Biases in comparative analyses of extinction risk: mind the gap

1. Comparative analyses are used to address the key question of what makes a species more prone to extinction by exploring the links between vulnerability and intrinsic species’ traits and/or extrinsic factors. This approach requires comprehensive species data but information is rarely available for all species of interest. As a result comparative analyses often rely on subsets of relatively few species that are assumed to be representative samples of the overall studied group. 2. Our study challenges this assumption and quantifies the taxonomic, spatial, and data type biases associated with the quantity of data available for 5415 mammalian species using the freely available life-history database PanTHERIA. 3. Moreover, we explore how existing biases influence results of comparative analyses of extinction risk by using subsets of data that attempt to correct for detected biases. In particular, we focus on links between four species’ traits commonly linked to vulnerability (distribution range area, adult body mass, population density and gestation length) and conduct univariate and multivariate analyses to understand how biases affect model predictions. 4. Our results show important biases in data availability with c.22% of mammals completely lacking data. Missing data, which appear to be not missing at random, occur frequently in all traits (14–99% of cases missing). Data availability is explained by intrinsic traits, with larger mammals occupying bigger range areas being the best studied. Importantly, we find that existing biases affect the results of comparative analyses by overestimating the risk of extinction and changing which traits are identified as important predictors. 5. Our results raise concerns over our ability to draw general conclusions regarding what makes a species more prone to extinction. Missing data represent a prevalent problem in comparative analyses, and unfortunately, because data are not missing at random, conventional approaches to fill data gaps, are not valid or present important challenges. These results show the importance of making appropriate inferences from comparative analyses by focusing on the subset of species for which data are available. Ultimately, addressing the data bias problem requires greater investment in data collection and dissemination, as well as the development of methodological approaches to effectively correct existing biases.

A morphometric comparison of the Namib and southwest Kalahari dunefields using ASTER GDEM data

The increased availability of digital elevation models and satellite image data enable testing of morphometric relationships between sand dune variables (dune height, spacing and equivalent sand thickness), which were originally established using limited field survey data. These long-established geomorphological hypotheses can now be tested against very much larger samples than were possible when available data were limited to what could be collected by field surveys alone. This project uses ASTER Global Digital Elevation Model (GDEM) data to compare morphometric relationships between sand dune variables in the southwest Kalahari dunefield to those of the Namib Sand Sea, to test whether the relationships found in an active sand sea (Namib) also hold for the fixed dune system of the nearby southwest Kalahari. The data show significant morphometric differences between the simple linear dunes of the Namib sand sea and the southwest Kalahari; the latter do not show the expected positive relationship between dune height and spacing. The southwest Kalahari dunes show a similar range of dune spacings, but they are less tall, on average, than the Namib sand sea dunes. There is a clear spatial pattern to these morphometric data; the tallest and most closely spaced dunes are towards the southeast of the Kalahari dunefield; and this is where the highest values of equivalent sand thickness result. We consider the possible reasons for the observed differences and highlight the need for more studies comparing sand seas and dunefields from different environmental settings.

Impact of an intervention on the availability and consumption of fruits and vegetables in the workplace

Objective: To evaluate the impact of an educational and environmental intervention on the availability and consumption of fruits and vegetables in workplace cafeterias. Design: This was a randomized intervention study involving a sample of companies that were divided into intervention and control groups. The intervention, which focused on change in the work environment, was based on an ecological model for health promotion. It involved several different aspects including menu planning, food presentation and motivational strategies to encourage the consumption of fruits and vegetables. The impact of the intervention was measured by changes (between baseline and follow-up) in the availability of fruits and vegetables that were eaten per consumer in meals and the consumption of fruits and vegetables in the workplace by workers. We also evaluated the availability of energy, macronutrients and fibre. Settings: Companies of Sao Paulo, Brazil. Subjects: Twenty-nine companies and 2510 workers. Results: After the intervention we found an average increase in the availability of fruits and vegetables of 49 g in the intervention group, an increase of approximately 15 %, whereas the results for the control group remained practically equal to baseline levels. During the follow-up period, the intervention group also showed reduced total fat and an increase in fibre in the meals offered. The results showed a slight but still positive increase in the workers` consumption of fruits and vegetables (about 11 g) in the meals offered by the companies. Conclusions: Interventions focused on the work environment can be effective in promoting the consumption of healthy foods.

Random primordial magnetic fields and the gas content of dark matter haloes

We recently predicted the existence of random primordial magnetic fields (RPMFs) in the form of randomly oriented cells with dipole-like structure with a cell size L(0) and an average magnetic field B(0). Here, we investigate models for primordial magnetic field with a similar web-like structure, and other geometries, differing perhaps in L(0) and B(0). The effect of RPMF on the formation of the first galaxies is investigated. The filtering mass, M(F), is the halo mass below which baryon accretion is severely depressed. We show that these RPMF could influence the formation of galaxies by altering the filtering mass and the baryon gas fraction of a halo, f(g). The effect is particularly strong in small galaxies. We find, for example, for a comoving B(0) = 0.1 mu G, and a reionization epoch that starts at z(s) = 11 and ends at z(e) = 8, for L(0) = 100 pc at z = 12, the f(g) becomes severely depressed for M < 10(7) M(circle dot), whereas for B(0) = 0 the f(g) becomes severely depressed only for much smaller masses, M < 10(5) M(circle dot). We suggest that the observation of M(F) and f(g) at high redshifts can give information on the intensity and structure of primordial magnetic fields.

Effect of fires on soil nutrient availability in an open savanna in Central Brazil

Fire is common in savannas but its effects on soil are poorly understood. We analyzed long-term effects of fire on surface soil of an open Brazilian savanna (campo sujo) in plots submitted to different fire regimes during 18 years. The five fire regimes were: unburned, quadrennial fires in middle dry season, and biennial fires in early, middle or late dry season. Soil was collected during the wet and the middle dry season of 2008, and analyzed for pH, organic matter, total N, potential acidity, exchangeable cations and available P, S, Mn, Cu, Zn and Fe. We applied multivariate analysis to search for patterns related to fire regimes, and to local climate, fuel, and fire behavior. Spearman test was used to establish correlations between soil variables and the multivariate analysis gradient structure. Seasonal differences were tested using t-test. We found evidence of long-term fire effects: the unburned plot was segregated mainly by lower soil pH; the quadrennial plot was also segregated by lower soil pH and higher amount of exchangeable cations; the time of burning during the dry season in biennial plots did not significantly affect soil availability of nutrients. Differences in elements amounts due to the season of soil sampling (wet or dry) were higher than due to the effect of fires. Higher availability of nutrients in the soil during the wet season was probably related to higher nutrient inputs via rainfall and higher microbial activity.

Non-random reef use by fishes at two dominant zones in a tropical, algal-dominated coastal reef

Habitat use and the processes which determine fish distribution were evaluated at the reef flat and reef crest zones of a tropical, algal-dominated reef. Our comparisons indicated significant differences in the majority of the evaluated environmental characteristics between zones. Also, significant differences in the abundances of twelve, from thirteen analyzed species, were observed within and between-sites. According to null models, non-random patterns of species co-occurrences were significant, suggesting that fish guilds in both zones were non-randomly structured. Unexpectedly, structural complexity negatively affected overall species richness, but had a major positive influence on highly site-attached species such as a damselfish. Depth and substrate composition, particularly macroalgae cover, were positive determinants for the fish assemblage structure in the studied reef, prevailing over factors such as structural complexity and live coral cover. Our results are conflicting with other studies carried out in coral-dominated reefs of the Caribbean and Pacific, therefore supporting the idea that the factors which may potentially influence reef fish composition are highly site-dependent and variable.

The Prospective and Retrospective Memory Questionnaire: A population-based random sampling study

The Prospective and Retrospective Memory Questionnaire (PRMQ) has been shown to have acceptable reliability and factorial, predictive, and concurrent validity. However, the PRMQ has never been administered to a probability sample survey representative of all ages in adulthood, nor have previous studies controlled for factors that are known to influence metamemory, such as affective status. Here, the PRMQ was applied in a survey adopting a probabilistic three-stage cluster sample representative of the population of Sao Paulo, Brazil, according to gender, age (20-80 years), and economic status (n=1042). After excluding participants who had conditions that impair memory (depression, anxiety, used psychotropics, and/or had neurological/psychiatric disorders), in the remaining 664 individuals we (a) used confirmatory factor analyses to test competing models of the latent structure of the PRMQ, and (b) studied effects of gender, age, schooling, and economic status on prospective and retrospective memory complaints. The model with the best fit confirmed the same tripartite structure (general memory factor and two orthogonal prospective and retrospective memory factors) previously reported. Women complained more of general memory slips, especially those in the first 5 years after menopause, and there were more complaints of prospective than retrospective memory, except in participants with lower family income.

Conversion coefficients from air kerma to personal dose equivalent in mammography

In this work, the scattered X-ray beams produced by a mammography unit with a Mo/Mo, Mo/Rh and W/Rh anode/filter combinations were applied in the evaluation of the Hp(10, 0) and mean conversion coefficients from air kerma to the personal dose equivalent ((C) over barH(p(10,0 degrees))). The higher values of H(p)(10,0 degrees) are related to the Mo/Rh combination whereas the lower ones are for the W/Rh target/filter. (C) over barH(p(10,0 degrees)) values are in the range 0.19-0.54 Sv/Gy, where the higher values comprise the W/Rh combination. (C) 2009 Elsevier Ltd. All rights reserved.

Conformal deformation of equilibrium measures in normal random ensembles

We investigate the eigenvalue statistics of ensembles of normal random matrices when their order N tends to infinite. In the model, the eigenvalues have uniform density within a region determined by a simple analytic polynomial curve. We study the conformal deformations of equilibrium measures of normal random ensembles to the real line and give sufficient conditions for it to weakly converge to a Wigner measure.

Nonlinear Schrodinger equation with chaotic, random, and nonperiodic nonlinearity

In this Letter we deal with a nonlinear Schrodinger equation with chaotic, random, and nonperiodic cubic nonlinearity. Our goal is to study the soliton evolution, with the strength of the nonlinearity perturbed in the space and time coordinates and to check its robustness under these conditions. Here we show that the chaotic perturbation is more effective in destroying the soliton behavior, when compared with random or nonperiodic perturbation. For a real system, the perturbation can be related to, e.g., impurities in crystalline structures, or coupling to a thermal reservoir which, on the average, enhances the nonlinearity. We also discuss the relevance of such random perturbations to the dynamics of Bose-Einstein condensates and their collective excitations and transport. (C) 2010 Elsevier B.V. All rights reserved.

Approach to Equilibrium for a Class of Random Quantum Models of Infinite Range

We consider random generalizations of a quantum model of infinite range introduced by Emch and Radin. The generalizations allow a neat extension from the class l (1) of absolutely summable lattice potentials to the optimal class l (2) of square summable potentials first considered by Khanin and Sinai and generalised by van Enter and van Hemmen. The approach to equilibrium in the case of a Gaussian distribution is proved to be faster than for a Bernoulli distribution for both short-range and long-range lattice potentials. While exponential decay to equilibrium is excluded in the nonrandom l (1) case, it is proved to occur for both short and long range potentials for Gaussian distributions, and for potentials of class l (2) in the Bernoulli case. Open problems are discussed.

Perturbation treatment of symmetry breaking within random matrix theory

We discuss the applicability, within the random matrix theory, of perturbative treatment of symmetry breaking to the experimental data on the flip symmetry breaking in quartz crystal. We found that the values of the parameter that measures this breaking are different for the spacing distribution as compared to those for the spectral rigidity. We consider both two-fold and three-fold symmetries. The latter was found to account better for the spectral rigidity than the former. Both cases, however, underestimate the experimental spectral rigidity at large L. This discrepancy can be resolved if an appropriate number of eigenfrequencies is considered to be missing in the sample. Our findings are relevant for symmetry violation studies in general. (C) 2008 Elsevier B.V. All rights reserved.

Performance of GEANT4 in dosimetry applications: Calculation of X-ray spectra and kerma-to-dose equivalent conversion coefficients

In order to validate the Geant4 toolkit for dosimetry applications, simulations were performed to calculate conversion coefficients h(10, alpha) from air kerma free-in-air to personal dose equivalent Hp(10, a). The simulations consisted of two parts: the production of X-rays with radiation qualities of narrow and wide spectra, and the interaction of radiation with ICRU tissue-equivalent and ISO water slab phantoms. The half-value layers of the X-ray spectra obtained by simulation were compared with experimental results. Mean energy, spectral resolution, half-value layers and conversion coefficients were compared with ISO reference values. The good agreement between results from simulation and reference data shows that the Geant4 is suitable for dosimetry applications which involve photons with energies in the range of ten to a few hundreds of keV. (C) 2008 Elsevier Ltd. All rights reserved.

Bose systems in spatially random or time-varying potentials

Bose systems, subject to the action of external random potentials, are considered. For describing the system properties, under the action of spatially random potentials of arbitrary strength, the stochastic mean-field approximation is employed. When the strength of disorder increases, the extended Bose-Einstein condensate fragments into spatially disconnected regions, forming a granular condensate. Increasing the strength of disorder even more transforms the granular condensate into the normal glass. The influence of time-dependent external potentials is also discussed. Fastly varying temporal potentials, to some extent, imitate the action of spatially random potentials. In particular, strong time-alternating potential can induce the appearance of a nonequilibrium granular condensate.