The effects of extended exposure to traffic noise on parid social and risk-taking behavior

Traffic noise is a prevalent and yet poorly understood anthropogenic disturbance associated with reduced avian diversity, population densities and pairing and mating success. How these systems are affected is not clear as a direct experimental link between noise and behavior underlying these patterns is missing. Here we provide the first empirical evidence of the effects of long-term exposure to simulated traffic noise on social and risk-taking behavior of Carolina chickadees (Poecile carolinensis) and tufted titmice (Baeolophus bicolor). In testing for these effects we compare two hypotheses regarding the effects of noise on behavior. We found that noise increases sociality by reducing nearest neighbor distances and increasing the number of close-perches within study flocks. These behavioral responses mimic those of species in high-risk situations, such as birds in the presence of a predator. These results provide support for the 'Increased Threat Hypothesis,' which argues that chronic traffic noise affects behavior by increasing the perceived level of threat. Although the adaptive value or function of these responses to noise is unknown, they may serve to mitigate any negative effects of traffic noise. If true, species lacking behavioral plasticity may be more susceptible to effects of traffic noise and other similar acoustic disturbances.     

What determines the normal water content of a living cell?

Most living cells contain a large amount of water. To improve our understanding of this fundamental phenomenon of cell physiology, five theories are critically examined in the light of three sets of relevant experimental findings. These findings are: (1) the diversity and specificity of the percentage water content to tissue type; (2) the limitation imposed by the Law of the Conservation of Energy on postulating membrane pumps and (3) the non-extractability of cell water from the open ends of muscle cells whose membrane covering has been surgically removed. Two of the five theories examined are called respectively the accidental theory (Theory I) and the direct water pump-leak theory (Theory III); both are introduced for the first time here as working hypotheses. Three others theories examined were published; they comprise the Donnan membrane equilibrium theory (Theory II), the indirect pump-leak (Theory IV) and the polarized-oriented multilayer (PM) theory of cell water (Theory V.) The PM (Theory V) alone is in harmony with, and supported by all three sets of the experimental findings. The remaining theories are shown to be non-applicable to cell water by at least two of the findings     

Asynchronous functional linear regression models for longitudinal data in reproducing kernel Hilbert space

Motivated by the analysis of longitudinal neuroimaging studies, we study the longitudinal functional linear regression model under asynchronous data setting for modeling the association between clinical outcomes and functional (or imaging) covariates. In the asynchronous data setting, both covariates and responses may be measured at irregular and mismatched time points, posing methodological challenges to existing statistical methods. We develop a kernel weighted loss function with roughness penalty to obtain the functional estimator and derive its representer theorem. The rate of convergence, a Bahadur representation, and the asymptotic pointwise distribution of the functional estimator are obtained under the reproducing kernel Hilbert space framework. We propose a penalized likelihood ratio test to test the nullity of the functional coefficient, derive its asymptotic distribution under the null hypothesis, and investigate the separation rate under the alternative hypotheses. Simulation studies are conducted to examine the finite-sample performance of the proposed procedure. We apply the proposed methods to the analysis of multitype data obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) study, which reveals significant association between 21 regional brain volume density curves and the cognitive function. Data used in preparation of this paper were obtained from the ADNI database (adni.loni.usc.edu).     

Geophagy among primates: adaptive significance and ecological consequences

We review geophagy, or soil ingestion, in primates. This behaviour is widespread and is presumed to be important to health and nutrition. Primates may engage in geophagy for one or a combination of reasons. Here we present, and make a preliminary assessment of, six nonexclusive hypotheses that may contribute to the prevalence of geophagy. Four hypotheses relate to geophagy in alleviating gastrointestinal disorders or upsets: (1) soils adsorb toxins such as phenolics and secondary metabolites; (2) soil ingestion has an antacid action and adjusts the gut pH; (3) soils act as an antidiarrhoeal agent; and (4) soils counteract the effects of endoparasites. Two hypotheses pertain to geophagy in supplementing minerals and/or elements: (5) soils supplement nutrient-poor diets and (6) soils provide extra iron at high altitudes. In addition to these hypotheses, geophagy may satiate olfactory senses, serve as a famine food and finally may have no function at all. We draw together a large body of information from various sources to assess these hypotheses and suggest some tests to understand the function of geophagy. Our review suggests that primates engage in geophagy for a number of reasons that are nonexclusive. We conclude that mineral supplementation, adsorption of toxins, treatment of diarrhoea and pH adjustment of the gut seem the most plausible reasons why primates engage in geophagy. Copyright 2000 The Association for the Study of Animal Behaviour.     

The function of teeth chattering in male Barbary macaques (Macaca sylvanus)

Teeth chattering is seen in many primate species and has been proposed to have a range of social functions. This observational study tested specific hypotheses relating to the function of teeth chattering in a semi-free-ranging group of Barbary macaques, Macaca sylvanus. During focal watches of males, the outcome of male-male dyadic social interactions in which teeth chattering was present or absent was compared. Using these data, we tested the predictions of four hypotheses: teeth chattering functions as a signal of submission, appeasement, affiliation or reassurance. Support was found for all four hypotheses. In addition, in some contexts, an exchange of teeth chattering appeared to have a greater impact on the outcome of interactions than one male alone giving this signal. These findings suggest that teeth chattering serves an important role in coordinating the social interactions of male Barbary macaques.     

Competition and community structure in diurnal arboreal geckos (genus Phelsuma) in the Indian Ocean

In this study, we investigate community structure in day geckos (genus Phelsuma ) in the Indian Ocean. Much of what we know about communities of diurnal arboreal lizards comes from studies of Caribbean Anolis . Phelsuma in the Indian Ocean are ecologically similar to Anolis but not closely related. Using field observations and an experiment, we test three hypotheses for Phelsuma communities, all derived from work on Anolis : (1) Phelsuma species richness will be correlated with the diversity of available perches, (2) sympatric species will partition their habitat use, shifting their habitat use depending on which other species of Phelsuma are present, and (3) experimentally removing individuals of one species will lead to changes in the microhabitat use and/or abundance of sympatric congeners. We find support for all three hypotheses. We also describe some unique aspects of Phelsuma communities, such as partitioning of palm vs. non-palm trees. This study identifies some potentially general features of diurnal arboreal lizard communities, and suggests that some aspects of community assembly might be repeatable.     

A phylogenetic analysis of sleep architecture in mammals: the integration of anatomy, physiology, and ecology

Among mammalian species, the time spent in the two main "architectural" states of sleep--slow-wave sleep (SWS) and rapid-eye-movement (REM) sleep--varies greatly. Previous comparative studies of sleep architecture found that larger mammals, those with bigger brains, and those with higher absolute basal metabolic rates (BMR) tended to engage in less SWS and REM sleep. Species experiencing a greater risk of predation also exhibited less SWS and REM sleep. In all cases, however, these studies lacked a formal phylogenetic and theoretical framework and used mainly correlational analyses. Using independent contrasts and an updated data set, we extended existing approaches with path analysis to examine the integrated influence of anatomy, physiology, and ecology on sleep architecture. Path model structure was determined by nonmutually exclusive hypotheses for the function of sleep. We found that species with higher relative BMRs engage in less SWS, whereas species with larger relative brain masses engage in more REM sleep. REM sleep was the only sleep variable strongly influenced by predation risk; mammals sleeping in riskier environments engage in less REM sleep. Overall, we found support for some hypotheses for the function of sleep, such as facilitating memory consolidation or learning, but not others, such as energy conservation.     

Genetic modelling: an analysis of a colour polymorphism in the Snow Goose (Anser caerulescens)

Previous studies of colour polymorphism in the Snow Goose [ Anser caerulescens ; failed to consider and reject alternative hypotheses to that of a single locus with incomplete dominance. Utilizing data from a long-term study of a wild population, we test the validity of these earlier results by considering two alternatives: (1) a single locus with multiple allelism and (2) a threshold polygenic system. Our analyses corroborate the original model, but emphasize the importance of testing all plausible hypotheses.     

Electromechanical and Chemical Sensing at the Nanoscale: Molecular Modeling Applications

Atomistic modeling and simulations are becoming increasingly important in the design of new devices at the nanoscale. Of the myriad of potential application areas commonly associated with Nanotechnology, sensors based on carbon nanotubes (CNT) and metal-oxide nanoribbons are one of the closest to commercial reality. In this work, we review some recent molecular modeling investigations on: (1) CNT-based electromechanical sensors, and (2) gas-sensing properties of SnO² nanoribbons. Simulation methods include: First-Principles Density Functional Theory (DFT), classical molecular mechanics, and Green's-function-based tight-binding transport.     

Wildfire Selectivity for Land Cover Type: Does Size Matter?

Previous research has shown that fires burn certain land cover types disproportionally to their abundance. We used quantile regression to study land cover proneness to fire as a function of fire size, under the hypothesis that they are inversely related, for all land cover types. Using five years of fire perimeters, we estimated conditional quantile functions for lower (avoidance) and upper (preference) quantiles of fire selectivity for five land cover types - annual crops, evergreen oak woodlands, eucalypt forests, pine forests and shrublands. The slope of significant regression quantiles describes the rate of change in fire selectivity (avoidance or preference) as a function of fire size. We used Monte-Carlo methods to randomly permutate fires in order to obtain a distribution of fire selectivity due to chance. This distribution was used to test the null hypotheses that 1) mean fire selectivity does not differ from that obtained by randomly relocating observed fire perimeters; 2) that land cover proneness to fire does not vary with fire size. Our results show that land cover proneness to fire is higher for shrublands and pine forests than for annual crops and evergreen oak woodlands. As fire size increases, selectivity decreases for all land cover types tested. Moreover, the rate of change in selectivity with fire size is higher for preference than for avoidance. Comparison between observed and randomized data led us to reject both null hypotheses tested ( = 0.05) and to conclude it is very unlikely the observed values of fire selectivity and change in selectivity with fire size are due to chance.     

What does the male function hypothesis claim?

Paternal, rather than maternal, fitness consequences of reproductive traits are the lynchpin in many hypotheses about reproductive evolution in hermaphroditic angiosperms. These hypotheses often differ in their predictions, so that supporting or contradictory evidence for one hypothesis may not reflect similarly on another, even though both may be referred to as ‘the male function hypothesis’. We provide graphical representations of four male function hypotheses from the recent literature in order to highlight their differences. We offer and explain two recommendations to reduce ambiguity in terminology: (1) male function hypotheses should address the evolution of excess flowers per se, rather than total flower number, which is usually highly plastic in modular organisms with open growth form; and (2) attention must be given to whole plant fitness, rather than fitness per flower or per inflorescence. In empirical studies, we recommend the use of path analysis to dissect the multiple pathways (through both male and female function) by which selection may act on excess flower number.     

Trait‐based tests of coexistence mechanisms

Recent functional trait studies have shown that trait differences may favour certain species (environmental filtering) while simultaneously preventing competitive exclusion (niche partitioning). However, phenomenological trait‐dispersion analyses do not identify the mechanisms that generate niche partitioning, preventing trait‐based prediction of future changes in biodiversity. We argue that such predictions require linking functional traits with recognised coexistence mechanisms involving spatial or temporal environmental heterogeneity, resource partitioning and natural enemies. We first demonstrate the limitations of phenomenological approaches using simulations, and then (1) propose trait‐based tests of coexistence, (2) generate hypotheses about which plant functional traits are likely to interact with particular mechanisms and (3) review the literature for evidence for these hypotheses. Theory and data suggest that all four classes of coexistence mechanisms could act on functional trait variation, but some mechanisms will be stronger and more widespread than others. The highest priority for future research is studies of interactions between environmental heterogeneity and trait variation that measure environmental variables at within‐community scales and quantify species' responses to the environment in the absence of competition. Evidence that similar trait‐based coexistence mechanisms operate in many ecosystems would simplify biodiversity forecasting and represent a rare victory for generality over contingency in community ecology.     

Testing equality of survival functions of quality-adjusted lifetime

We present a method for comparing the survival functions of quality-adjusted lifetime from two treatments. This test statistic becomes the ordinary log-rank test when quality-adjusted lifetime is the same as the survival time. Simulation experiments are conducted to examine the behavior of our proposed test statistic under both null and alternative hypotheses. In addition, we apply our method to a breast cancer trial for comparing the distribution of quality-adjusted lifetime between two treatment regimes.     

COMPARATIVE ETHOLOGY OF THE CICONIIDAE. THE WOOD-STORKS (GENERA MYCTERIA AND IBIS)*

This paper reports on an 11-year study of the comparative behaviour of the four species of wood-storks. All species were studied under natural conditions at breeding colonies in the U.S.A., East Africa, India, and Indonesia. In addition, observations were made on hand-reared young of two species (Mycteria americana and Ibis ibis). Various aspects of signal (display) and non-signal behaviour are described. The most common ritualised display away from the nest is the Forward Threat. At the neBt, the following displays are seen, mainly during courtship and pair-formation: Aerial Clattering Threat, Forward Clattering Threat, Snap Display, Anxiety Stretch, Flying Around, Gaping, Balancing Posture, Swaying Twig-Grasping, Display Preening, Up-Down, and Copulation Clattering. Each of these patterns is described in the text and many of them are illustrated. The four species treated here are similar to each other in most behaviour patterns. They do show some quantitative differences in courtship displays, particularly in the Up-Down, a common “greeting” display shown to the mate at the nest. The behavioural and morphological evidence now available does not justify the separation of M. americana into a monotypic genus, and I suggest that all four wood-storks be combined in the genus Mycteria. Thus, the wood-storks include: M. americana, M. cinerea, M. ibis, and M. leucocephala.     

Design and analysis of bridging studies with prior probabilities on the null and alternative hypotheses

The pharmaceutical industry and regulatory agencies are increasingly interested in conducting bridging studies in order to bring an approved drug product from the original region (eg, United States or European Union) to a new region (eg, Asian-Pacific countries). In this article, we provide a new methodology for the design and analysis of bridging studies by assuming prior knowledge on how the null and alternative hypotheses in the original, foreign study are related to the null and alternative hypotheses in the bridging study and setting the type I error for the bridging study according to the strength of the foreign-study evidence. The new methodology accounts for randomness in the foreign-study evidence and controls the average type I error of the bridging study over all possibilities of the foreign-study evidence. In addition, the new methodology increases statistical power, when compared to approaches that do not use foreign-study evidence, and it allows for the possibility of not conducting the bridging study when the foreign-study evidence is unfavorable. Finally, we conducted extensive simulation studies to demonstrate the usefulness of the proposed methodology.     

COP9 signalosome: a multifunctional regulator of SCF and other cullin-based ubiquitin ligases

COP9 Signalosome (CSN) is a fascinating protein complex whose biochemical and physiological functions are only beginning to be understood. It is conserved throughout eukaryotes and is critical to the proper development of all multicellular organisms in which its function has been explored. Recent work suggests that CSN plays a key role in sustaining the activity of SCF and other cullin-based ubiquitin ligases, which may account for its essential roles in development. Here, we summarize what is known about CSN, and discuss hypotheses for how CSN promotes the activity of SCF ubiquitin ligases.     

Semiparametric Bayes Multiple Testing: Applications to Tumor Data

Summary In National Toxicology Program (NTP) studies, investigators want to assess whether a test agent is carcinogenic overall and specific to certain tumor types, while estimating the dose‐response profiles. Because there are potentially correlations among the tumors, a joint inference is preferred to separate univariate analyses for each tumor type. In this regard, we propose a random effect logistic model with a matrix of coefficients representing log‐odds ratios for the adjacent dose groups for tumors at different sites. We propose appropriate nonparametric priors for these coefficients to characterize the correlations and to allow borrowing of information across different dose groups and tumor types. Global and local hypotheses can be easily evaluated by summarizing the output of a single Monte Carlo Markov chain (MCMC). Two multiple testing procedures are applied for testing local hypotheses based on the posterior probabilities of local alternatives. Simulation studies are conducted and an NTP tumor data set is analyzed illustrating the proposed approach.     

More Specific Signal Detection in Functional Magnetic Resonance Imaging by False Discovery Rate Control for Hierarchically Structured Systems of Hypotheses

Signal detection in functional magnetic resonance imaging (fMRI) inherently involves the problem of testing a large number of hypotheses. A popular strategy to address this multiplicity is the control of the false discovery rate (FDR). In this work we consider the case where prior knowledge is available to partition the set of all hypotheses into disjoint subsets or families, e. g., by a-priori knowledge on the functionality of certain regions of interest. If the proportion of true null hypotheses differs between families, this structural information can be used to increase statistical power. We propose a two-stage multiple test procedure which first excludes those families from the analysis for which there is no strong evidence for containing true alternatives. We show control of the family-wise error rate at this first stage of testing. Then, at the second stage, we proceed to test the hypotheses within each non-excluded family and obtain asymptotic control of the FDR within each family at this second stage. Our main mathematical result is that this two-stage strategy implies asymptotic control of the FDR with respect to all hypotheses. In simulations we demonstrate the increased power of this new procedure in comparison with established procedures in situations with highly unbalanced families. Finally, we apply the proposed method to simulated and to real fMRI data.