Random marginal agreement coefficients: rethinking the adjustment for chance when measuring agreement

Agreement coefficients quantify how well a set of instruments agree in measuring some response on a population of interest. Many standard agreement coefficients (e.g. kappa for nominal, weighted kappa for ordinal, and the concordance correlation coefficient (CCC) for continuous responses) may indicate increasing agreement as the marginal distributions of the two instruments become more different even as the true cost of disagreement stays the same or increases. This problem has been described for the kappa coefficients; here we describe it for the CCC. We propose a solution for all types of responses in the form of random marginal agreement coefficients (RMACs), which use a different adjustment for chance than the standard agreement coefficients. Standard agreement coefficients model chance agreement using expected agreement between two independent random variables each distributed according to the marginal distribution of one of the instruments. RMACs adjust for chance by modeling two independent readings both from the mixture distribution that averages the two marginal distributions. In other words, both independent readings represent first a random choice of instrument, then a random draw from the marginal distribution of the chosen instrument. The advantage of the resulting RMAC is that differences between the two marginal distributions will not induce greater apparent agreement. As with the standard agreement coefficients, the RMACs do not require any assumptions about the bivariate distribution of the random variables associated with the two instruments. We describe the RMAC for nominal, ordinal and continuous data, and show through the delta method how to approximate the variances of some important special cases.     

Coalescent processes when the distribution of offspring number among individuals is highly skewed

We report a complex set of scaling relationships between mutation and reproduction in a simple model of a population. These follow from a consideration of patterns of genetic diversity in a sample of DNA sequences. Five different possible limit processes, each with a different scaled mutation parameter, can be used to describe genetic diversity in a large population. Only one of these corresponds to the usual population genetic model, and the others make drastically different predictions about genetic diversity. The complexity arises because individuals can potentially have very many offspring. To the extent that this occurs in a given species, our results imply that inferences from genetic data made under the usual assumptions are likely to be wrong. Our results also uncover a fundamental difference between populations in which generations are overlapping and those in which generations are discrete. We choose one of the five limit processes that appears to be appropriate for some marine organisms and use a sample of genetic data from a population of Pacific oysters to infer the parameters of the model. The data suggest the presence of rare reproduction events in which approximately 8% of the population is replaced by the offspring of a single individual.     

Lipopolysaccharide is the receptor for kappa phage inSerratia marcescens

Kappa phage active onSerratia marcescens can form plaques on white and red strains with identical efficiencies. To identify the kappa phage receptor, the inactivation of the phage was studied after incubation with several bacterial subcellular fractions. The experiments demonstrated that kappa phage adsorbs to outer membrane fractions of susceptible cells. Proteinase K did not affect the rate of inactivation. Lipopolysaccharide proved to be the primary receptor for kappa phage. Prodigiosin content of the lipopolysaccharide fraction was low.     

small bristles is required for the morphogenesis of multiple tissues during Drosophila development.

We found that mutations in small bristles (sbr) affect several tissues during the development of the fruit fly. In sbr embryos, neurons have defects in pathfinding and the body wall muscles have defective morphology. As adults, sbr flies have smaller and thinner bristles with a reduced diameter, suggesting a defective cytoskeleton within. The phenotypes we observe are consistent with defects in cell morphogenesis. We identified DmNXF1, the Drosophila homolog of a mRNA export protein that has been characterized in human (NXF1/TAP) and yeast (Mex67p) as the protein encoded by the small bristles locus. Given that a global decrease in mRNA export in these mutants is likely, the phenotypes we observe suggest that certain tissues are acutely sensitive to lower levels of cytoplasmic mRNA and the resultant decrease in protein synthesis during key stages of cellular morphogenesis.     

Capillary filtration coefficient is independent of number of perfused capillaries in cat skeletal muscle

The capillary filtration coefficient (CFC) is assumed to reflect both microvascular hydraulic conductivity and the number of perfused capillaries at a given moment (precapillary sphincter activity). Estimation of hydraulic conductivity in vivo with the CFC method has therefore been performed under conditions of unchanged vascular tone and metabolic influence. There are studies, however, that did not show any change in CFC after changes in vascular tone and metabolic influence, and these studies indicate that CFC may not be influenced by alteration in the number of perfused capillaries. The present study reexamined to what extent CFC in a pressure-controlled preparation depends on the vascular tone and number of perfused capillaries by analyzing how CFC is influenced by 1) vasoconstriction, 2) increase in metabolic influence by decrease in arterial blood pressure, and 3) occlusion of precapillary microvessels by arterial infusion of microspheres. CFC was calculated from the filtration rate induced by a fixed decrease in tissue pressure. Vascular tone was increased in two steps by norepinephrine (n = 7) or angiotensin II (n = 6), causing a blood flow reduction from 7.2 +/- 0.8 to at most 2.7 +/- 0.2 ml x min(-1) x 100 g(-1) (P < 0.05). The decrease in arterial pressure reduced blood flow from 4.8 +/- 0.4 to 1.40 +/- 0.1 ml x min(-1) x 100 g(-1) (n = 6). Vascular resistance increased to 990 +/- 260% of control after the infusion of microspheres (n = 6). CFC was not significantly altered from control after any of the experimental interventions. We conclude that CFC under these conditions is independent of the vascular tone and number of perfused capillaries and that variation in CFC reflects variation in microvascular hydraulic conductivity.     

Thirteen is the lucky number for doublecortin

Doublecortin is a microtubule-associated protein that is essential for normal brain development. A recent report published in Molecular Cell shows that doublecortin associates preferentially with microtubules made of 13 protofilaments, by recognizing a novel site between the protofilaments. These findings explain how doublecortin stabilizes microtubules and provide clues about its function during neuronal migration.     

Monogamy when there is potential for polygyny: tests of multiple hypotheses in a group-living fish

Monogamy within social groups where there exists a high potentialfor polygyny poses a challenge to our understanding of matingsystem evolution. Specifically, the traditional explanationthat monogamy evolves due to wide female dispersion, affordingmales little opportunity to defend multiple females, cannotapply. Instead, monogamy in groups potentially arises becausefemales compete for breeding resources such as breeding sites,food, and paternal care. We conducted manipulative experimentsto determine whether females compete over limiting resourceswithin groups of the obligate coral-dwelling goby, Paragobiodonxanthosomus (Gobiidae). Breeding females behaved aggressivelytoward individuals of their own sex and evicted subordinatefemales that were large and mature from the group. Experimentalremoval of nest sites caused breeding partners to breed in alternativenest sites, demonstrating that nest site limitation was notthe cause of female competition. Supplemental feeding resultedin an increase in the fecundity of breeding females but no maturationof subordinate females, demonstrating that food-limited femalefecundity was a likely cause of female competition. Finally,supplemental feeding of breeding pairs demonstrated that thedifference in eggs hatched by fed versus unfed males was lessthan the difference in eggs laid by fed versus unfed females,suggesting that paternal care limitation might also drive femalecompetition. These results suggest that competition over foodand possibly paternal care selects for dominant, breeding femalesto suppress the maturation of subordinate females to minimizecompetition. Monogamy in association with group living is thereforelikely to have evolved because female competition prevents malesfrom utilizing the potential for polygyny.     

Response to genomic selection: The Bulmer effect and the potential of genomic selection when the number of phenotypic records is limiting

Background

Over the last ten years, genomic selection has developed enormously. Simulations and results on real data suggest that breeding values can be predicted with high accuracy using genetic markers alone. However, to reach high accuracies, large reference populations are needed. In many livestock populations or even species, such populations cannot be established when traits are difficult or expensive to record, or when the population size is small. The value of genomic selection is then questionable.

Methods

In this study, we compare traditional breeding schemes based on own performance or progeny information to genomic selection schemes, for which the number of phenotypic records is limiting. Deterministic simulations were performed using selection index theory. Our focus was on the equilibrium response obtained after a few generations of selection. Therefore, we first investigated the magnitude of the Bulmer effect with genomic selection.

Results

Results showed that the reduction in response due to the Bulmer effect is the same for genomic selection as for selection based on traditional BLUP estimated breeding values, and is independent of the accuracy of selection. The reduction in response with genomic selection is greater than with selection based directly on phenotypes without the use of pedigree information, such as mass selection. To maximize the accuracy of genomic estimated breeding values when the number of phenotypic records is limiting, the same individuals should be phenotyped and genotyped, rather than genotyping parents and phenotyping their progeny. When the generation interval cannot be reduced with genomic selection, large reference populations are required to obtain a similar response to that with selection based on BLUP estimated breeding values based on own performance or progeny information. However, when a genomic selection scheme has a moderate decrease in generation interval, relatively small reference population sizes are needed to obtain a similar response to that with selection on traditional BLUP estimated breeding values.

Conclusions

When the trait of interest cannot be recorded on the selection candidate, genomic selection schemes are very attractive even when the number of phenotypic records is limited, because traditional breeding requires progeny testing schemes with long generation intervals in those cases.     

Retardance coefficient of vegetated channels estimated by the Froude number

The Manning Equation is widely adopted to estimate open channel flows, and selecting retardance coefficient is always one of the most difficult tasks for estimating velocity and discharge. In cases of estimating accurate retardance coefficient values of vegetated channels, countless trials and errors are to be made before reaching conclusive results due to conditions created by various aquatic plants. The majority of past studies on this subject, however, are established based on terrestrial plants and plastic moulds as laboratorial factors, and only few are done with natural aquatic vegetations. Hence, in this study, two different types of natural aquatic plants are applied to estimate retardance coefficients; and the result indicates that each type of plant affects differently in terms of flow resistance. Analysis of hydraulic parameters indicates there are strong correlations between the retardance coefficient and the Froude number. The Froude number is most important and commonly used parameter of open channel hydraulics. The retardance coefficient and Froude number are exponentially related. Therefore, the Froude number can replace the product of velocity and hydraulic radius (VR) to estimate the retardance coefficient, in which VR (product of velocity (V) and hydraulic radius (R)). Additionally, it can be used accurately to estimate velocity and discharge during river and wetland restoration.     

Renin cells are precursors for multiple cell types that switch to the renin phenotype when homeostasis is threatened

Renin-synthesizing cells are crucial in the regulation of blood pressure and fluid-electrolyte homeostasis. Adult mammals subjected to manipulations that threaten homeostasis increase circulating renin by increasing the number of renin-expressing/-releasing cells. We hypothesize that the ability of adult cells to synthesize renin does not occur randomly in any cell type, depending instead on the cell's lineage. To determine the fate of renin-expressing cells, we generated knockin mice expressing cre recombinase in renin-expressing cells and crossed them with reporter mice. Results show that renin-expressing cells are precursors for a variety of cells that differentiate into non-renin-expressing cells such as smooth-muscle, epithelial, mesangial, and extrarenal cells. In the kidney, these cells retain the capability to synthesize renin when additional hormone is required to reestablish homeostasis: specific subpopulations of apparently differentiated cells are "held in reserve" to respond (repeatedly) by de-differentiating and expressing renin in response to stress, and re-differentiating when the crisis passes.     

The frequency of multiple recombination events occurring at the human Ig kappa L chain locus

Products of Ig kappa L chain gene rearrangement in a variety of human B cell samples were investigated by sequential Southern blot hybridization analysis. By application of four region-specific probes (C kappa, J kappa, U' kappa and kappa de) a complete spectrum of kappa rearrangements, including both predicted and novel products, were detected. Nearly 30% of the products detected reflect multiple recombination of the kappa locus. The kappa-deleting element was responsible for 70% of the multiple rearrangements that were detected. Interestingly, eight kappa-expressing samples exhibited rearrangement of the kappa-deleting element. The remaining multiple recombination products were characteristic of double V kappa-J kappa rearrangement. This frequency reveals that secondary V-J rearrangement may significantly contribute to the expression of kappa L chains in humans.     

The ideal free distribution when the resource is variable

On the basis of the ideal free distribution (IFD) model, twostochastic models that incorporate the uncertainty of the informationused for decision making were considered to investigate theeffects of the variability in the resource supply rate on theIFD under continuous input conditions. In the uncertain-informationmodel, competitors cannot trace the variation of the supplyrate and use the expectation of the supply rate or previouspayoffs for decision making. Both submodels predict matchingof means, in which the average number of competitors for eachpatch is proportional to the average supply rate in the patch.In the perfect-information model, competitors continuously knowand trace the environment conditions. Numerical predictionsdepend on the relative size of the resource variance betweenpatches. When the resource variance in the good patch is sufficientlylarger than that in the poor patch, it predicts undermatchingof means; when the variance of the supply rate for each patchis small and proportional to the average of the supply ratein the patch, it predicts matching of means; and when the resourcevariance in the poor patch is larger than (or equal to) thatin the good patch, it predicts overmatching of means. Theseresults indicate the importance of clarifying the assumptionon the uncertainty in information for decision making and thetype of the resource variance for the test of the IFD underconditions where the resource supply rate is stochastic.     

A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given

Among the fundamental problems in molecular evolution and in the analysisof homologous sequences are alignment, phylogeny reconstruction, and thereconstruction of ancestral sequences. This paper presents a fast, combinedsolution to these problems. The new algorithm gives an approximation to theminimal history in terms of a distance function on sequences. The distancefunction on sequences is a minimal weighted path length constructed fromsubstitutions and insertions-deletions of segments of any length.Substitutions are weighted with an arbitrary metric on the set ofnucleotides or amino acids, and indels are weighted with a gap penaltyfunction of the form gk = a + (bxk), where k is the length of the indel anda and b are two positive numbers. A novel feature is the introduction ofthe concept of sequence graphs and a generalization of the traditionaldynamic sequence comparison algorithm to the comparison of sequence graphs.Sequence graphs ease several computational problems. They are used torepresent large sets of sequences that can then be compared simultaneously.Furthermore, they allow the handling of multiple, equally good, alignments,where previous methods were forced to make arbitrary choices. A programwritten in C implemented this method; it was tested first on 22 5S RNAsequences.     

The number of equilibria in the diallelic Levene model with multiple demes

The Levene model is the simplest mathematical model to describe the evolution of gene frequencies in spatially subdivided populations. It provides insight into how locally varying selection promotes a population’s genetic diversity. Despite its simplicity, interesting problems have remained unsolved even in the diallelic case.In this paper we answer an open problem by establishing that for two alleles at one locus and J demes, up to 2J−1 polymorphic equilibria may coexist. We first present a proof for the case of stable monomorphisms and then show that the result also holds for protected alleles. These findings allow us to prove that any odd number (up to 2J−1) of equilibria is possible, before we extend the proof to even numbers. We conclude with some numerical results and show that for J>2, the proportion of parameter space affording this maximum is extremely small.     

The relationship between dietary intake and the number of teeth in elderly Japanese subjects

Objective: This study used a precise weighing method to assess whether tooth loss was related to nutrient intake in elderly Japanese subjects. Material and methods: Fifty‐seven subjects aged 74 years were randomly selected from a longitudinal interdisciplinary study of ageing. Complete 3‐day food intake data were obtained by a precise weighing method. The dietary intakes of energy and nutrients were calculated based on the Standard Tables of Food Composition in Japan (5th ed.). A clinical evaluation of the number of teeth present was carried out. Multiple regression standardised coefficients for each nutrient was estimated based on a continuous scale adjusted for gender, smoking habits, and educational level. After dividing the subjects into two groups according to the number of teeth present (0–19, 20+), the difference in the intake of nutrients and the amount of food consumed per day was evaluated. Results: The number of teeth present had a significant relationship with the intake of several nutrients. In particular, total protein, animal protein, sodium, vitamin D, vitamin B₁, vitamin B₆, niacin, and pantothenic acid were significantly associated with the number of teeth present and with the two groups (0–19, 20+). The intake of vegetables and fish, shellfish, and their products was significantly lower among subjects with fewer teeth. Conclusion: This study suggests that there was a significant relationship between nutrient intake, such as minerals and vitamins from food, and tooth loss.     

On the number of subjects used in animal behaviour experiments

Experiments published in Animal Behaviour in 1979 are reviewed, and it is concluded that there are grounds for thinking that the numbers of animals used could sometimes be reduced without loss of scientific rigour. Principles underlying the choice of number of subjects (N) are outlined, and illustrated with examples from the 1979 sample. Several alternatives to increasing N in order to increase power are given, including better design, larger α, and sequential methods. The logic of inference from experiments with small N is discussed.