference method and we have inverted it by means of a numerical procedure. The results have been compared with those obtained by the direct application of the cable equation to a simplified nonmodular model with "equivalent" electrical parameters. The implication of our work in the analysis of the time and space course of the potential of real fibers has been discussed. In particular, we have shown that the simplified ("equivalent") model is a very good representation of the segmented model for the nodal regions of myelinated fibers in a steady situation and in every condition for muscle fibers. An approximate solution for the steady potential of myelinated fibers has been derived for both nodal and internodal regions. The applications of our work to other cases dealing with repeating structures, such as earthworm giant fibers, have been discussed and our results have been compared with other attempts to solve similar problems.     

Crystal structures of human glycerol 3-phosphate dehydrogenase 1 (GPD1)

Homo sapiens L-alpha-glycerol-3-phosphate dehydrogenase 1 (GPD1) catalyzes the reversible biological conversion of dihydroxyacetone (DHAP) to glycerol-3-phosphate. The GPD1 protein was expressed in Escherichia coli, and purified as a fusion protein with glutathione S-transferase. Here we report the apoenzyme structure of GPD1 determined by multiwavelength anomalous diffraction phasing, and other complex structures with small molecules (NAD+ and DHAP) by the molecular replacement method. This enzyme structure is organized into two distinct domains, the N-terminal eight-stranded beta-sheet sandwich domain and the C-terminal helical substrate-binding domain. An electrophilic catalytic mechanism by the epsilon-NH3+ group of Lys204 is proposed on the basis of the structural analyses. In addition, the inhibitory effects of zinc and sulfate on GPDHs are assayed and discussed.     

Gpd1 and Gpd2 fine-tuning for sustainable reduction of glycerol formation in Saccharomyces cerevisiae

Gpd1 and Gpd2 are the two isoforms of glycerol 3-phosphate dehydrogenase (GPDH), which is the rate-controlling enzyme of glycerol formation in Saccharomyces cerevisiae. The two isoenzymes play crucial roles in osmoregulation and redox balancing. Past approaches to increase ethanol yield at the cost of reduced glycerol yield have most often been based on deletion of either one or two isogenes (GPD1 and GPD2). While single deletions of GPD1 or GPD2 reduced glycerol formation only slightly, the gpd1Δ gpd2Δ double deletion strain produced zero glycerol but showed an osmosensitive phenotype and abolished anaerobic growth. Our current approach has sought to generate "intermediate" phenotypes by reducing both isoenzyme activities without abolishing them. To this end, the GPD1 promoter was replaced in a gpd2Δ background by two lower-strength TEF1 promoter mutants. In the same manner, the activity of the GPD2 promoter was reduced in a gpd1Δ background. The resulting strains were crossed to obtain different combinations of residual GPD1 and GPD2 expression levels. Among our engineered strains we identified four candidates showing improved ethanol yields compared to the wild type. In contrast to a gpd1Δ gpd2Δ double-deletion strain, these strains were able to completely ferment the sugars under quasi-anaerobic conditions in both minimal medium and during simultaneous saccharification and fermentation (SSF) of liquefied wheat mash (wheat liquefact). This result implies that our strains can tolerate the ethanol concentration at the end of the wheat liquefact SSF (up to 90 g liter(-1)). Moreover, a few of these strains showed no significant reduction in osmotic stress tolerance compared to the wild type.     

Structural homology between glycophorins C and D of human erythrocytes

Glycophorin C (GPC) and D (GPD) are minor glycoproteins which are believed to be important for the structural integrity of the red cell membrane. We have investigated the structural relationship between these glycoproteins by both immunological and structural investigations: 1. A rabbit anti-serum produced against GPD reacts strongly with GPC and the abnormal glycoproteins of Gerbich: -2, -3 and Gerbich: -2,3 red cells, and recognizes most probably the homologous C-terminal portions of GPC and GPD. The two molecules however differ at their N-terminus. 2. One-dimensional mapping of the peptides obtained after tryptic, chymotryptic, V8 protease or acid cleavage of 125I-labelled GPC and GPD, indicated that GPC and GPD are structurally related but some differences were found indicating that additional peptides were generated from GPC. 3. The partial primary structure of GPD was determined. The sequencing data are consistent with the assumption that GPD represents an abridged version of GPC that comprises residues approximately 21/29-128 and exhibits a N-terminal residue that is blocked by an as yet undefined group.     

GPD1L inhibits renal cell carcinoma progression by regulating PINK1/Parkin-mediated mitophagy

Few approaches have been conducted in the treatment of renal cell carcinoma (RCC) after nephrectomy, resulting in a high mortality rate in urological tumours. Mitophagy is a mechanism of mitochondrial quality control that enables selective degradation of damaged and unnecessary mitochondria. Previous studies have found that glycerol-3-phosphate dehydrogenase 1-like (GPD1L) is associated with the progression of tumours such as lung cancer, colorectal cancer and oropharyngeal cancer, but the potential mechanism in RCC is still unclear. In this study, microarrays from tumour databases were analysed. The expression of GPD1L was confirmed by RT–qPCR and western blotting. The effect and mechanism of GPD1L were explored using cell counting kit 8, wound healing, invasion, flow cytometry and mitophagy-related experiments. The role of GPD1L was further confirmed in vivo. The results showed that GPD1L expression was downregulated and positively correlated with prognosis in RCC. Functional experiments revealed that GPD1L prevented proliferation, migration and invasion while promoting apoptosis and mitochondrial injury in vitro. The mechanistic results indicated that GPD1L interacted with PINK1, promoting PINK1/Parkin-mediated mitophagy. However, inhibition of PINK1 reversed GPD1L-mediated mitochondrial injury and mitophagy. Moreover, GPD1L prevented tumour growth and promoted mitophagy by activating the PINK1/Parkin pathway in vivo. Our study shows that GPD1L has a positive correlation with the prognosis of RCC. The potential mechanism involves interacting with PINK1 and regulating the PINK1/Parkin pathway. In conclusion, these results reveal that GPD1L can act as a biomarker and target for RCC diagnosis and therapy.     

Rectangular tolerance regions and multivariate normal reference regions in laboratory medicine

Reference intervals are widely used in the interpretation of results of biochemical and physiological tests of patients. When there are multiple biochemical analytes measured from each subject, a multivariate reference region is needed. Because of their greater specificity against false positives, such reference regions are more desirable than separate univariate reference intervals that disregard the cross-correlations between variables. Traditionally, under multivariate normality, reference regions have been constructed as ellipsoidal regions. This approach suffers from a major drawback: it cannot detect component-wise extreme observations. In the present work, procedures are developed to construct rectangular reference regions in the multivariate normal setup. The construction is based on the criteria for tolerance intervals. The problems addressed include the computation of a rectangular tolerance region and simultaneous tolerance intervals. Also addressed is the computation of mixed reference intervals that include both two-sided and one-sided limits, simultaneously. A parametric bootstrap approach is used in the computations, and the accuracy of the proposed methodology is assessed using estimated coverage probabilities. The problem of sample size determination is also addressed, and the results are illustrated using examples that call for the computation of reference regions.     

正态总体均值与标准差比在半序约束下的最大似然估计

考虑两个正态总体X_i～N(μ_i,σ_i~2) i=1,2,均值μ_i和方差σ_i~2>0是未知参数,它们的比在半序约束μ_1/σ_1≤μ_2/σ_2下的最大似然估计(MLE)问题,给出了计算MLE的方法,对三个正态总体的情况,给出了相关的结果,这些方法在生物遗传和药物检验等方面都有广泛应用。     

The Ginsenoside 20-O-β-D-Glucopyranosyl-20(S)-Protopanaxadiol Induces Autophagy and Apoptosis in Human Melanoma via AMPK/JNK Phosphorylation

Studies have shown that a major metabolite of the red ginseng ginsenoside Rb1, called 20-O-β-D-glucopyranosyl-20(S)-protopanaxadiol (GPD), exhibits anticancer properties. However, the chemotherapeutic effects and molecular mechanisms behind GPD action in human melanoma have not been previously investigated. Here we report the anticancer activity of GPD and its mechanism of action in melanoma cells. GPD, but not its parent compound Rb1, inhibited melanoma cell proliferation in a dose-dependent manner. Further investigation revealed that GPD treatment achieved this inhibition through the induction of autophagy and apoptosis, while Rb1 failed to show significant effect at the same concentrations. The inhibitory effect of GPD appears to be mediated through the induction of AMPK and the subsequent attenuation of mTOR phosphorylation. In addition, GPD activated c-Jun by inducing JNK phosphorylation. Our findings suggest that GPD suppresses melanoma growth by inducing autophagic cell death and apoptosis via AMPK/JNK pathway activation. GPD therefore has the potential to be developed as a chemotherapeutic agent for the treatment of human melanoma.     

Confidence Limits for the Onset and Duration of Treatment Effect

Studies of biological variables such as those based on blood chemistry often have measurements taken over time at closely spaced intervals for groups of individuals. Natural scientific questions may then relate to the first time that the underlying population curve crosses a threshold (onset) and to how long it stays above the threshold (duration). In this paper we give general confidence regions for these population quantities. The regions are based on the intersection-union principle and may be applied to totally nonparametric, semiparametric, or fully parametric models where level-α tests exist pointwise at each time point. A key advantage of the approach is that no modeling of the correlation over time is required.     

Microwave Hall effect measurements in biomacromolecular systems

Microwave Hall effect measurements have recently been applied to the study of the electronic properties of biological materials. A basic outline of the relevance of the Hall effect for such biological studies is given, together with a brief summary of the various techniques available for its detection. Particular emphasis is given to the bimodal cavity microwave technique, since this appears to be the most suitable for the investigation of biological materials. Some of the results reported in the literature are discussed in order to give, hopefully, a realistic appraisal of their worth.     

Glycerol-3-phosphate dehydrogenase isozyme variation in insects

Glycerol-3-phosphate dehydrogenase (GPD) serves a central function in the metabolism of carbohydrate for insect flight. This paper reports that the function is supported in a wide range of species by thorax-specific GPD isozymes. These have been discovered in nine of 14 orders in which winged forms have been tested, including all of the major orders except Lepidoptera and Odonata. Examples have been found in each of the Polyneoptera, Paraneoptera and Holometabola, occurring predominantly in larger, stronger fliers which use carbohydrate as a fuel. Thorax-specific GPD isozymes have been found only once (in a tiphiid female) in a flightless insect and in the Palaeoptera not at all.     

Nonlinear biological oscillators: Action-angle variable approach with an application to Cowan's model of neuroelectric activity

We obtain within the action-angle variable approach new expressions, involving the Dirac delta function, for time periods and time averages of dynamical variables which are useful for nonlinear biological oscillator problems. We combine these with Laplace transformation techniques for evaluating the required perturbation expansions. The radii of convergence of these series are determined through a complex variable approach. The method is powerful enough to yield explicit results for such systems as the two species Volterra model, Goodwin's model of protein synthesis etc. and as an illustration, is applied here to Cowan's model of neuroelectric activity. We also point out the usefulness of the action integral in the case where parameters occurring in dynamics have slow time variations.