Tabling as a Library with Delimited Control

Tabling is probably the most widely studied extension of Prolog. But despite its importance and practicality, tabling is not implemented by most Prolog systems. Existing approaches require substantial changes to the Prolog engine, which is an investment out of reach of most systems. To enable more widespread adoption, we present a new implementation of tabling in under 600 lines of Prolog code. Our lightweight approach relies on delimited control and provides reasonable performance.Comment: 15 pages. To appear in Theory and Practice of Logic Programming (TPLP), Proceedings of ICLP 201

Trait evolution and historical biogeography shape assemblages of annual killifish

International audienceAim: Different species assemblages of annual killifish possess replicated body size distributions yet have unique sets of species in each area of endemism. Here, we use models of trait evolution and historical biogeography to discover how size variation originated and has been restructured.Location: South America.Taxon: Austrolebias (Cyprinodontiformes).Methods: We sampled 63 individuals from 26 Austrolebias species. Using phylogenetic trees (BEAST2), data on environmental variables at sampling locations and size data, we compare different models for trait evolution (SURFACE, l1OU) of body size and niche traits. We model the historical biogeography of the areas of endemism (BioGeoBEARS) and use both analyses in combination to reconstruct the history of four species assemblages.Results: We present new phylogenetic trees for Austrolebias and use them to show that large size principally arose within a single area driven by a shifted selection optimum for a subset of the species in that area. We suggest that ecological interactions triggered size divergence and that this large‐bodied lineage subsequently spread to two other areas. A second assemblage may have been shaped by adaptation to a new environment without an associated increase in size divergence. A third assemblage, which has the smallest size range and the most recent origin, is phylogenetically clustered, and we found no evidence of environmental filtering.Main conclusions: Assemblage similarity in Austrolebias is the result of contrasting ecological, evolutionary and historical processes. Modelling trait evolution together with historical biogeography can help to disentangle the complex histories of multispecies assemblages. This approach provides context to commonly used tests investigating the role of ecological processes from phylogenetic data and generates new testable hypotheses on the processes that generated trait diversity and assemblage similarit

Proximate causes of intraspecific variation in locomotor performance in the lizard Gallotia galloti

ABSTRACT To understand the evolution of biological traits, information on the degree and origins of intraspecific variation is essential. Because adaptation can take place only if the trait shows heritable variation, it is important to know whether (at least) part of the trait variation is genetically based. We describe intraand interindividual variation in three performance measures (sprint speed, climbing, and clambering speed) in juvenile Gallotia galloti lizards from three populations and examine how genetic, environmental (incubation temperature), and ontogenetic (age, size) effects interact to cause performance variation. Moreover, we test whether the three performance traits are intercorrelated phenotypically and genetically. Sprint speed is highest in juveniles incubated at the lowest temperature (26ЊC) irrespective of population. Climbing speed differs among populations, and the differences persist at least until the lizards are 30 wk old. This suggests that the three populations experience different selective pressures. Moreover, mass, snoutvent length, and hindlimb length seem to affect climbing performance differently in the three populations. The variation in sprinting and climbing ability appears to be genetically based. Moreover, the two performance traits are intercorrelated and thus will not evolve independently from each other. Clambering speed (i.e., capacity to climb up an inclined mesh) varies among individuals, but the origin of this variation remains obscure

Modifying Rap1-signalling by targeting Pde6δ is neuroprotective in models of Alzheimer’s disease

Background: Neuronal Ca2+ dyshomeostasis and hyperactivity play a central role in Alzheimer's disease pathology arid progression. Amyloid-beta together with non-genetic risk-factors of Alzheimer's disease contributes to increased Ca2+ influx and aberrant neuronal activity, which accelerates neurodegeneration in a feed-forward fashion. As such, identifying new targets and drugs to modulate excessive Ca2+ signalling and neuronal hyperactivity, without overly suppressing them, has promising therapeutic potential. Methods: Here we show, using biochemical, electrophysiological, imaging, and behavioural tools, that pharmacological modulation of Rap1 signalling by inhibiting its interaction with Pde6 delta normalises disease associated Ca2+ aberrations and neuronal activity, conferring neuroprotection in models of Alzheimer's disease. Results: The newly identified inhibitors of the Rap1-Pde6 delta interaction counteract AD phenotypes, by reconfiguring Rapt signalling underlying synaptic efficacy, Ca2+ influx, and neuronal repolarisation, without adverse effects in-cellulo or invivo. Thus, modulation of Rap1 by Pde6 delta accommodates key mechanisms underlying neuronal activity, and therefore represents a promising new drug target for early or late intervention in neurodegenerative disorders. Conclusion: Targeting the Pde6 delta-Rap1 interaction has promising therapeutic potential for disorders characterised by neuronal hyperactivity, such as Alzheimer's disease

Enriched biodiversity data as a resource and service

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts

Clinical characteristics of women captured by extending the definition of severe postpartum haemorrhage with 'refractoriness to treatment': a cohort study

Background: The absence of a uniform and clinically relevant definition of severe postpartum haemorrhage hampers comparative studies and optimization of clinical management. The concept of persistent postpartum haemorrhage, based on refractoriness to initial first-line treatment, was proposed as an alternative to common definitions that are either based on estimations of blood loss or transfused units of packed red blood cells (RBC). We compared characteristics and outcomes of women with severe postpartum haemorrhage captured by these three types of definitions. Methods: In this large retrospective cohort study in 61 hospitals in the Netherlands we included 1391 consecutive women with postpartum haemorrhage who received either ≥4 units of RBC or a multicomponent transfusion. Clinical characteristics and outcomes of women with severe postpartum haemorrhage defined as persistent postpartum haemorrhage were compared to definitions based on estimated blood loss or transfused units of RBC within 24 h following birth. Adverse maternal outcome was a composite of maternal mortality, hysterectomy, arterial embolisation and intensive care unit admission. Results: One thousand two hundred sixty out of 1391 women (90.6%) with postpartum haemorrhage fulfilled the definition of persistent postpartum haemorrhage. The majority, 820/1260 (65.1%), fulfilled this definition within 1 h following birth, compared to 819/1391 (58.7%) applying the definition of ≥1 L blood loss and 37/845 (4.4%) applying the definition of ≥4 units of RBC. The definition persistent postpartum haemorrhage captured 430/471 adverse maternal outcomes (91.3%), compared to 471/471 (100%) for ≥1 L blood loss and 383/471 (81.3%) for ≥4 units of RBC. Persistent postpartum haemorrhage did not capture all adverse outcomes because of missing data on timing of initial, first-line treatment. Conclusion: The definition persistent postpartum haemo

Adaptational lags during periods of environmental change

Abstract Effects of climate change can be handled by means of mitigation and adaptation. In the biological sciences, adaptations are solutions which evolved when organisms needed to match an ecological challenge. Based on Adaptive Dynamics theory, a definition is proposed of adapted states and adaptational lags applicable during periods with environmental change of any speed. Adaptation can thus be studied when it emerges from complex eco-evolutionary processes or when targets for adaptation are not defined a priori. The approach is exemplified with a model for delayed germination in an annual plant. Plasticity and maternal effects are often presumed to be adaptive and added to the model to investigate lags in these modes of trait determination. Adaptational lags can change sign and to understand their dynamics, effects of trait space boundaries and characteristics of years with large numbers of recruits had to be considered. Adaptational lags can be crucial elements of adaptive control strategies for managed ecosystems. To demonstrate their practical relevance, examples from pest management show that evolutionary adaptation has been used to infer targets of control. Adaptational lags then serve as measures of the distance to the control target and become integral elements of strategies for adaptive pest population management

Stasis and the phenotypic gambit

International audienceA recommendation – based on reviews by Katja Räsänen, Jacob Johansson and one anonymous reviewer – of the article: Coulson, T. (2020) Environmental perturbations and transitions between ecological and evolutionary equilibria: an eco-evolutionary feedback framework. bioRxiv, 509067, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/50906