Using strong conflicts to detect quality issues in component-based complex systems

The mainstream adoption of free and open source software (FOSS) has widely popularised notions like software packages or plugins, maintained in a distributed fashion and evolving at a very quick pace. Each of these components is equipped with metadata, such as dependencies, which define the other components it needs to function properly, and the incompatible components it cannot work with. In this paper, we introduce the notion of strong conflicts, defined from the component dependencies, that can be effectively computed. It gives important insights on the quality issues faced when adding or upgrading components in a given component repository, which is one of the facets of the predictable assembly problem.Our work contains concrete examples drawn from the world of GNU/Linux distributions, that validate the proposed approach. It also shows that the measures defined can be easily applied to the Eclipse world, or to any other coarse-grained software component model

Optimal and Automated Deployment for Microservices

Microservices are highly modular and scalable Service Oriented Architectures. They underpin automated deployment practices like Continuous Deployment and Autoscaling. In this paper, we formalize these practices and show that automated deployment - proven undecidable in the general case - is algorithmically treatable for microservices. Our key assumption is that the configuration life-cycle of a microservice is split into two phases: (i) creation, which entails establishing initial connections with already available microservices, and (ii) subsequent binding/unbinding with other microservices. To illustrate the applicability of our approach, we implement an automatic optimal deployment tool and compute deployment plans for a realistic microservice architecture, modeled in the Abstract Behavioral Specification (ABS) language

Recording electrical activity from the brain of behaving octopus

: Octopuses, which are among the most intelligent invertebrates,1,2,3,4 have no skeleton and eight flexible arms whose sensory and motor activities are at once autonomous and coordinated by a complex central nervous system.5,6,7,8 The octopus brain contains a very large number of neurons, organized into numerous distinct lobes, the functions of which have been proposed based largely on the results of lesioning experiments.9,10,11,12,13 In other species, linking brain activity to behavior is done by implanting electrodes and directly correlating electrical activity with observed animal behavior. However, because the octopus lacks any hard structure to which recording equipment can be anchored, and because it uses its eight flexible arms to remove any foreign object attached to the outside of its body, in vivo recording of electrical activity from untethered, behaving octopuses has thus far not been possible. Here, we describe a novel technique for inserting a portable data logger into the octopus and implanting electrodes into the vertical lobe system, such that brain activity can be recorded for up to 12 h from unanesthetized, untethered octopuses and can be synchronized with simultaneous video recordings of behavior. In the brain activity, we identified several distinct patterns that appeared consistently in all animals. While some resemble activity patterns in mammalian neural tissue, others, such as episodes of 2 Hz, large amplitude oscillations, have not been reported. By providing an experimental platform for recording brain activity in behaving octopuses, our study is a critical step toward understanding how the brain controls behavior in these remarkable animals

Archiving and referencing source code with Software Heritage

Software, and software source code in particular, is widely used in modern research. It must be properly archived, referenced, described and cited in order to build a stable and long lasting corpus of scientic knowledge. In this article we show how the Software Heritage universal source code archive provides a means to fully address the first two concerns, by archiving seamlessly all publicly available software source code, and by providing intrinsic persistent identifiers that allow to reference it at various granularities in a way that is at the same time convenient and effective. We call upon the research community to adopt widely this approach.Comment: arXiv admin note: substantial text overlap with arXiv:1909.1076

MicroRNAs are deeply linked to the emergence of the complex octopus brain

Soft-bodied cephalopods such as octopuses are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their nervous tissues, we hypothesized that RNA regulation may play a major role in the cognitive success of this group. We thus profiled messenger RNAs and small RNAs in three cephalopod species including 18 tissues of the Octopus vulgaris. We show that the major RNA innovation of soft-bodied cephalopods is an expansion of the microRNA (miRNA) gene repertoire. These evolutionarily novel miRNAs were primarily expressed in adult neuronal tissues and during the development and had conserved and thus likely functional target sites. The only comparable miRNA expansions happened, notably, in vertebrates. Thus, we propose that miRNAs are intimately linked to the evolution of complex animal brains

Identification and Characterization of a Rhodopsin Kinase Gene in the Suckers of Octopus vulgaris: Looking around Using Arms?

In their foraging behavior octopuses rely on arm search movements outside the visual field of the eyes. In these movements the environment is explored primarily by the suckers that line the entire length of the octopus arm. In this study, for the first time, we report the complete characterization of a light-sensing molecule, Ov-GRK1, in the suckers, skin and retina of Octopus vulgaris. We sequenced the O. vulgaris GRK1 gene, defining a phylogenetic tree and performing a 3D structure model prediction. Furthermore, we found differences in relative mRNA expression in different sucker types at several arm levels, and localized it through in situ hybridization. Our findings suggest that the suckers in octopus arms are much more multimodal than was previously shown, adding the potential for light sensing to the already known mechanical and chemical sensing abilities

MicroRNAs are deeply linked to the emergence of the complex octopus brain

Soft-bodied cephalopods such as octopuses are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their nervous tissues, we hypothesized that RNA regulation may play a major role in the cognitive success of this group. We thus profiled messenger RNAs and small RNAs in three cephalopod species including 18 tissues of the (Octopus vulgaris). We show that the major RNA innovation of soft-bodied cephalopods is an expansion of the microRNA (miRNA) gene repertoire. These evolutionarily novel miRNAs were primarily expressed in adult neuronal tissues and during the development and had conserved and thus likely functional target sites. The only comparable miRNA expansions happened, notably, in vertebrates. Thus, we propose that miRNAs are intimately linked to the evolution of complex animal brains

Multi-proxy dating the ‘Millennium Eruption’ of Changbaishan to late 946 CE

Ranking among the largest volcanic eruptions of the Common Era (CE), the ‘Millennium Eruption’ of Changbaishan produced a widely-dispersed tephra layer (known as the B-Tm ash), which represents an important tie point for palaeoenvironmental studies in East Asia. Hitherto, there has been no consensus on its age, with estimates spanning at least the tenth century CE. Here, we identify the cosmogenic radiocarbon signal of 775 CE in a subfossil larch engulfed and killed by pyroclastic currents emplaced during the initial rhyolitic phase of the explosive eruption. Combined with glaciochemical evidence from Greenland, this enables us to date the eruption to late 946 CE. This secure date rules out the possibility that the Millennium Eruption contributed to the collapse of the Bohai Kingdom (Manchuria/Korea) in 926 CE, as has previously been hypothesised. Further, despite the magnitude of the eruption, we do not see a consequent cooling signal in tree-ring-based reconstructions of Northern Hemisphere summer temperatures. A tightly-constrained date for the Millennium Eruption improves the prospect for further investigations of historical sources that may shed light on the eruption's impacts, and enhances the value of the B-Tm ash as a chronostratigraphic marker.Ranking among the largest volcanic eruptions of the Common Era (CE), the ‘Millennium Eruption’ of Changbaishan produced a widely-dispersed tephra layer (known as the B-Tm ash), which represents an important tie point for palaeoenvironmental studies in East Asia. Hitherto, there has been no consensus on its age, with estimates spanning at least the tenth century CE. Here, we identify the cosmogenic radiocarbon signal of 775 CE in a subfossil larch engulfed and killed by pyroclastic currents emplaced during the initial rhyolitic phase of the explosive eruption. Combined with glaciochemical evidence from Greenland, this enables us to date the eruption to late 946 CE. This secure date rules out the possibility that the Millennium Eruption contributed to the collapse of the Bohai Kingdom (Manchuria/Korea) in 926 CE, as has previously been hypothesised. Further, despite the magnitude of the eruption, we do not see a consequent cooling signal in tree-ring-based reconstructions of Northern Hemisphere summer temperatures. A tightly-constrained date for the Millennium Eruption improves the prospect for further investigations of historical sources that may shed light on the eruption's impacts, and enhances the value of the B-Tm ash as a chronostratigraphic marker