Inaugural BMC Ecology and Evolution image competition: the winning images

The inaugural BMC Ecology and Evolution image competition attracted entries from talented ecologists and evolutionary biologists worldwide. Together, these photos beautifully capture biodiversity, how it arose and why we should conserve it. This editorial celebrates the winning images as selected by the Editor of BMC Ecology and Evolution and senior members of the journal’s editorial board

Support for public provision of a private good with top-up and opt-out: A controlled laboratory experiment

This paper presents the results of a revealed-choice experiment testing the theoretical predictions of political economy models regarding public support for a publicly provided private good financed with proportional income taxes when individuals can purchase the good privately and either continue to consume public provision (‘top-up’) or forego public provision (‘opt-out’), but in each case continue to pay income taxes. Our laboratory results confirm behavior is consistent with the predicted majority-preferred tax rate under mixed financing with top-up, but we identify preferences for significantly higher rates of public provision than predicted under mixed financing with opt-out. Using non parametric regression analysis, we explore the relationship between individuals’ top-up and opt-out decisions and both their income levels and the implemented tax rates

Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots

<p>Abstract</p> <p>Background</p> <p>An important and yet rather neglected question related to bioinformatics predictions is the estimation of the amount of data that is needed to allow reliable predictions. Bioinformatics predictions are usually validated through a series of figures of merit, like for example sensitivity and precision, and little attention is paid to the fact that their performance may depend on the amount of data used to make the predictions themselves.</p> <p>Results</p> <p>Here I describe a tool, named Fragmented Prediction Performance Plot (FPPP), which monitors the relationship between the prediction reliability and the amount of information underling the prediction themselves. Three examples of FPPPs are presented to illustrate their principal features. In one example, the reliability becomes independent, over a certain threshold, of the amount of data used to predict protein features and the intrinsic reliability of the predictor can be estimated. In the other two cases, on the contrary, the reliability strongly depends on the amount of data used to make the predictions and, thus, the intrinsic reliability of the two predictors cannot be determined. Only in the first example it is thus possible to fully quantify the prediction performance.</p> <p>Conclusion</p> <p>It is thus highly advisable to use FPPPs to determine the performance of any new bioinformatics prediction protocol, in order to fully quantify its prediction power and to allow comparisons between two or more predictors based on different types of data.</p

Canada and The Marshall Plan, June — December 1947

La position et les réactions du Canada au début des discussions du Plan Marshall furent typiques des principales caractéristiques des relations canado-américaines durant l'après-guerre : accommodement des intérêts politiques des Etats-Unis et des intérêts économiques canadiens. Malgré des plans de restriction des importations américaines au Canada afin de réaliser une meilleure balance commerciale, le Canada se montra prêt à proposer un tarif moins discriminatoire en échange d'une réduction du tarif américain et d'une participation au bénéfices du plan Marshall. Lorsque le Congrès américain accepta que des denrées puissent être exportées d'en dehors des Etats-Unis jusqu'à concurrence de 25% des crédits alloués pour le plan, le Canada se vit assuré d'un débouché important pour certaines des ses exportations

Ontogenetic changes in the body plan of the sauropodomorph dinosaur Mussaurus patagonicus reveal shifts of locomotor stance during growth

Ontogenetic information is crucial to understand life histories and represents a true challenge in dinosaurs due to the scarcity of growth series available. Mussaurus patagonicus was a sauropodomorph dinosaur close to the origin of Sauropoda known from hatchling, juvenile and mature specimens, providing a sufficiently complete ontogenetic series to reconstruct general patterns of ontogeny. Here, in order to quantify how body shape and its relationship with locomotor stance (quadruped/biped) changed in ontogeny, hatchling, juvenile (~1 year old) and adult (8+ years old) individuals were studied using digital models. Our results show that Mussaurus rapidly grew from about 60 g at hatching to ~7 kg at one year old, reaching >1000 kg at adulthood. During this time, the body’s centre of mass moved from a position in the mid-thorax to a more caudal position nearer to the pelvis. We infer that these changes of body shape and centre of mass reflect a shift from quadrupedalism to bipedalism occurred early in ontogeny in Mussaurus. Our study indicates that relative development of the tail and neck was more influential in determining the locomotor stance in Sauropodomorpha during ontogeny, challenging previous studies, which have emphasized the influence of hindlimb vs. forelimb lengths on sauropodomorph stance

Structural and electronic properties of Pb1-xCdxTe and Pb1-xMnxTe ternary alloys

A systematic theoretical study of two PbTe-based ternary alloys, Pb1-xCdxTe and Pb1-xMnxTe, is reported. First, using ab initio methods we study the stability of the crystal structure of CdTe - PbTe solid solutions, to predict the composition for which rock-salt structure of PbTe changes into zinc-blende structure of CdTe. The dependence of the lattice parameter on Cd (Mn) content x in the mixed crystals is studied by the same methods. The obtained decrease of the lattice constant with x agrees with what is observed in both alloys. The band structures of PbTe-based ternary compounds are calculated within a tight-binding approach. To describe correctly the constituent materials new tight-binding parameterizations for PbTe and MnTe bulk crystals as well as a tight-binding description of rock-salt CdTe are proposed. For both studied ternary alloys, the calculated band gap in the L point increases with x, in qualitative agreement with photoluminescence measurements in the infrared. The results show also that in p-type Pb1-xCdxTe and Pb1-xMnxTe mixed crystals an enhancement of thermoelectrical power can be expected.Comment: 10 pages, 13 figures, submitted to Physical Review

Status and trends of the fish community in the Flemish Cap (NAFO Div. 3M) bioregion

This report summarizes fish community trends for the Flemish Cap (NAFO Div. 3M) based on European Union summer trawl research vessel surveys between 1988 and 2018. Species were classified into eight functional groups and trends were described using biomass indices, biomass and abundance anomalies, and fish size (Biomass/Abundance Ratio) anomalies. In 2003, a replacement of the research vessel allowed extending the depth coverage of the survey from 700m to 1400m. The vessel change had an impact on survey catchability, so to account for it conversion factors were applied. Considering the change in depth coverage, trends were examined for 1988-2018 with data up to 700m, and for 2004-2018 with data up to 1400m. Fish community trends were similar between the two datasets, but the analyses including deeper waters showed a comparatively higher levels of benthivores, reflecting the changes in community structure with depth. Generally speaking, trends in average fish size as tracked by the Biomass/Abundance Ratio appeared driven by recruitment, where general declines in abundance and absences of good recruitments got reflected in increases of this ratio. Biomass of plankpiscivores (mostly Sebastes sp.) experienced a sharp increase in the early 2000s but then returned to levels comparable to the 1990s. Piscivores biomass showed a strong decline in the early 1990s due to the collapse of cod but has since shown signs of recovery. Shellfish, driven by northern shrimp, saw a sustained increase in biomass from the early 1990s until 2002, when started a decline that has persisted until 2018. The biomass of large benthivores decline in the late 1990s and remains low to this date

Control of human cytomegalovirus replication by liver resident natural killer cells

Natural killer cells are considered to be important for control of human cytomegalovirus– a major pathogen in immune suppressed transplant patients. Viral infection promotes the development of an adaptive phenotype in circulating natural killer cells that changes their anti-viral function. In contrast, less is understood how natural killer cells that reside in tissue respond to viral infection. Here we show natural killer cells resident in the liver have an altered phenotype in cytomegalovirus infected individuals and display increased anti-viral activity against multiple viruses in vitro and identify and characterise a subset of natural killer cells responsible for control. Crucially, livers containing natural killer cells with better capacity to control cytomegalovirus replication in vitro are less likely to experience viraemia post-transplant. Taken together, these data suggest that virally induced expansion of tissue resident natural killer cells in the donor organ can reduce the chance of viraemia post-transplant

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

CATH version 3.3 (class, architecture, topology, homology) contains 128 688 domains, 2386 homologous superfamilies and 1233 fold groups, and reflects a major focus on classifying structural genomics (SG) structures and transmembrane proteins, both of which are likely to add structural novelty to the database and therefore increase the coverage of protein fold space within CATH. For CATH version 3.4 we have significantly improved the presentation of sequence information and associated functional information for CATH superfamilies. The CATH superfamily pages now reflect both the functional and structural diversity within the superfamily and include structural alignments of close and distant relatives within the superfamily, annotated with functional information and details of conserved residues. A significantly more efficient search function for CATH has been established by implementing the search server Solr (http://lucene.apache.org/solr/). The CATH v3.4 webpages have been built using the Catalyst web framework