Developing a methodology for the National Frog Survey of Ireland: a pilot study in Co. Mayo.

A National Frog Survey of Ireland is planned for spring 2011. We conducted a pilot survey of 25 water bodies in ten 0.25 km2 survey squares in Co. Mayo during spring 2010. Drainage ditches were the most commonly available site for breeding and, generally, two 100 m stretches of ditch were surveyed in each square. The restricted period for peak spawning activity renders any methodology utilizing only one site visit inherently risky. Consequently, each site was visited three times from late March to early April. Occurrence of spawn declined significantly from 72 % to 44 % between the first and third visit whilst the overall occurrence of spawn at all sites was 76 %. As the breeding season advanced, spawn either hatched or was predated and, therefore, disappeared. In those water bodies where spawning was late, however, greater densities of spawn were deposited than in those sites where breeding was early. Consequently, spawn density and estimated frog density did not differ significantly between site visits. Future surveys should nevertheless include multiple site visits to avoid biased estimation of species occurrence and distribution. Ecological succession was identified as the main threat present at 44 % of sites.

Atomistic Insights into Rhodopsin Activation from a Dynamic Model

Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy.

A survey of sidedness in Northern Irish schoolchildren: The interaction of sex, age, and task

The study examined lateral preference in use of hands, feet, eyes, and ears in a group of nearly 5000 schoolchildren in Northern Ireland. Performance tests were carried out by student teachers during their school-based work in 2002 and data were submitted on-line. Six tasks were used-writing, throwing a ball, kicking a ball, hopping, listening to quiet sounds, and looking through a cardboard tube. There was right bias in every task but the extent of it differed between tasks. Males were generally less right biased than females, and younger children less than older ones; for hearing, the changes with age were markedly different in the two sexes, with females showing a strong increase in right bias but males showing none. These observational results do little to illuminate the reasons for the patterns observed.

Simulated predator extinctions: Predator identity affects survival and recruitment of oysters

The rate of species loss is increasing at a global scale, and human-induced extinctions are biased toward predator species. We examined the effects of predator extinctions on a foundation species, the eastern oyster (Crassostrea virginica). We performed a factorial experiment manipulating the presence and abundance of three of the most common predatory crabs, the blue crab (Callinectes sapidus), stone crab (Menippe mercenaria), and mud crab (Panopeus herbstii) in estuaries in the eastern United States. We tested the effects of species richness and identity of predators on juvenile oyster survival, oyster recruitment, and organic matter content of sediment. We also manipulated the density of each of the predators and controlled for the loss of biomass of species by maintaining a constant mass of predators in one set of treatments and simultaneously using an additive design. This design allowed us to test the density dependence of our results and test for functional compensation by other species. The identity of predator species, but not richness, affected oyster populations. The loss of blue crabs, alone or in combination with either of the other species, affected the survival rate of juvenile oysters. Blue crabs and stone crabs both affected oyster recruitment and sediment organic matter negatively. Mud crabs at higher than ambient densities, however, could fulfill some of the functions of blue and stone crabs, suggesting a level of ecological redundancy. Importantly, the strong effects of blue crabs in all processes measured no longer occurred when individuals were present at higher-than-ambient densities. Their role as dominant predator is, therefore, dependent on their density within the system and the density of other species within their guild (e.g., mud crabs). Our findings support the hypothesis that the effects of species loss at higher trophic levels are determined by predator identity and are subject to complex intraguild interactions that are largely density dependent. Understanding the role of biodiversity in ecosystem functioning or addressing practical concerns, such as loss of predators owing to overharvesting, remains complicated because accurate predictions require detailed knowledge of the system and should be drawn from sound experimental evidence, not based on observations or generalized models.

Necessary conditions for demand revelation in double referenda

This paper demonstrates a set of necessary conditions that should generate unbiased, internally consistent estimates of willingness to pay (WTP) from a double referendum mechanism. These conditions are also sufficient for demand revelation in an experimental laboratory environment. However, the control over the mechanism achieved in the lab may not be transferrable to the field and WTP estimates derived from field surveys may remain biased. (c) 2008 Elsevier Inc. All rights reserved.

Resolving questions about bias in real and hypothetical referenda

Despite 10 years of research on behavior in hypothetical referenda, conflict remains in the literature on whether or not the mechanism generates biased responses compared to real referenda, and the nature and source of any such bias. Almost all previous inquiry in respect of this issue has concentrated on bias at the aggregate level. This paper reports a series of three experiments which focuses on bias at the individual level and how this can translate to bias at the aggregate level. The authors argue that only an individual approach to hypothetical bias is consistent with the concept of incentive compatibility. The results of these experiments reflect these previous conflicting findings but go on to show that individual hypothetical bias is a robust result driven by the differing influence of pure self-interest and other-regarding preferences in real and hypothetical situations, rather than by a single behavioral theory such as free riding. In a hypothetical situation these preferences cause yea-saying and non-demand revealing voting. This suggests that investigation of individual respondents in other hypothetical one-shot binary choices may also provide us with insights into aggregate behavior in these situations.

Estimating the Density of Honeybee Colonies across Their Natural Range to Fill the Gap in Pollinator Decline Censuses

Although pollinator declines are a global biodiversity threat, the demography of the western honeybee (Apis mellifera) has not been considered by conservationists because it is biased by the activity of beekeepers. To fill this gap in pollinator decline censuses and to provide a broad picture of the current status of honeybees across their natural range, we used microsatellite genetic markers to estimate colony densities and genetic diversity at different locations in Europe, Africa, and central Asia that had different patterns of land use. Genetic diversity and colony densities were highest in South Africa and lowest in Northern Europe and were correlated with mean annual temperature. Confounding factors not related to climate, however, are also likely to influence genetic diversity and colony densities in honeybee populations. Land use showed a significantly negative influence over genetic diversity and the density of honeybee colonies over all sampling locations. In Europe honeybees sampled in nature reserves had genetic diversity and colony densities similar to those sampled in agricultural landscapes, which suggests that the former are not wild but may have come from managed hives. Other results also support this idea: putative wild bees were rare in our European samples, and the mean estimated density of honeybee colonies on the continent closely resembled the reported mean number of managed hives. Current densities of European honeybee populations are in the same range as those found in the adverse climatic conditions of the Kalahari and Saharan deserts, which suggests that beekeeping activities do not compensate for the loss of wild colonies. Our findings highlight the importance of reconsidering the conservation status of honeybees in Europe and of regarding beekeeping not only as a profitable business for producing honey, but also as an essential component of biodiversity conservation.

A Robust Co-Localisation Measurement Utilising Z-Stack Image Intensity Similarities for Biological Studies

Background: Co-localisation is a widely used measurement in immunohistochemical analysis to determine if fluorescently labelled biological entities, such as cells, proteins or molecules share a same location. However the measurement of co-localisation is challenging due to the complex nature of such fluorescent images, especially when multiple focal planes are captured. The current state-of-art co-localisation measurements of 3-dimensional (3D) image stacks are biased by noise and cross-overs from non-consecutive planes.

Method: In this study, we have developed Co-localisation Intensity Coefficients (CICs) and Co-localisation Binary Coefficients (CBCs), which uses rich z-stack data from neighbouring focal planes to identify similarities between image intensities of two and potentially more fluorescently-labelled biological entities. This was developed using z-stack images from murine organotypic slice cultures from central nervous system tissue, and two sets of pseudo-data. A large amount of non-specific cross-over situations are excluded using this method. This proposed method is also proven to be robust in recognising co-localisations even when images are polluted with a range of noises.

Results: The proposed CBCs and CICs produce robust co-localisation measurements which are easy to interpret, resilient to noise and capable of removing a large amount of false positivity, such as non-specific cross-overs. Performance of this method of measurement is significantly more accurate than existing measurements, as determined statistically using pseudo datasets of known values. This method provides an important and reliable tool for fluorescent 3D neurobiological studies, and will benefit other biological studies which measure fluorescence co-localisation in 3D.

An Empirical Analysis of Scale and Scope Economies and Technical Change in an Irish Multiproduct Banking Firm

In contrast to most empirical investigations of the efficiency of multiproduct financial institutions, which either estimate scale and scope economies with a given state of technology, or only analyse technical change in the presence of overall scale economies, this study estimates overall scale economies, product-specific scale economies and scope economies in the presence of both neutral and non-neutral technical change. Also, in contrast to most other empirical studies in this area, standard errors are computed for all relevant statistics. The findings indicate diseconomies of scope; overall diseconomies of scale; product-specific economies are decreasing for investments and increasing for loans; in addition to substantial neutral technical change, biased technical change is labour- and capital-saving and deposits-using in character.

Beyond the ideal free distribution: More general models of predator distribution

The ideal free distribution model which relates the spatial distribution of mobile consumers to that of their resource is shown to be a limiting case of a more general model which we develop using simple concepts of diffusion. We show how the ideal free distribution model can be derived from a more general model and extended by incorporating simple models of social influences on predator spacing. First, a free distribution model based on patch switching rules, with a power-law interference term, which represents instantaneous biased diffusion is derived. A social bias term is then introduced to represent the effect of predator aggregation on predator fitness, separate from any effects which act through intake rate. The social bias term is expanded to express an optimum spacing for predators and example solutions of the resulting biased diffusion models are shown. The model demonstrates how an empirical interference coefficient, derived from measurements of predator and prey densities, may include factors expressing the impact of social spacing behaviour on fitness. We conclude that empirical values of log predator/log prey ratio may contain information about more than the relationship between consumer and resource densities. Unlike many previous models, the model shown here applies to conditions without continual input. (C) 1997 Academic Press Limited.</p>

Red-shifts and red herrings in geographical ecology

I draw attention to the need for ecologists to take spatial structure into account more seriously in hypothesis testing. If spatial autocorrelation is ignored, as it usually is, then analyses of ecological patterns in terms of environmental factors can produce very misleading results. This is demonstrated using synthetic but realistic spatial patterns with known spatial properties which are subjected to classical correlation and multiple regression analyses. Correlation between an autocorrelated response variable and each of a set of explanatory variables is strongly biased in favour of those explanatory variables that are highly autocorrelated - the expected magnitude of the correlation coefficient increases with autocorrelation even if the spatial patterns are completely independent. Similarly, multiple regression analysis finds highly autocorrelated explanatory variables "significant" much more frequently than it should. The chances of mistakenly identifying a "significant" slope across an autocorrelated pattern is very high if classical regression is used. Consequently, under these circumstances strongly autocorrelated environmental factors reported in the literature as associated with ecological patterns may not actually be significant. It is likely that these factors wrongly described as important constitute a red-shifted subset of the set of potential explanations, and that more spatially discontinuous factors (those with bluer spectra) are actually relatively more important than their present status suggests. There is much that ecologists can do to improve on this situation. I discuss various approaches to the problem of spatial autocorrelation from the literature and present a randomisation test for the association of two spatial patterns which has advantages over currently available methods.

Bending It Like Beckham: How to Visually Fool the Goalkeeper

Background: As bending free-kicks becomes the norm in modern day soccer, implications for goalkeepers have largely been ignored. Although it has been reported that poor sensitivity to visual acceleration makes it harder for expert goalkeepers to perceptually judge where the curved free-kicks will cross the goal line, it is unknown how this affects the goalkeeper's actual movements.

Methodology/Principal Findings: Here, an in-depth analysis of goalkeepers' hand movements in immersive, interactive virtual reality shows that they do not fully account for spin-induced lateral ball acceleration. Hand movements were found to be biased in the direction of initial ball heading, and for curved free-kicks this resulted in biases in a direction opposite to those necessary to save the free-kick. These movement errors result in less time to cover a now greater distance to stop the ball entering the goal. These and other details of the interceptive behaviour are explained using a simple mathematical model which shows how the goalkeeper controls his movements online with respect to the ball's current heading direction. Furthermore our results and model suggest how visual landmarks, such as the goalposts in this instance, may constrain the extent of the movement biases.

Conclusions: While it has previously been shown that humans can internalize the effects of gravitational acceleration, these results show that it is much more difficult for goalkeepers to account for spin-induced visual acceleration, which varies from situation to situation. The limited sensitivity of the human visual system for detecting acceleration, suggests that curved free-kicks are an important goal-scoring opportunity in the game of soccer.

The Unification of Asymmetry Signatures of Type Ia Supernovae

We present a compilation of the geometry measures acquired using optical and IR spectroscopy and optical spectropolarimetry to probe the explosion geometry of Type Ia supernovae (SNe Ia). Polarization measurements are sensitive to asymmetries in the plane of the sky, whereas line profiles in nebular phase spectra are expected to trace asymmetries perpendicular to the plane of the sky. The combination of these two measures can overcome their respective projection effects, completely probing the structures of these events. For nine normal SNe Ia, we find that the polarization of Si II ?6355 at 5 days before maximum (p Si II ) is well correlated with its velocity evolution (\dot{v}_Si II), implying that \dot{v}_Si II is predominantly due to the asymmetry of the SNe. We find only a weak correlation between the polarization of Si II and the reported velocities (v neb) for peak emission of optical Fe II and Ni II lines in nebular spectra. Our sample is biased, with polarization measurements being only available for normal SNe that subsequently exhibited positive (i.e., redshifted) v neb. In unison these indicators are consistent with an explosion in which the outer layers are dominated by a spherical oxygen layer, mixed with an asymmetric distribution of intermediate-mass elements. The combination of spectroscopic and spectropolarimetric indicators suggests a single geometric configuration for normal SNe Ia, with some of the diversity of observed properties arising from orientation effects.

Logic feels so good-I like it! Evidence for intuitive detection of logicality in syllogistic reasoning

When people evaluate syllogisms, their judgments of validity are often biased by the believability of the conclusions of the problems. Thus, it has been suggested that syllogistic reasoning performance is based on an interplay between a conscious and effortful evaluation of logicality and an intuitive appreciation of the believability of the conclusions (e.g., Evans, Newstead, Allen, & Pollard, 1994). However, logic effects in syllogistic reasoning emerge even when participants are unlikely to carry out a full logical analysis of the problems (e.g., Shynkaruk & Thompson, 2006). There is also evidence that people can implicitly detect the conflict between their beliefs and the validity of the problems, even if they are unable to consciously produce a logical response (e.g., De Neys, Moyens, & Vansteenwegen, 2010). In 4 experiments we demonstrate that people intuitively detect the logicality of syllogisms, and this effect emerges independently of participants' conscious mindset and their cognitive capacity. This logic effect is also unrelated to the superficial structure of the problems. Additionally, we provide evidence that the logicality of the syllogisms is detected through slight changes in participants' affective states. In fact, subliminal affective priming had an effect on participants' subjective evaluations of the problems. Finally, when participants misattributed their emotional reactions to background music, this significantly reduced the logic effect.

Regulation of Foxp3+ Inducible Regulatory T Cell Stability by SOCS2

Suppressor of cytokine signaling (SOCS) proteins are key regulators of CD4+ T cell differentiation, and in particular, we have recently shown that SOCS2 inhibits the development of Th2 cells and allergic immune responses. Interestingly, transcriptome analyses have identified SOCS2 as being preferentially expressed in both natural regulatory T cells (Tregs) and inducible Tregs (iTregs); however, the role of SOCS2 in Foxp3+ Treg function or development has not been fully elucidated. In this study, we show that despite having no effect on natural Treg development or function, SOCS2 is highly expressed in iTregs and required for the stable expression of Foxp3 in iTregs in vitro and in vivo. Indeed, SOCS2-deficient CD4+ T cells upregulated Foxp3 following in vitro TGF-ß stimulation, but failed to maintain stable expression of Foxp3. Moreover, in vivo generation of iTregs following OVA feeding was impaired in the absence of SOCS2 and could be rescued in the presence of IL-4 neutralizing Ab. Following IL-4 stimulation, SOCS2-deficient Foxp3+ iTregs secreted elevated IFN-? and IL-13 levels and displayed enhanced STAT6 phosphorylation. Therefore, we propose that SOCS2 regulates iTreg stability by downregulating IL-4 signaling. Moreover, SOCS2 is essential to maintain the anti-inflammatory phenotype of iTregs by preventing the secretion of proinflammatory cytokines. Collectively, these results suggest that SOCS2 may prevent IL-4-induced Foxp3+ iTreg instability. Foxp3+ iTregs are key regulators of immune responses at mucosal surfaces; therefore, this dual role of SOCS2 in both Th2 and Foxp3+ iTregs reinforces SOCS2 as a potential therapeutic target for Th2-biased diseases.