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Public natures : evolutionary infrastructures
\"As elements of the constructed landscape, infrastructure is a means rather than an end--rail and subway lines, distribution grids, waterways, traffic signals and signs, on-and-off ramps, highways, and bridges of our cities are essential in a practical sense but dead in a social one. They create boundaries and perform as agents of separation, preventing one metropolis from physically connecting with another. But their very physical presence may reveal latent qualities of places that are key to vitalizing urban life, and by leveraging that presence to support a broader range of ecological, institutional, and cultural imperatives, these utilitarian structures could transcend their pragmatic roles and become points of meaningful public exchange. In Public Natures: Evolutionary Infrastructures, New York City-based firm Weiss/Manfredi tests such a possibility and takes the pursuit to practice, in turn crafting a manifesto/monograph hybrid replete with essays, roundtable discussions, and projects that explore new obligations and opportunities for infrastructure\"-- Provided by publisher.
Book
Splitting the chains: ultra-basal insulin analog uncovers a redox mechanism of hormone clearance
Reporting in
Nature Communications
, Kjeldsen and colleagues describe a redox mechanism of insulin clearance based on separation of A- and B chains. Exploiting an ultra-long-acting analog protected from classical clearance pathways, the study highlights principles of protein stability in pharmacology.
Journal Article
Sebacinales – one thousand and one interactions with land plants
Root endophytism and mycorrhizal associations are complex derived traits in fungi that shape plant physiology. Sebacinales (Agaricomycetes, Basidiomycota) display highly diverse interactions with plants. Although early-diverging Sebacinales lineages are root endophytes and/or have saprotrophic abilities, several more derived clades harbour obligate biotrophs forming mycorrhizal associations. Sebacinales thus display transitions from saprotrophy to endophytism and to mycorrhizal nutrition within one fungal order. This review discusses the genomic traits possibly associated with these transitions. We also show how molecular ecology revealed the hyperdiversity of Sebacinales and their evolutionary diversification into two sister families: Sebacinaceae encompasses mainly ectomycorrhizal and early-diverging saprotrophic species; the second family includes endophytes and lineages that repeatedly evolved ericoid, orchid and ectomycorrhizal abilities.Wepropose the name Serendipitaceae for this family and, within it, we transfer to the genus Serendipita the endophytic cultivable species Piriformospora indica and P. williamsii. Such cultivable Serendipitaceae species provide excellent models for root endophytism, especially because of available genomes, genetic tractability, and broad host plant range including important crop plants and the model plant Arabidopsis thaliana. We review insights gained with endophytic Serendipitaceae species into the molecular mechanisms of endophytism and of beneficial effects on host plants, including enhanced resistance to abiotic and pathogen stress.
Journal Article
Comparison of Bayesian and frequentist methods for prevalence estimation under misclassification
Background
Various methods exist for statistical inference about a prevalence that consider misclassifications due to an imperfect diagnostic test. However, traditional methods are known to suffer from truncation of the prevalence estimate and the confidence intervals constructed around the point estimate, as well as from under-performance of the confidence intervals’ coverage.
Methods
In this study, we used simulated data sets to validate a Bayesian prevalence estimation method and compare its performance to frequentist methods, i.e. the Rogan-Gladen estimate for prevalence,
RGE
, in combination with several methods of confidence interval construction. Our performance measures are (i) error distribution of the point estimate against the simulated true prevalence and (ii) coverage and length of the confidence interval, or credible interval in the case of the Bayesian method.
Results
Across all data sets, the Bayesian point estimate and the
RGE
produced similar error distributions with slight advantages of the former over the latter. In addition, the Bayesian estimate did not suffer from the
RGE
’s truncation problem at zero or unity. With respect to coverage performance of the confidence and credible intervals, all of the traditional frequentist methods exhibited strong under-coverage, whereas the Bayesian credible interval as well as a newly developed frequentist method by Lang and Reiczigel performed as desired, with the Bayesian method having a very slight advantage in terms of interval length.
Conclusion
The Bayesian prevalence estimation method should be prefered over traditional frequentist methods. An acceptable alternative is to combine the Rogan-Gladen point estimate with the Lang-Reiczigel confidence interval.
Journal Article
The evolution of menopause in toothed whales
Understanding how and why menopause has evolved is a long-standing challenge across disciplines. Females can typically maximize their reproductive success by reproducing for the whole of their adult life. In humans, however, women cease reproduction several decades before the end of their natural lifespan
1
,
2
. Although progress has been made in understanding the adaptive value of menopause in humans
3
,
4
, the generality of these findings remains unclear. Toothed whales are the only mammal taxon in which menopause has evolved several times
5
, providing a unique opportunity to test the theories of how and why menopause evolves in a comparative context. Here, we assemble and analyse a comparative database to test competing evolutionary hypotheses. We find that menopause evolved in toothed whales by females extending their lifespan without increasing their reproductive lifespan, as predicted by the ‘live-long’ hypotheses. We further show that menopause results in females increasing their opportunity for intergenerational help by increasing their lifespan overlap with their grandoffspring and offspring without increasing their reproductive overlap with their daughters. Our results provide an informative comparison for the evolution of human life history and demonstrate that the same pathway that led to menopause in humans can also explain the evolution of menopause in toothed whales.
A comparative analysis tests competing evolutionary hypotheses in toothed whales in which menopause has evolved many times as females extended their overall lifespan but not their reproductive lifespan, increasing their opportunity for intergenerational help without increasing intergenerational reproductive competition.
Journal Article
BISoN: A Bayesian framework for inference of social networks
Animal social networks are often constructed from point estimates of edge weights. In many contexts, edge weights are inferred from observational data, and the uncertainty around estimates can be affected by various factors. Though this has been acknowledged in previous work, methods that explicitly quantify uncertainty in edge weights have not yet been widely adopted and remain undeveloped for many common types of data. Furthermore, existing methods are unable to cope with some of the complexities often found in observational data, and do not propagate uncertainty in edge weights to subsequent statistical analyses. We introduce a unified Bayesian framework for modelling social networks based on observational data. This framework, which we call BISoN, can accommodate many common types of observational social data, can capture confounds and model effects at the level of observations and is fully compatible with popular methods used in social network analysis. We show how the framework can be applied to common types of data and how various types of downstream statistical analyses can be performed, including non‐random association tests and regressions on network properties. Our framework opens up the opportunity to test new types of hypotheses, make full use of observational datasets, and increase the reliability of scientific inferences. We have made both an R package and example R scripts available to enable adoption of the framework.
Journal Article