Multivariate relationships and spatial distribution of geochemical features of soils in Jamaica

Abstract

Concentrations of 31 chemical elements in 165 soil samples from the tropical island of Jamaica were analyzed during the island-wide soil survey. Multivariate outliers were detected and remedied for quality control of the database. Multivariate analyses including principal component analysis (PCA), cluster analysis, and analysis of variance (ANOVA), and a geographic information system (GIS) were applied to study the geochemical features of element associations and sample clusters. The results show that rare earth elements, most of the heavy metals and trace elements (including As, Al, Cd, Ce, Co, Cr, Dy, Eu, Fe, Hf, Hg, La, Lu, Mn, Pb, Sb, Sc, Sm, Th, Ti, U, V, Yb, Zn) are enriched in the bauxitic soils relative to the non-bauxitic soils, and closely correlated with one another. Negative correlations between the bauxite-enriched elements and the mobile alkali and alkaline earth elements including Ca, Sr, Mg and Na are observed, showing the opposite tendencies of enrichment of the immobile elements and leaching of the mobile elements during the soil formation processes. The halogen elements of Br and I are also relatively enriched in the bauxitic soils, but they appear to be rather affected by sea-spray. Copper has poor correlations with all the other elements, which is likely to be related to mineralization. Significantly different concentrations of the bauxite-enriched elements are observed between the bauxitic and non-bauxitic soils.     

Statistical analysis of a dynamic model for dietary contaminant exposure

This paper is devoted to the statistical analysis of a stochastic model introduced in [P. Bertail, S. Clémençon, and J. Tressou, A storage model with random release rate for modelling exposure to food contaminants, Math. Biosci. Eng. 35 (1) (2008), pp. 35–60] for describing the phenomenon of exposure to a certain food contaminant. In this modelling, the temporal evolution of the contamination exposure is entirely determined by the accumulation phenomenon due to successive dietary intakes and the pharmacokinetics governing the elimination process inbetween intakes, in such a way that the exposure dynamic through time is described as a piecewise deterministic Markov process. Paths of the contamination exposure process are scarcely observable in practice, therefore intensive computer simulation methods are crucial for estimating the time-dependent or steady-state features of the process. Here we consider simulation estimators based on consumption and contamination data and investigate how to construct accurate bootstrap confidence intervals (CI) for certain quantities of considerable importance from the epidemiology viewpoint. Special attention is also paid to the problem of computing the probability of certain rare events related to the exposure process path arising in dietary risk analysis using multilevel splitting or importance sampling (IS) techniques. Applications of these statistical methods to a collection of data sets related to dietary methyl mercury contamination are discussed thoroughly.     

A comparison of methods for estimating common vole (Microtus arvalis) abundance in agricultural habitats

Rodent outbreaks cause significant crop damages in agricultural areas worldwide, but routinely monitoring large areas at low cost remains a challenge. The common vole Microtus arvalis has recently colonized the agricultural plains of the northern Iberian Plateau, an area where it has started to produce population outbreaks with important impacts in agriculture, the environment and human health. Vole monitoring has become of prime importance to implement preventive management measures to control populations. In order to find a simple and reliable vole monitoring method to be applied in large areas, we compared abundance estimates derived from three methods: capture–mark–recapture (CMR), single capture events (SCE) and presence/absence of vole activity signs (VAS) during three seasons and on the main agricultural habitats in the study area. We show that an activity index based on the presence of fresh droppings and/or clippings had a similar performance to SCE in a large sample of plots (n = 222) across habitats and seasons. Data obtained with both methods (SCE, VAS) were also well correlated with those obtained with CMR, despite a limited sample size (n = 23 CMR plots). We suggest that the VAS method, which is a cheaper and easier alternative to trapping methods, provides a promising tool for scientists and managers to implement large scale monitoring of common vole in agricultural areas.     

A cautionary note on Bayesian estimation of population size by removal sampling with diffuse priors

We consider the problem of estimating a population size by removal sampling when the sampling rate is unknown. Bayesian methods are now widespread and allow to include prior knowledge in the analysis. However, we show that Bayes estimates based on default improper priors lead to improper posteriors or infinite estimates. Similarly, weakly informative priors give unstable estimators that are sensitive to the choice of hyperparameters. By examining the likelihood, we show that population size estimates can be stabilized by penalizing small values of the sampling rate or large value of the population size. Based on theoretical results and simulation studies, we propose some recommendations on the choice of the prior. Then, we applied our results to real datasets.     

Correlates of ecological dominance within Pheidole ants (Hymenoptera: Formicidae)

1. In any group of organisms, one can almost invariably find some species that are ecologically dominant (i.e. disproportionately more abundant and widespread), whereas others are comparatively less prevalent. Understanding of the causes of variation in ecological dominance has been elusive, particularly given that dominant and subordinate species often lack obvious features that could predict their abundance in nature. 2. In this study, physiological, behavioural, morphological, and phylogenetic information is integrated in an effort to understand the mechanisms underlying ecological dominance in ants using the hyperdiverse ant genus Pheidole (Formicidae: Myrmicinae) as a model system. Field estimates of the relative abundance of 10 Pheidole species were compared with potential correlates, which included behavioural (walking velocity), physiological (tolerance to high and low temperatures and desiccation), and morphological traits (body size and degree of dimorphism in the worker caste). A molecular phylogeny of the tested species was also generated to account for potential confounding effects of phylogenetic non‐independence. 3. Dominant Pheidole species were characterised by higher environmental tolerance with respect to temperature and humidity, as well as faster walking speeds. On the other hand, no morphological correlates of ecological dominance were detected. Interestingly, subordinate species showed no evidence of trade‐off in performance, being both more fragile to environmental challenges and slower in their walking speeds. 4. These results provide important insights into the mechanisms involved in local species coexistence in Pheidole.     

New technologies in the mix: Assessing N‐mixture models for abundance estimation using automated detection data from drone surveys

1. Reliable estimates of abundance are critical in effectively managing threatened species, but the feasibility of integrating data from wildlife surveys completed using advanced technologies such as remotely piloted aircraft systems (RPAS) and machine learning into abundance estimation methods such as N‐mixture modeling is largely unknown due to the unique sources of detection errors associated with these technologies.
2. We evaluated two modeling approaches for estimating the abundance of koalas detected automatically in RPAS imagery: (a) a generalized N‐mixture model and (b) a modified Horvitz–Thompson (H‐T) estimator method combining generalized linear models and generalized additive models for overall probability of detection, false detection, and duplicate detection. The final estimates from each model were compared to the true number of koalas present as determined by telemetry‐assisted ground surveys.
3. The modified H‐T estimator approach performed best, with the true count of koalas captured within the 95% confidence intervals around the abundance estimates in all 4 surveys in the testing dataset (n = 138 detected objects), a particularly strong result given the difficulty in attaining accuracy found with previous methods.
4. The results suggested that N‐mixture models in their current form may not be the most appropriate approach to estimating the abundance of wildlife detected in RPAS surveys with automated detection, and accurate estimates could be made with approaches that account for spurious detections.

     

Trials, Travails and Triumphs: An Account of RNA Catalysis in RNase P

Last December marked the 20th anniversary of the Nobel Prize in Chemistry to Sidney Altman and Thomas Cech for their discovery of RNA catalysts in bacterial ribonuclease P (an enzyme catalyzing 5′ maturation of tRNAs) and a self-splicing rRNA of Tetrahymena, respectively. Coinciding with the publication of a treatise on RNase P,¹ this review provides a historical narrative, a brief report on our current knowledge, and a discussion of some research prospects on RNase P.

“…the great thing about science is that you can actually solve a problem. You can take something which is confused, a mess, and not only find a solution, but prove it's the right one.”²

-Sydney Brenner

“In research the front line is almost always in a fog.”³

-Francis Crick

     

The Mechanism of l-Canavanine Cytotoxicity: Arginyl tRNA Synthetase as a Novel Target for Anticancer Drug Discovery

There is a clear need for agents with novel mechanisms of action to provide new therapeutic approaches for the treatment of pancreatic cancer. Owing to its structural similarity to l-arginine, l-canavanine, the δ-oxa-analog of l-arginine, is a substrate for arginyl tRNA synthetase and is incorporated into nascent proteins in place of l-arginine. Although l-arginine and l-canavanine are structurally similar, the oxyguanidino group of l-canavanine is significantly less basic than the guanidino group of l-arginine. Consequently, l-canavanyl proteins lack the capacity to form crucial ionic interactions, resulting in altered protein structure and function, which leads to cellular death. Since l-canavanine is selectively sequestered by the pancreas, it may be especially useful as an adjuvant therapy in the treatment of pancreatic cancer. This novel mechanism of cytotoxicity forms the basis for the anticancer activity of l-canavanine and thus, arginyl tRNA synthetase may represent a novel target for the development of such therapeutic agents.