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

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

Isomorphisms of types in the presence of higher-order references (extended version)

We investigate the problem of type isomorphisms in the presence of higher-order references. We first introduce a finitary programming language with sum types and higher-order references, for which we build a fully abstract games model following the work of Abramsky, Honda and McCusker. Solving an open problem by Laurent, we show that two finitely branching arenas are isomorphic if and only if they are geometrically the same, up to renaming of moves (Laurent's forest isomorphism). We deduce from this an equational theory characterizing isomorphisms of types in our language. We show however that Laurent's conjecture does not hold on infinitely branching arenas, yielding new non-trivial type isomorphisms in a variant of our language with natural numbers

A Serum Resistin and Multicytokine Inflammatory Pathway Is Linked With and Helps Predict All-cause Death in Diabetes

Context: Type 2 diabetes (T2D) shows a high mortality rate, partly mediated by atherosclerotic plaque instability. Discovering novel biomarkers may help identify high-risk patients who would benefit from more aggressive and specific managements. We recently described a serum resistin and multicytokine inflammatory pathway (REMAP), including resistin, interleukin (IL)-1 beta, IL-6, IL-8, and TNF-alpha, that is associated with cardiovascular disease.Objective: We investigated whether REMAP is associated with and improves the prediction of mortality in T2D.Methods: A REMAP score was investigated in 3 cohorts comprising 1528 patients with T2D (409 incident deaths) and in 59 patients who underwent carotid endarterectomy (CEA; 24 deaths). Plaques were classified as unstable/stable according to the modified American Heart Association atherosclerosis classification.Results: REMAP was associated with all-cause mortality in each cohort and in all 1528 individuals (fully adjusted hazard ratio [HR] for 1 SD increase=1.34, P<.001). In CEA patients, REMAP was associated with mortality (HR=1.64, P=.04) and a modest change was observed when plaque stability was taken into account (HR=1.58; P=.07). REMAP improved discrimination and reclassification measures of both Estimation of Mortality Risk in Type 2 Diabetic Patients and Risk Equations for Complications of Type 2 Diabetes, well-established prediction models of mortality in T2D (P<.05-<.001).Conclusion: REMAP is independently associated with and improves predict all-cause mortality in T2D; it can therefore be used to identify high-risk individuals to be targeted with more aggressive management. Whether REMAP can also identify patients who are more responsive to IL-6 and IL-1 beta monoclonal antibodies that reduce cardiovascular burden and total mortality is an intriguing possibility to be tested

La création du nouveau type de dépôt scientifique - Le logiciel

International audienceLes logiciels sont devenus le support indissociable des connaissances techniques et scientifiques de l'humanité tout entière. Ils constituent un véritable socle pour les sciences. La préservation des logiciels est à la base de la reproductibilité. L'utilisation des logiciels intervient à toutes les étapes de la recherche, dans tous les domaines scientifiques, et se révèle essentielle à de multiples égards. La collaboration entre Software Heritage (SWH), Hal-Inria et le CCSD a permis l'ouverture de Hal vers le nouveau type de données scientifiques: le logiciel

Urine Proteome Analysis May Allow Noninvasive Differential Diagnosis of Diabetic Nephropathy

AbstractObjective: Chronic renal insufficiency and/or proteinuria in type 2 diabetes may stem from chronic renal diseases (CKD) other than classic diabetic nephropathy (DN) in over one third of cases. We interrogated urine proteomic profiles generated by SELDI-TOF/MS with the aim to isolate a set of biomarkers able to reliably identify biopsy-proven DN and to establish a stringent correlation with the different patterns of renal injury. Research design and methods: Ten mug urine proteins from 190 subjects [20 healthy subjects (HS), 20 normoalbuminuric (NAD) and 18 microalbuminuric (MICRO) diabetic patients, and 132 patients with biopsy-proven nephropathy (65 DN, 10 diabetics with non-diabetic CKD (nd-CKD) and 57 non-diabetic patients with CKD)] were run by CM10 ProteinChip array and analysed by supervised learning methods (CART analysis). Results: The classification model correctly identified 75% NAD, 87.5% MICRO and 87.5% DN when applied to a blinded testing set. Most importantly, it was able to reliably differentiate DN from nd-CKD in both diabetic and non-diabetic patients. Among the best predictors of the classification model, we identified and validated 2 proteins, ubiquitin and ss2-microglobulin. Conclusions: Our data suggest the presence of a specific urine proteomic signature able to reliably identify type 2 diabetic patients with diabetic glomerulosclerosis

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