Redefining the community: a species-based approach

We propose that effective community size can be defined on the basis of the web of indirect interactions experienced on average by each individual species. Indirect interaction chains are composed of links provided by direct interactions. We analyzed previously published data on 20 assemblages of species. Chain strengths were estimated by the weakest link and by the product of link strength. The average strength of the interaction chain decreased with increasing numbers of links with both models. Positive indirect interactions in chains with an even number of links offset negative direct interactions. We set the community size by the chain length where 95% of the indirect interactions are weaker than 10% of the mean of the absolute value of direct interaction strength. Using the multiplicative model, seven assemblages had a community size (web of interaction length) of three links, one of four links, and the remainder of communities were too small to set community size. The analysis suggests that effective communities of size are rarely investigated in ecological experiments.     

Concomitant Information in Competing Risk Analysis

A competing risk model, accommodating both Type I censoring and random withdrawals, is expanded to incorporate concomitant information by allowing the parameters of the underlying distributions to be a linear function of two covariates. The model is developed for two competing risks, one following a Weibull distribution and the other a Rayleigh distribution, and random withdrawals following a Weibull distribution. A method is developed for testing the equality of the coefficients for a given covariate for each of the competing risks using MLE'.     

Mean-field calculations of chain packing and conformational statistics in lipid bilayers: comparison with experiments and molecular dynamics studies.

A molecular, mean-field theory of chain packing statistics in aggregates of amphiphilic molecules is applied to calculate the conformational properties of the lipid chains comprising the hydrophobic cores of dipalmitoyl-phosphatidylcholine (DPPC), dioleoyl-phosphatidylcholine (DOPC), and palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayers in their fluid state. The central quantity in this theory, the probability distribution of chain conformations, is evaluated by minimizing the free energy of the bilayer assuming only that the segment density within the hydrophobic region is uniform (liquidlike). Using this distribution we calculate chain conformational properties such as bond orientational order parameters and spatial distributions of the various chain segments. The lipid chains, both the saturated palmitoyl (-(CH2)14-CH3) and the unsaturated oleoyl (-(CH2)7-CH = CH-(CH2)7-CH3) chains are modeled using rotational isomeric state schemes. All possible chain conformations are enumerated and their statistical weights are determined by the self-consistency equations expressing the condition of uniform density. The hydrophobic core of the DPPC bilayer is treated as composed of single (palmitoyl) chain amphiphiles, i.e., the interactions between chains originating from the same lipid headgroup are assumed to be the same as those between chains belonging to different molecules. Similarly, the DOPC system is treated as a bilayer of oleoyl chains. The POPC bilayer is modeled as an equimolar mixture of palmitoyl and oleoyl chains. Bond orientational order parameter profiles, and segment spatial distributions are calculated for the three systems above, for several values of the bilayer thickness (or, equivalently, average area/headgroup) chosen, where possible, so as to allow for comparisons with available experimental data and/or molecular dynamics simulations. In most cases the agreement between the mean-field calculations, which are relatively easy to perform, and the experimental and simulation data is very good, supporting their use as an efficient tool for analyzing a variety of systems subject to varying conditions (e.g., bilayers of different compositions or thicknesses at different temperatures).     

Intermediate filament structure: 1. Analysis of IF protein sequence data

Amino acid sequence data for intermediate filament proteins have been analysed with a view to identifying structurally invariant segments and determining their likely secondary structure. The sequences in these segments have also been analysed for periodic distributions of particular types of residue. The results support the classification of intermediate filament proteins into three main groups and also reinforce the concept of a molecular structure with a central domain of coiled-coil segments, together with essentially non-helical N-terminal and C-terminal domains of variable size and composition. Regions exhibiting the greatest homology between the three types of IF chain are identified and significant variation in charged residue disposition along the length of individual chains is noted. The conservation in all IF protein chains of specific sites of coiled-coil rope interruption are discussed in terms of the probable molecular structure. Stabilizing ionic interactions between coiled-coil chain segments have been investigated quantitatively as a function of the relative chain stagger. In all cases and calculations favour ropes in which the constituent chains are in-register and parallel rather than antiparallel.     

Vesicle size distributions measured by flow field-flow fractionation coupled with multiangle light scattering.

The separation method, flow field-flow fractionation (flow FFF), is coupled on-line with multiangle laser light scattering (MALLS) for simultaneous measurement of the size and concentration of vesicles eluting continuously from the fractionator. These size and concentration data, gathered as a function of elution time, may be used to construct both number- and mass-weighted vesicle size distributions. Unlike most competing, noninvasive methods, this flow FFF/MALLS technique enables measurement of vesicle size distributions without a separate refractive index detector, calibration using particle size standards, or prior assumptions about the shape of the size distribution. Experimentally measured size distributions of vesicles formed by extrusion and detergent removal are non-Gaussian and are fit well by the Weibull distribution. Flow FFF/MALLS reveals that both the extrusion and detergent dialysis vesicle formation methods can yield nearly size monodisperse populations with standard deviations of approximately 8% about the mean diameter. In contrast to the rather low resolution of dynamic light scattering in analyzing bimodal systems, flow FFF/MALLS is shown to resolve vesicle subpopulations that differ by much less than a factor of two in mean size.     

Models for antigen receptor gene rearrangement: CDR3 length

Despite the various processing steps involved in V(D)J recombination, which could potentially introduce many biases in the length distribution of complementarity determining region 3 (CDR3) segments, the observed CDR3 length distributions for complete repertoires are very close to a normal-like distribution. This raises the question of whether this distribution is simply a result of the random steps included in the process of gene rearrangement, or has been optimized during evolution. We have addressed this issue by constructing a simulation of gene rearrangement, which takes into account the DNA modification steps included in the process, namely hairpin opening, nucleotide additions, and nucleotide deletions. We found that the near-Gaussian- shape of CDR3 length distribution can only be obtained under a relatively narrow set of parameter values, and thus our model suggests that specific biases govern the rearrangement process. In both B-cell receptor (BCR) heavy chain and T-cell receptor beta chain, we obtained a Gaussian distribution using identical parameters, despite the difference in the number and the lengths of the D segments. Hence our results suggest that these parameters most likely reflect the optimal conditions under which the rearrangement process occurs. We have subsequently used the insights gained in this study to estimate the probability of occurrence of two exactly identical BCRs over the course of a human lifetime. Whereas identical rearrangements of the heavy chain are highly unlikely to occur within one human lifetime, for the light chain we found that this probability is not negligible, and hence the light chain CDR3 alone cannot serve as an indicator of B-cell clonality.     

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.     

Nonparametric inference on cause‐specific quantile residual life

In medical research, investigators are often interested in inferring time‐to‐event distributions under competing risks. It is well known, however, that the naive approach based on the Kaplan–Meier method to estimate the proportion of cause‐specific events overestimates the true quantity. In this paper, we show that the quantile residual life function, a natural and popular summary measure of survival data, could be also seriously affected by the competing events. An existing two‐sample test statistic for inference on median residual life is modified for competing risks data, which does not involve estimation of the improper probability density function of the subdistribution of cause‐specific events under censoring. Simulation results demonstrate that the test statistic controls the type 1 error probabilities reasonably well. The proposed method is applied to a real data example from a large‐scale phase III breast cancer study.     

The anchoring protein RACK1 links protein kinase Cepsilon to integrin beta chains. Requirements for adhesion and motility

Integrin affinity is modulated by intracellular signaling cascades, in a process known as "inside-out" signaling, leading to changes in cell adhesion and motility. Protein kinase C (PKC) plays a critical role in integrin-mediated events; however, the mechanism that links PKC to integrins remains unclear. Here, we report that PKCepsilon positively regulates integrin-dependent adhesion, spreading, and motility of human glioma cells. PKCepsilon activation was associated with increased focal adhesion and lamellipodia formation as well as clustering of select integrins, and it is required for phorbol 12-myristate 13-acetate-induced adhesion and motility. We provide novel evidence that the scaffolding protein RACK1 mediates the interaction between integrin beta chain and activated PKCepsilon. Both depletion of RACK1 by antisense strategy and overexpression of a truncated form of RACK1 which lacks the integrin binding region resulted in decreased PKCepsilon-induced adhesion and migration, suggesting that RACK1 links PKCepsilon to integrin beta chains. Altogether, these results provide a novel mechanistic link between PKC activation and integrin-mediated adhesion and motility.     

Measures of stratigraphic fit to phylogeny and their sensitivity to tree size, tree shape, and scale

Measures of stratigraphic fit to phylogeny are analyzed to test how they are affected by the shape and size of the phylogenetic trees and by the number of stratigraphic intervals encompassed. Monte Carlo randomizations are used to investigate the sensitivity of three commonly used measures (SCI, GER and MSM*) approximating their distribution of possible values under certain conditions. All are shown to vary in different ways as parameters are varied, although MSM* seems to be the most invariant in the analyzed parameter space. These results suggest that the raw metrics should not be used for comparing the fit of different taxonomic groups or competing phylogenetic trees of the same group that differ in tree size or balance. Tree balance also affects the distributions used in significance tests based on randomization and therefore their results should not be interpreted in terms of the amount of conflict implied by a phylogenetic tree.     

Relative noncovalent association constant between immunoglobulin H and L chains is unrelated to their expression or antigen-binding activity

With H and L chains derived from the murine hybridoma and myeloma proteins NQ5-89.4, 93G7, AIDA10/3, AIDA10/16, HyHEL-10, HyHEL-9, HyHEL-8, HyHEL-5, XRPC25, J539, UPC10, 6684, and C101, the relationship between the relative affinity between H-L pairs, their antigen-binding characteristics, and the primary structure of their VH and VL domains was assessed. Using competitive chain reassociation assays in which two different L chains were allowed to compete for a limiting amount of an H chain, it was observed that different pairs of L chains tended to compete to the same degree regardless of which H chain was used as the limiting reagent and regardless of whether they were the autologous or heterologous L chain. In agreement with our previous results, it was also observed that when there was limited diversity between the Vk segments of the competing L chains, the relative competitive ability of an L chain was dictated by the nature of the first residue of the Jk segment, residue 96. However, when a high degree of diversity existed between the Vk segments of the competing L chains, the relative affinity was dictated by the V segment. It was further demonstrated that junctional diversity in the L chain may not necessarily be essential for antibody activity, determined using autologous and heterologous, noncovalently reassociated immunoglobulin molecules in antigen-binding assays. Combined with the results of the competitive reassociation assays, it was evident that no correlation between the competitive ability of these L chains existed or, by inference, the relative mutual affinity between different H-L pairs and their ability to form an antigen-binding site. These results were in agreement with the random rearrangement of VH and VL domain gene segments and argue against any restrictions in the expression of the full repertoire of immunoglobulin molecules due to combinatorial (H-L pairing) mechanisms.     

Flexible generalized t-link models for binary response data

A critical issue in modelling binary response data is the choiceof the links. We introduce a new link based on the generalizedt-distribution. There are two parameters in the generalizedt-link: one parameter purely controls the heaviness of the tailsof the link and the second parameter controls the scale of thelink. Two major advantages are offered by the generalized t-links.First, a symmetric generalized t-link with an unknown shapeparameter is much more identifiable than a Student t-link withunknown degrees of freedom and a known scale parameter. Secondly,skewed generalized t-links with both unknown shape and scaleparameters provide much more flexible and improved skewed linkregression models than the existing skewed links. Various theoreticalproperties and attractive features of the proposed links areexamined and explored in detail. An efficient Markov chain MonteCarlo algorithm is developed for sampling from the posteriordistribution. The deviance information criterion measure isused for guiding the choice of links. The proposed methodologyis motivated and illustrated by prostate cancer data.     

J chain in Rana catesbeiana high molecular weight Ig

A polypeptide homologous to human and mouse J chain has been identified in the high molecular weight (HMW) Ig of the bullfrog, Rana catesbeiana. In previous studies, we had detected a component that was similar in size to mammalian J chains and that, relative to L chains, migrated rapidly to the anode in alkaline-urea PAGE; however, its mobility was less than that of mammalian J chains. We now demonstrate that this component is covalently linked to the H chain of R. catesbeiana HMW Ig. All of the disulfide bridges of this polypeptide, like those of human and mouse J chain, can be cleaved by reducing agents even in the absence of denaturing solvents. The putative frog J chain was isolated by a procedure that did not require preliminary purification of the HMW Ig. The chain differed in amino acid composition from L chains but resembled J chains from several other species. Tryptic peptides were isolated and sequenced. Except for a single heptapeptide, the peptides could be aligned by virtue of their similarity to segments of human and mouse J chain. Of the 116 residues that were placed, 55 were identical with residues in human J chain and 60 with residues in mouse J chain. The six cysteine residues identified in the frog J chain are at the same positions as six of the eight cysteines in the human and mouse J chains. The results indicate significant conservation in structure between amphibian and mammalian Ig J chains.     

Survival analysis of three clones of Brachionus plicatilis (Rotifera)

Age-specific survival schedules of females from three genetically different clones of Brachionus plicatilis were analyzed at several environmental conditions in the laboratory.Lifespan showed the expected decrease with increasing temperature, but a general trend with salinity or genotype was not observed. Probability of death increased with age, as tested by polynomial regression analysis of the survival curve and using theoretical mortality distributions. Three two-parameter models (linear-exponential model, Weibull model, and Gompertz model) were fitted to the survival data. Fitting of these models to data was rather poor, but the Gompertz model and, to a lesser extent, the Weibull model fitted the data better than the linear-exponential model. Parameters obtained from the survival curve analyses were related to other demographic parameters. A significant relationship between the shape parameter of the Gompertz model and the cohort generation time was detected, suggesting, but not proving, an effect of reproductive effort on aging.     

Flexible cloglog links for binomial regression models as an alternative for imbalanced medical data

The complementary log-log link was originally introduced in 1922 to R. A. Fisher, long before the logit and probit links. While the last two links are symmetric, the complementary log-log link is an asymmetrical link without a parameter associated with it. Several asymmetrical links with an extra parameter were proposed in the literature over last few years to deal with imbalanced data in binomial regression (when one of the classes is much smaller than the other); however, these do not necessarily have the cloglog link as a special case, with the exception of the link based on the generalized extreme value distribution. In this paper, we introduce flexible cloglog links for modeling binomial regression models that include an extra parameter associated with the link that explains some unbalancing for binomial outcomes. For all cases, the cloglog is a special case or the reciprocal version loglog link is obtained. A Bayesian Markov chain Monte Carlo inference approach is developed. Simulations study to evaluate the performance of the proposed algorithm is conducted and prior sensitivity analysis for the extra parameter shows that a uniform prior is the most convenient for all models. Additionally, two applications in medical data (age at menarche and pulmonary infection) illustrate the advantages of the proposed models.     

Competing Risk Analysis of Censored Survival Data

A competing risk model is developed to accommodate both planned Type I censoring and random withdrawals. MLE's, their properties, confidence regions for parameters and mean lifetimes are obtained for a model regarding random censoring as a competing risk and compared to those obtained for the model in which withdrawals are regarded as random censoring. Estimated net and crude probabilities are calculated and compared for the two models. The model is developed for two competing risks, one following a Weibull distribution and the other a Rayleigh distribution, and random withdrawals following a Weibull distribution.     

The effects of amylose content on the molecular size of amylose, and on the distribution of amylopectin chain length in maize starches

The amylose to amylopectin ratios in six maize starch samples of differing amylose contents were measured by enzymatic debranching, followed by high performance size exclusion chromatography (HPSEC). The molecular size of amyloses, estimated by -log K_wav, shows progressive decrease with the increase in amylose content in maize starches. The gel permeation chromatographs of the corresponding amylopectins, debranched with isoamylase, showed bimodal distributions containing long and short chains. The average chain length of amylopectin has a correlation with amylose content. The correlation coefficients between amylose content and average chain length, long chain length, weight ratio and the mole ratio of long and short chain length, were 0.97, 0.92, 0.96, 0.94 respectively. The maize starch with the highest amylose content has the lowest amylose molecular size and the longest chains, with a high ratio of long to short chains in its amylopectin fraction. Comparing the values of amylose content determined by HPSEC of starch or debranched starch with those of the iodinecomplex method, we conclude that long chains of amylopectin in high amylose starches contribute significantly to apparent amylose content.     

Standardized tumor rates for chronic bioassays

If crude experimental proportions of animals with tumors from chronic bioassays for carcinogenicity are used for low-dose extrapolation in a risk analysis, different dose-specific patterns of mortality due to competing risks can bias the results. In order to adjust tumor rates for differential mortality across dose groups, Farmer, Kodell, and Gaylor (1982, Risk Analysis 2, 27-34) recommended using nonparametric estimates of probability distributions of times to onset of tumors, with competing causes of death removed, when performing a risk analysis. This paper extends the approach of Farmer et al. by proposing a method for adjusting tumor rates to reflect lifetime or near-lifetime tumor incidences that would be obtained if all dose groups experienced the control mortality rate from causes other than the tumor of interest. Thus, natural mortality due to competing risks is explicitly included, rather than removed. The proposed standardized tumor rates are calculated as a summation of adjusted age-specific probabilities of dying with a tumor during the course of an animal bioassay for carcinogenicity plus the probability of being alive with a tumor at the terminal sacrifice.     

Facilitation of fisheries by natural predators depends on life history of shared prey

Predators commonly share prey with human exploiters, intuitively suggesting that there is an inherent human–predator conflict through competition for prey. Here we studied the effects of fishing and predation mortality on biomass distributions and yields of shared prey using a size‐structured model of competing populations, describing the life histories of Baltic Sea sprat and herring. Whereas both species responded in a similar fashion to increased fishing mortality, with decreasing juvenile and adult biomasses, we found that responses to predation mortality differed between species. Sprat only display weak compensatory responses with increasing predation mortality, while over a substantial range of mortalities there was a strong increase in adult (and total) herring biomass, i.e. overcompensation. The observed biomass overcompensation results from relaxed intraspecific competition as predation mortality increased, allowing for faster individual growth rates that in turn lead to a change in population composition (juvenile:adult biomass ratio). Our results suggest that the potential for biomass overcompensation is higher for species exhibiting substantial growth after maturation. Differences in size‐selectivity of predators and fishing mortality resulted in a positive effect of predation mortality on fisheries yields, which can be explained by an overcompensatory response in adult herring biomass. Thus, somewhat counter intuitive, our results suggest that fishermen, depending on prey life history, may actually benefit from allowing for a higher abundance of predators, despite competing for shared prey.