Further nonparametric tests for comparing dissimilarity matrices based on the relative neighborhood graph

Using the edge sets of their relative neighborhood graphs, contingency tables may be constructed to compare dissimilarity matrices. Two kinds of tests of independence are considered, one based on the relationship between the minimum path lengths in the relative neighborhood graphs, the other on the product-moment correlation coefficient between the dissimilarities corresponding to the unit path lengths of the intersection. To compare a dissimilarity matrix with a transformation of it, such as by a clustering, various elements of the contingency table are compared with the binomial distribution having known parameters, while for independently obtained dissimilarity matrices, standard tests of marginal independence are appropriate.     

Evaluation of the Taguchi methods for the simultaneous assessment of the effects of multiple variables in the tumour microenvironment

BACKGROUND: The control of proliferation, differentiation and survival of normal and malignant cells in the tumour microenvironment is under the control of a wide range of different factors, including cell:cell interactions, cytokines, growth factors and hormonal influences. However, the ways in which these factors interact are poorly understood. In order to compare the effects of multiple variables, experimental design becomes complex and difficult to manage. We have therefore evaluated the use of a novel approach to multifactorial experimental design, the Taguchi methods, to approach this problem. METHOD: The Taguchi methods are widely used by quality engineering scientists to compare the effects of multiple variables, together with their interactions, with a simple and manageable experimental design. In order to evaluate these methods, we have used a simple and robust system to compare a traditional experimental design with the Taguchi Methods. The effect of G-CSF, GM-CSF, IL3 and M-CSF on daunorubicin mediated cytotoxicity in K562 cells was measured using the MTT assay. RESULTS: Both methods demonstrated that the same combination of growth factors at the same concentrations minimised daunorubicin cytotoxicity in this assay. CONCLUSIONS: These findings demonstrate that Taguchi methods may be a valuable tool for the investigation of the interactions of multiple variables in the tumour microenvironment.     

Choosing the Most Effective Pattern Classification Model under Learning-Time Constraint

Nowadays, large datasets are common and demand faster and more effective pattern analysis techniques. However, methodologies to compare classifiers usually do not take into account the learning-time constraints required by applications. This work presents a methodology to compare classifiers with respect to their ability to learn from classification errors on a large learning set, within a given time limit. Faster techniques may acquire more training samples, but only when they are more effective will they achieve higher performance on unseen testing sets. We demonstrate this result using several techniques, multiple datasets, and typical learning-time limits required by applications.     

Differences in Patterns of Reproductive Allocation between the Sexes in Nicrophorus orbicollis

Organisms are selected to maximize lifetime reproductive success by balancing the costs of current reproduction with costs to future survival and fecundity. Males and females typically face different reproductive costs, which makes comparisons of their reproductive strategies difficult. Burying beetles provide a unique system that allows us to compare the costs of reproduction between the sexes because males and females are capable of raising offspring together or alone and carcass preparation and offspring care represent the majority of reproductive costs for both sexes. Because both sexes perform the same functions of carcass preparation and offspring care, we predict that they would experience similar costs and have similar life history patterns. In this study we assess the cost of reproduction in male Nicrophorus orbicollis and compare to patterns observed in females. We compare the reproductive strategies of single males and females that provided pre- and post-hatching parental care. There is a cost to reproduction for both males and females, but the sexes respond to these costs differently. Females match brood size with carcass size, and thus maximize the lifetime number of offspring on a given size carcass. Males cull proportionately more offspring on all carcass sizes, and thus have a lower lifetime number of offspring compared to females. Females exhibit an adaptive reproductive strategy based on resource availability, but male reproductive strategies are not adaptive in relation to resource availability.     

Close encounters during a pandemic: Social habits and inter-generational links in the first two waves of COVID-19

Social habits are ingrained in a community and affect human behaviour. Have they played any role in the spread of the pandemic? We use high-frequency data for 220 regions in 15 European countries from March to December 2020 to compare the association between social contacts outside the family and within inter-generational families, on the one hand, and cases and excess mortality on the other. We find that a standard deviation increase in the percentage of people having daily face-to-face contacts outside the household is associated with 5 new daily cases and 2.6 additional weekly deaths, while the incidence of inter-generational households exhibits a less robust association with both COVID-19 transmission and mortality. We compare results across the first and the second wave of pandemic and show that differences are related to the average age of the most affected groups. Our findings are robust to the inclusion of a number of controls, fixed effects, the chosen sample of countries, and the estimation method. We argue that type and frequency of social interactions are interweaved with a region culture and habits and are informative on the potential transmission of contagion and on its lethality.     

Causal inference on the difference of the restricted mean lifetime between two groups

When comparing survival times between two treatment groups, it may be more appropriate to compare the restricted mean lifetime, i.e., the expectation of lifetime restricted to a time L, rather than mean lifetime in order to accommodate censoring. When the treatments are not assigned to patients randomly, as in observational studies, we also need to account for treatment imbalances in confounding factors. In this article, we propose estimators for the difference of the restricted mean lifetime between two groups that account for treatment imbalances in prognostic factors assuming a proportional hazards relationship. Large-sample properties of our estimators based on martingale theory for counting processes are also derived. Simulation studies were conducted to compare these estimators and to assess the adequacy of the large-sample approximations. Our methods are also applied to an observational database of acute coronary syndrome patients from Duke University Medical Center to estimate the treatment effect on the restricted mean lifetime over 5 years.     

Enzymatic activity on a chip: the critical role of protein orientation

We compare the catalytic activities of enzymes immobilized on silicon surfaces with and without orientation. While oriented sulfotransferases selectively immobilized on an otherwise zero-background surface via 6xHis tags faithfully reflect activities of solution phase enzymes, those with random orientation on the surface do not. This finding demonstrates that controlling the orientation of immobilized protein molecules and designing an ideal local chemical environment on the solid surface are both essential if protein microarrays are to be used as quantitative tools in biomedical research.     

Estimating the Antimicrobial Log Reduction: Part 1. Quantitative Assays

In quantitative antimicrobial assays, the responses are counts of viable microbes in two treatment groups. One group is treated with a chemical germicide and the other group is control, treated with an inactive chemical. This is part 1 of a pair of papers that pertain to assays that estimate the log reduction (LR), in the density of viable microbes, attributable to the germicide treatment (part 2 is concerned with presence/absence responses). Such assays are used by producers, consumers, and regulatory agencies to assess the efficacy of liquid germicides. We define and compare the two different mathematical formulations for LR that are commonly used in practice when there are replicate density measurements. One LR parameter is based on the mean of the log-transformed densities; the other is based on the logarithm of the mean of densities. We build a statistical model relating microbial count data to the LR parameters, derive maximum likelihood and method of moments estimators for each LR parameter, and compare the estimators according to both their asymptotic characteristics and the results of a simulation study utilizing realistic sample sizes. Standard error formulas for the estimators are derived, and they are evaluated via simulation studies. The results of this investigation lead us to recommend the method of moments estimator, regardless of which definition of LR is chosen.     

Linkage analysis of the simulated data - evaluations and comparisons of methods

The goal of this study is to evaluate, compare, and contrast several standard and new linkage analysis methods. First, we compare a recently proposed confidence set approach with MAPMAKER/SIBS. Then, we evaluate a new Bayesian approach that accounts for heterogeneity. Finally, the newly developed software SIMPLE is compared with GENEHUNTER. We apply these methods to several replicates of the Genetic Analysis Workshop 13 simulated data to assess their ability to detect the high blood pressure genes on chromosome 21, whose positions were known to us prior to the analyses. In contrast to the standard methods, most of the new approaches are able to identify at least one of the disease genes in all the replicates considered.     

Estimating the body size of eocene primates: A comparison of results from dental and postcranial variables

Estimating body weights for fossil primates is an important step in reconstructing aspects of their behavior and ecology. To date, the body size of Eocene euprimates—the Adapidae and Omomyidae—has been estimated only from molar area. Studies on other primates and mammals demonstrate that body weights estimated from teeth are not always concordant with those estimated from postcranial variables. We derive estimates for Eocene primates based on tarsal bone variables to compare with previously published values derived from dental measures. Stepsirhine-wide, family-level, and subfamily-level models are developed and compared. We also compare the accuracy and precision of dental- and tarsal-based regression models for predicting weight in extant species. Tarsal bone and dental area measures prove to be equally robust in predicting body weight; however, highly disparate estimates are often obtained from different variables. Equations based on lower-level taxonomic groups perform better than more widely based models. However, all equations considered yield fairly large errors, which can affect interpretations of paleoecology. The choice of the more robust prediction is not straightforward.     

Bayesian Estimation of the Distribution Function of the Poisson Model

This paper presents the Bayes estimators of the Poisson distribution function based on complete and truncated data under a natural conjugate prior. Laplace transform of the incomplete gamma function and the Gauss hypergeometric function have been employed in order to overcome the intractability of the integrals. Numerical examples from biosciences are given to illustrate the results. A Monte Carlo study has been carried out to compare Bayes estimators under complete data with the corresponding maximum liklihood estimators.     

Recent changes in the food of the Grey Heron Ardea cinerea in central-west Spain

As far as we know, there are no data on how changes in the freshwater fauna within the same area affect the feeding preference of the Grey Heron Ardea cinerea . We present data on the diet of the bird during the breeding seasons of 1990 and 1991 in central-west Spain and compare these data with those obtained from the same colonies in 1986–1987.     

Comparison of the effects of sodium chloride, pH and temperature on the growth of Listeria monocytogenes on gradient plates and in liquid medium

Gradient plates provide a convenient means of assessing the effect of sodium chloride and pH in combination with different temperatures on the growth of microorganisms. The effects of these variables on the growth of Listeria monocytogenes in gradient plates at four temperatures are compared with growth in a micro-well system. The growth-limiting conditions in the two systems are in good agreement, and also compare favourably with data in the literature. The gradient plates gave a good illustration of the concentrations of sodium chloride required to inhibit growth at different temperatures and pHs, although incubation time is limited to 72 h.     

The application of radiography to the study of fish nutrition

The measurement of individual food consumption rates of fish held in groups using radiography has enabled the development of a new approach to fish nutrition trials. In order to compare diets, groups of individually numbered fish are fed different experimental diets over extended periods of time (similar to standard nutrition trials) and food consumption rates are measured regularly over the course of the experiment. Analysis of covariance is then used to compare regression coefficients, obtained from mean consumption-growth relationships, from each diet. The advantages of the approach are several: (1) differences in appetite between fish fed different diets are monitored; (2) fewer fish are needed to establish consumption-growth curves over a large range of consumption rates; (3) measured food consumption rates, not ration levels, are used to calculate 'true' growth efficiencies; and (4) other factors, such as absorption efficiency, trypsin activity, the concentration of free amino acids in tissues and protein turnover can be measured for individual fish and related to differences in food consumption between fish in the same group. The approach has been used successfully with a variety of species to compare the growth response of groups fed two or more diets.     

A note on the false discovery rate and inconsistent comparisons between experiments

MOTIVATION: The false discovery rate (FDR) has been widely adopted to address the multiple comparisons issue in high-throughput experiments such as microarray gene-expression studies. However, while the FDR is quite useful as an approach to limit false discoveries within a single experiment, like other multiple comparison corrections it may be an inappropriate way to compare results across experiments. This article uses several examples based on gene-expression data to demonstrate the potential misinterpretations that can arise from using FDR to compare across experiments. Researchers should be aware of these pitfalls and wary of using FDR to compare experimental results. FDR should be augmented with other measures such as p-values and expression ratios. It is worth including standard error and variance information for meta-analyses and, if possible, the raw data for re-analyses. This is especially important for high-throughput studies because data are often re-used for different objectives, including comparing common elements across many experiments. No single error rate or data summary may be appropriate for all of the different objectives.     

Five statistical questions about the tree of life

Stochastic modeling of phylogenies raises five questions that have received varying levels of attention from quantitatively inclined biologists. 1) How large do we expect (from the model) the ratio of maximum historical diversity to current diversity to be? 2) From a correct phylogeny of the extant species of a clade, what can we deduce about past speciation and extinction rates? 3) What proportion of extant species are in fact descendants of still-extant ancestral species, and how does this compare with predictions of models? 4) When one moves from trees on species to trees on sets of species (whether traditional higher order taxa or clades within PhyloCode), does one expect trees to become more unbalanced as a purely logical consequence of tree structure, without signifying any real biological phenomenon? 5) How do we expect that fluctuation rates for counts of higher order taxa should compare with fluctuation rates for number of species? We present a mathematician's view based on an oversimplified modeling framework in which all these questions can be studied coherently.     

单肺通气时两种通气模式对PetCO2与PaCO2相关性的影响

目的：探讨胸科开胸手术单肺通气定容通气模式下和定压通气模式下PetC02（呼气末二氧化碳分压）与PaCO2（动脉二氧化碳分压）的相关性。方法：选择40例择期左侧开胸手术单肺通气成年患者,ASAI～II级,随机分为A组（n=20）采用VCV（容量控制通气）模式通气、B组（n=20）采用PCV（压力控制通气）模式通气。比较两组各时段的PaCO2和PetCO2的差异及相关性。结果：经统计学分析,除第一时间点,两组同一时间点的PetC02比较及PaCO2比较差异均有统计学意义（P〈O．05）,A组PetC02四个时间点比较及PaCO2四个时间点比较差异均有有统计学意义（P〈0．001）,B组除PetCO2第三与第四个时间点比较差异无统计学意义外,余PetCO2各时间点相比较及PaCO2各时间点相比较差异均有统计学意义（P〈0．05）。单肺通气定压通气模式下PetCO2与PaCO2在各个时间点的相关系数均大于定容通气模式时。无论是定容还是定压通气模式,单肺通气时间越长,其PetCO2与PaCOz的相关系数也越小。结论：1．同双肺通气相比,单肺通气时定压通气模式下PaCO2及PetCO2的改变小于定容通气模式时。2．单肺通气时,定压通气模式下PetCO2与PaCO2的相关性好于定容通气模式时。3．在这两种通气模式下PetCO2与PaCO2的相关性与单肺通气的时间成反比。     

Phylogeography of the lacertid lizard, Psammodromus algirus, in Iberia and across the Strait of Gibraltar

Aim  To determine genetic substructuring within the lacertid lizard Psammodromus algirus . To compare levels of variation across a geological barrier, the Strait of Gibraltar, and to compare this against the known age of the barrier using a molecular clock hypothesis. To compare the effect of the barrier within this species with previously published data from other organisms.
Location  The Iberian Peninsula and North Africa.
Methods  Partial sequences from the mitochondrial cytochrome b , 12S rRNA and 16S rRNA genes were obtained from 101 specimens belonging to the subfamily Gallotiinae and used in this study. The data set was aligned using C lustal X and phylogenetic trees produced using both maximum-parsimony and maximum-likelihood methods. Maximum likelihood estimates of divergence times for the combined data set (12S + 16S + cytochrome b ) were obtained after discovery of lineage rate constancy across the tree using a likelihood ratio test.
Results  Psammodromus algirus contains divergent eastern and western mtDNA clades within the Iberian Peninsula. The western clade has northern and southern lineages in Iberia and one in North Africa. This phylogeographical pattern indicates that the lizard invaded North Africa after the opening of the Strait, presumably by natural rafting.
Main conclusions  As in several other species, current patterns of genetic diversity within P. algirus are not directly related to the opening of the Strait of Gibraltar. Widespread sampling on both sides of the barrier is necessary to determine its effect on species in this area accurately.