Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo

The rate at which a given site in a gene sequence alignment evolves over time may vary. This phenomenon-known as heterotachy-can bias or distort phylogenetic trees inferred from models of sequence evolution that assume rates of evolution are constant. Here, we describe a phylogenetic mixture model designed to accommodate heterotachy. The method sums the likelihood of the data at each site over more than one set of branch lengths on the same tree topology. A branch-length set that is best for one site may differ from the branch-length set that is best for some other site, thereby allowing different sites to have different rates of change throughout the tree. Because rate variation may not be present in all branches, we use a reversible-jump Markov chain Monte Carlo algorithm to identify those branches in which reliable amounts of heterotachy occur. We implement the method in combination with our 'pattern-heterogeneity' mixture model, applying it to simulated data and five published datasets. We find that complex evolutionary signals of heterotachy are routinely present over and above variation in the rate or pattern of evolution across sites, that the reversible-jump method requires far fewer parameters than conventional mixture models to describe it, and serves to identify the regions of the tree in which heterotachy is most pronounced. The reversible-jump procedure also removes the need for a posteriori tests of 'significance' such as the Akaike or Bayesian information criterion tests, or Bayes factors. Heterotachy has important consequences for the correct reconstruction of phylogenies as well as for tests of hypotheses that rely on accurate branch-length information. These include molecular clocks, analyses of tempo and mode of evolution, comparative studies and ancestral state reconstruction. The model is available from the authors' website, and can be used for the analysis of both nucleotide and morphological data.

Dynamics of QoI sensitivity in Mycosphaerella fijiensis in Costa Rica during 2000 to 2003

From 1997 onward, the strobilurin fungicide azoxystrobin was widely used in the main banana-production zone in Costa Rica against Mycosphaerella fijiensis var. difformis causing black Sigatoka of banana. By 2000, isolates of M. fijiensis with resistance to the quinolene oxidase inhibitor fungicides were common on some farms in the area. The cause was a single point mutation from glycine to alanine in the fungal target protein, cytochrome b gene. An amplification refractory mutation system Scorpion quantitative polymerase chain reaction assay was developed and used to determine the frequency of G 143A allele in samples of M. fijiensis. Two hierarchical surveys of spatial variability, in 2001 and 2002,found no significant variation in frequency on spatial scales <10 in. This allowed the frequency of G143A alleles on a farm to be estimated efficiently by averaging single samples taken at two fixed locations. The frequency of G 143A allele in bulk samples from I I farms throughout Costa Rica was determined at 2-month intervals. There was no direct relationship between the number of spray applications and the frequency of G143A on individual farms. Instead, the frequency converged toward regional averages, presumably due to the large-scale mixing of ascospores dispersed by wind. Using trap plants in an area remote from the main producing area, immigration of resistant ascospores was detected as far as 6 km away both with and against the prevailing wind.

Platelet PECAM-1 inhibits thrombus formation in vivo

Platelet endothelial cell adhesion molecule-1 (PECAM-1) is a cell surface glycoprotein receptor expressed on a range of blood cells, including platelets, and on vascular endothelial cells. PECAM-1 possesses adhesive and signaling properties, the latter being mediated by immunoreceptor tyrosine-based inhibitory motifs present on the cytoplasmic tail of the protein. Recent studies in vitro have demonstrated that PECAM-1 signaling inhibits the aggregation of platelets. In the present study we have used PECAM-1-deficient mice and radiation chimeras to investigate the function of this receptor in the regulation of thrombus formation. Using intravital microscopy and laser-induced injury to cremaster muscle arterioles, we show that thrombi formed in PECAM-1-deficient mice were larger, formed more rapidly than in control mice, and were more stable. Larger thrombi were also formed in control mice that received transplants of PECAM-1-deficient bone marrow, in comparison to mice that received control transplants. A ferric chloride model of thrombosis was used to investigate thrombus formation in carotid arteries. In PECAM-1-deficient mice the time to 75% vessel occlusion was significantly shorter than in control mice. These data provide evidence for the involvement of platelet PECAM-1 in the negative regulation of thrombus formation.

A decade of research and development in disability, virtual reality and associated technologies: review of ICDVRAT 1996−2006

The International Conference (series) on Disability, Virtual Reality and Associated Technologies (ICDVRAT) this year held its sixth biennial conference, celebrating ten years of research and development in this field. A total of 220 papers have been presented at the first six conferences, addressing potential, development, exploration and examination of how these technologies can be applied in disabilities research and practice. The research community is broad and multi-disciplined, comprising a variety of scientific and medical researchers, rehabilitation therapists, educators and practitioners. Likewise, technologies, their applications and target user populations are also broad, ranging from sensors positioned on real world objects to fully immersive interactive simulated environments. A common factor is the desire to identify what the technologies have to offer and how they can provide added value to existing methods of assessment, rehabilitation and support for individuals with disabilities. This paper presents a brief review of the first decade of research and development in the ICDVRAT community, defining technologies, applications and target user populations served.

Antoine de La Sale's 'La Sale': the cannonball and the prince's head

The elderly tutor La Sale's didactic treatise for his charges (dated 1451) includes an eye-witness account of the siege of Anjou-held Naples by the Aragonese in 1438. It narrates the accidental death (or miracle, depending on the perspective of the chroniclers) of the infante Pedro of Castille, brother of King Alfonso the Magnanimous of Aragon. This article explores how "La Sale", an adapted version of the Middle French translation of Valerius Maximus's 'Facta et dicta memorabilia', frames and skews the anecdote towards an exploration of the reliability and authority of the tutor-narrator.

Reliability, sufficiency, and the decomposition of proper scores

Scoring rules are an important tool for evaluating the performance of probabilistic forecasting schemes. A scoring rule is called strictly proper if its expectation is optimal if and only if the forecast probability represents the true distribution of the target. In the binary case, strictly proper scoring rules allow for a decomposition into terms related to the resolution and the reliability of a forecast. This fact is particularly well known for the Brier Score. In this article, this result is extended to forecasts for finite-valued targets. Both resolution and reliability are shown to have a positive effect on the score. It is demonstrated that resolution and reliability are directly related to forecast attributes that are desirable on grounds independent of the notion of scores. This finding can be considered an epistemological justification of measuring forecast quality by proper scoring rules. A link is provided to the original work of DeGroot and Fienberg, extending their concepts of sufficiency and refinement. The relation to the conjectured sharpness principle of Gneiting, et al., is elucidated.

Identifying uncertainties in Arctic climate change projections

Wide ranging climate changes are expected in the Arctic by the end of the 21st century, but projections of the size of these changes vary widely across current global climate models. This variation represents a large source of uncertainty in our understanding of the evolution of Arctic climate. Here we systematically quantify and assess the model uncertainty in Arctic climate changes in two CO2 doubling experiments: a multimodel ensemble (CMIP3) and an ensemble constructed using a single model (HadCM3) with multiple parameter perturbations (THC-QUMP). These two ensembles allow us to assess the contribution that both structural and parameter variations across models make to the total uncertainty and to begin to attribute sources of uncertainty in projected changes. We find that parameter uncertainty is an major source of uncertainty in certain aspects of Arctic climate. But also that uncertainties in the mean climate state in the 20th century, most notably in the northward Atlantic ocean heat transport and Arctic sea ice volume, are a significant source of uncertainty for projections of future Arctic change. We suggest that better observational constraints on these quantities will lead to significant improvements in the precision of projections of future Arctic climate change.

The DACCIWA project: dynamics-aerosol-chemistry-cloud interactions in West Africa

Massive economic and population growth, and urbanization are expected to lead to a tripling of anthropogenic emissions in southern West Africa (SWA) between 2000 and 2030. However, the impacts of this on human health, ecosystems, food security, and the regional climate are largely unknown. An integrated assessment is challenging due to (a) a superposition of regional effects with global climate change, (b) a strong dependence on the variable West African monsoon, (c) incomplete scientific understanding of interactions between emissions, clouds, radiation, precipitation, and regional circulations, and (d) a lack of observations. This article provides an overview of the DACCIWA (Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa) project. DACCIWA will conduct extensive fieldwork in SWA to collect high-quality observations, spanning the entire process chain from surface-based natural and anthropogenic emissions to impacts on health, ecosystems, and climate. Combining the resulting benchmark dataset with a wide range of modeling activities will allow (a) assessment of relevant physical, chemical, and biological processes, (b) improvement of the monitoring of climate and atmospheric composition from space, and (c) development of the next generation of weather and climate models capable of representing coupled cloud-aerosol interactions. The latter will ultimately contribute to reduce uncertainties in climate predictions. DACCIWA collaborates closely with operational centers, international programs, policy-makers, and users to actively guide sustainable future planning for West Africa. It is hoped that some of DACCIWA’s scientific findings and technical developments will be applicable to other monsoon regions.

Queering Philip Roth: homosocial discourse in 'An actor’s life for me', 'Letting go', 'Sabbath’s theater' and the 'American trilogy'

Much has been written on Roth’s representation of masculinity, but this critical discourse has tended to be situated within a heteronormative frame of reference, perhaps because of Roth’s popular reputation as an aggressively heterosexual, libidinous, masculinist, in some versions sexist or even misogynist author. In this essay I argue that Roth’s representation of male sexuality is more complex, ambiguous, and ambivalent than has been generally recognized. Tracing a strong thread of what I call homosocial discourse running through Roth’s oeuvre, I suggest that the series of intimate relationships with other men that many of Roth’s protagonists form are conspicuously couched in this discourse and that a recognition of this ought to reconfigure our sense of the sexual politics of Roth’s career, demonstrating in particular that masculinity in his work is too fluid and dynamic to be accommodated by the conventional binaries of heterosexual and homosexual, feminized Jew and hyper-masculine Gentile, the “ordinary sexual man” and the transgressively desiring male subject.

Mycoflora and fumonisin contamination in Brazilian sorghum from sowing to harvest

BACKGROUND: The aim of this study was to characterise the mycoflora and the presence of fumonisin in sorghum grains, correlating the results with the environment and abiotic factors. RESULTS: Fifty samples (five collections of ten samples each) of sorghum were analysed. All samples were found to be contaminated with fungi, with higher frequencies of Cladosporium spp. (61.8%) and Helminthosporium spp. (33.4%). Fusarium verticillioides was isolated from 15.1% of the samples, with 38% of them being contaminated with fumonisin B(1) (FB(1)) at levels ranging from 50 to 368.78 ng g(-1). Regarding abiotic factors, temperature, water activity and rainfall showed a positive correlation with the frequency of F. verticillioides and FB(1) production. There was a significant positive correlation between relative air humidity and FB(1) production. The results obtained from sexual crosses between standard F mating tester strains and the isolated strains confirmed that the strains isolated were F. verticillioides. CONCLUSION: It can be concluded that the decrease in F. verticillioides and fumonisin contamination occurred owing to atypical climatic factors during the period of sorghum cultivation, when there was any occurrence of rain and the level of water activity of grains did not reach 0.58. (C) 2010 Society of Chemical Industry

REIDEMEISTER TORSION AND ANALYTIC TORSION OF SPHERES

We provide a simple topological derivation of a formula for the Reidemeister and the analytic torsion of spheres.

An existence theorem for G-structure preserving affine immersions

We prove an existence result for local and global G-structure preserving affine immersions between affine manifolds. Several examples are discussed in the context of Riemannian and semi-Riemannian geometry, including the case of isometric immersions into Lie groups endowed with a left-invariant metric, and the case of isometric immersions into products of space forms.

A New Indirect Electrochemical Method for Determination of Ozone in Water Using Multiwalled Carbon Nanotubes

A new electrochemical methodology has been developed for the detection of ozone using multiwalled carbon nanotubes (MWCNT). The method presented here is based on the reaction of ozone with indigo blue dye producing anthranilic acid (ATN). The electrochemical profile of ATN on an electrode of glassy carbon (GC) modified with MWCNT showed an oxidation peak potential at 750 mV vs. Ag/AgCl. An analytical method was developed using differential pulse voltammetry (DPV) to determine ATN in a range of 50-400 nmol L(-1), with a detection limit of 9.7 nmol L(-1). Ozonated water samples were successfully analyzed by GC/MWCNT electrode and the recovery procedure yielded values between of 96.5 and 102.3%.