On Matrices, Automata, and Double Counting

Matrix models are ubiquitous for constraint problems. Many such problems have a matrix of variables M, with the same constraint defined by a finite-state automaton A on each row of M and a global cardinality constraint gcc on each column of M. We give two methods for deriving, by double counting, necessary conditions on the cardinality variables of the gcc constraints from the automaton A. The first method yields linear necessary conditions and simple arithmetic constraints. The second method introduces the cardinality automaton, which abstracts the overall behaviour of all the row automata and can be encoded by a set of linear constraints. We evaluate the impact of our methods on a large set of nurse rostering problem instances

Revisiting the tree Constraint

International audienceThis paper revisits the tree constraint introduced in [2] which partitions the nodes of a n-nodes, m-arcs directed graph into a set of node-disjoint anti-arborescences for which only certain nodes can be tree roots. We introduce a new filtering algorithm that enforces generalized arc-consistency in O(n + m) time while the original filtering algorithm reaches O(nm) time. This result allows to tackle larger scale problems involving graph partitioning

The role of the agent's outside options in principal-agent relationships

We consider a principal-agent model of adverse selection where, in order to trade with the principal, the agent must undertake a relationship-specific investment which affects his outside option to trade, i.e. the payoff that he can obtain by trading with an alternative principal. This creates a distinction between the agent’s ex ante (before investment) and ex post (after investment) outside options to trade. We investigate the consequences of this distinction, and show that whenever an agent’s ex ante and ex post outside options differ, this may equip the principal with an additional tool for screening among different agent types, by randomizing over the probability with which trade occurs once the agent has undertaken the investment. In turn, this may enhance the efficiency of the optimal second-best contract

Estimating the Number of Solutions of Cardinality Constraints through range and roots Decompositions

International audienceThis paper introduces a systematic approach for estimating the number of solutions of cardinality constraints. A main difficulty of solutions counting on a specific constraint lies in the fact that it is, in general, at least as hard as developing the constraint and its propaga-tors, as it has been shown on alldifferent and gcc constraints. This paper introduces a probabilistic model to systematically estimate the number of solutions on a large family of cardinality constraints including alldifferent, nvalue, atmost, etc. Our approach is based on their decomposition into range and roots, and exhibits a general pattern to derive such estimates based on the edge density of the associated variable-value graph. Our theoretical result is finally implemented within the maxSD search heuristic, that aims at exploring first the area where there are likely more solutions

Profound alterations of the chromatin architecture at chromosome 11p15.5 in cells from Beckwith-Wiedemann and Silver-Russell syndromes patients

Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS) are imprinting-related disorders associated with genetic/epigenetic alterations of the 11p15.5 region, which harbours two clusters of imprinted genes (IGs). 11p15.5 IGs are regulated by the methylation status of imprinting control regions ICR1 and ICR2. 3D chromatin structure is thought to play a pivotal role in gene expression control; however, chromatin architecture models are still poorly defined in most cases, particularly for IGs. Our study aimed at elucidating 11p15.5 3D structure, via 3C and 3D FISH analyses of cell lines derived from healthy, BWS or SRS children. We found that, in healthy cells, IGF2/H19 and CDKN1C/KCNQ1OT1 domains fold in complex chromatin conformations, that facilitate the control of IGs mediated by distant enhancers. In patient-derived cell lines, we observed a profound impairment of such a chromatin architecture. Specifically, we identified a cross-talk between IGF2/H19 and CDKN1C/KCNQ1OT1 domains, consisting in in cis, monoallelic interactions, that are present in healthy cells but lost in patient cell lines: an inter-domain association that sees ICR2 move close to IGF2 on one allele, and to H19 on the other. Moreover, an intra-domain association within the CDKN1C/KCNQ1OT1 locus seems to be crucial for maintaining the 3D organization of the region

Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards

Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for “Reporting” and “Serving” data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7th Framework Programme “Ocean of Tomorrow”, and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science

Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria

Understanding the functional diversity of specific microbial groups at the global scale is critical yet poorly developed. By combining the considerable knowledge accumulated through recent years on the molecular bases of photosynthetic pigment diversity in marine Synechococcus, a major phytoplanktonic organism, with the wealth of metagenomic data provided by the Tara Oceans expedition, we have been able to reliably quantify all known pigment types along its transect and provide a global distribution map. Unexpectedly, cells able to dynamically change their pigment content to match the ambient light color were ubiquitous and predominated in many environments. Altogether, our results unveiled the role of adaptation to light quality on niche partitioning in a key primary producer

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Ocean microbes drive global-scale biogeochemical cycling, but do so under constraints imposed by viruses on host community composition, metabolism, and evolutionary trajectories. Due to sampling and cultivation challenges, genome-level viral diversity remains poorly described and grossly understudied in nature such that <1% of observed surface ocean viruses, even those that are abundant and ubiquitous, are ′known′. Here we analyze a global map of abundant, double stranded DNA (dsDNA) viruses and viral-encoded auxiliary metabolic genes (AMGs) with genomic and ecological contexts through the Global Ocean Viromes (GOV) dataset, which includes complete genomes and large genomic fragments from both surface and deep ocean viruses sampled during the Tara Oceans and Malaspina research expeditions. A total of 15,222 epi- and mesopelagic viral populations were identified that comprised 867 viral clusters (VCs, approximately genus-level groups). This roughly triples known ocean viral populations, doubles known candidate bacterial and archaeal virus genera, and near-completely samples epipelagic communities at both the population and VC level. Thirty-eight of the 867 VCs were identified as the most impactful dsDNA viral groups in the oceans, as these were locally or globally abundant and accounted together for nearly half of the viral populations in any GOV sample. Most of these were predicted in silico to infect dominant, ecologically relevant microbes, while two thirds of them represent newly described viruses that lacked any cultivated representative. Beyond these taxon-specific ecological observations, we identified 243 viral-encoded AMGs in GOV, only 95 of which were known. Deeper analyses of 4 of these AMGs revealed that abundant viruses directly manipulate sulfur and nitrogen cycling, and do so throughout the epipelagic ocean. Together these data provide a critically-needed organismal catalog and functional context to begin meaningfully integrating viruses into ecosystem models as key players in nutrient cycling and trophic networks