Consensus Needs Broadcast in Noiseless Models but can be Exponentially Easier in the Presence of Noise

Consensus and Broadcast are two fundamental problems in distributed computing, whose solutions have several applications. Intuitively, Consensus should be no harder than Broadcast, and this can be rigorously established in several models. Can Consensus be easier than Broadcast? In models that allow noiseless communication, we prove a reduction of (a suitable variant of) Broadcast to binary Consensus, that preserves the communication model and all complexity parameters such as randomness, number of rounds, communication per round, etc., while there is a loss in the success probability of the protocol. Using this reduction, we get, among other applications, the first logarithmic lower bound on the number of rounds needed to achieve Consensus in the uniform GOSSIP model on the complete graph. The lower bound is tight and, in this model, Consensus and Broadcast are equivalent. We then turn to distributed models with noisy communication channels that have been studied in the context of some bio-inspired systems. In such models, only one noisy bit is exchanged when a communication channel is established between two nodes, and so one cannot easily simulate a noiseless protocol by using error-correcting codes. An $\Omega(\epsilon^{-2} n)$ lower bound on the number of rounds needed for Broadcast is proved by Boczkowski et al. [PLOS Comp. Bio. 2018] in one such model (noisy uniform PULL, where $\epsilon$ is a parameter that measures the amount of noise). In such model, we prove a new $\Theta(\epsilon^{-2} n \log n)$ bound for Broadcast and a $\Theta(\epsilon^{-2} \log n)$ bound for binary Consensus, thus establishing an exponential gap between the number of rounds necessary for Consensus versus Broadcast

Trinets encode tree-child and level-2 phylogenetic networks

Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from triplets, that is rooted trees on three species. However, although triplets determine or encode rooted phylogenetic trees, they do not in general encode rooted phylogenetic networks, which is a potential issue for any such method. Motivated by this fact, Huber and Moulton recently introduced trinets as a natural extension of rooted triplets to networks. In particular, they showed that level-1 level-1 phylogenetic networks are encoded by their trinets, and also conjectured that all “recoverable” rooted phylogenetic networks are encoded by their trinets. Here we prove that recoverable binary level-2 networks and binary tree-child networks are also encoded by their trinets. To do this we prove two decomposition theorems based on trinets which hold for all recoverable binary rooted phylogenetic networks. Our results provide some additional evidence in support of the conjecture that trinets encode all recoverable rooted phylogenetic networks, and could also lead to new approaches to construct phylogenetic networks from trinets

Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets

Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set T of binary binets or trinets over a taxon set X, and constructing such a network whenever it exists. We show that this is NP-hard for trinets but polynomial-time solvable for binets. Moreover, we show that the problem is still polynomial-time solvable for inputs consisting of binets and trinets as long as the cycles in the trinets have size three. Finally, we present an O(3^{|X|} poly(|X|)) time algorithm for general sets of binets and trinets. The latter two algorithms generalise to instances containing level-1 networks with arbitrarily many leaves, and thus provide some of the first supernetwork algorithms for computing networks from a set of rooted 1 phylogenetic networks

RecPhyloXML: a format for reconciled gene trees.

A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc.-along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities. http://phylariane.univ-lyon1.fr/recphyloxml/

Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae)

Background: Introgressive events (e.g., hybridization, gene flow, horizontal gene transfer) and incomplete lineage sorting of ancestral polymorphisms are a challenge for phylogenetic analyses since different genes may exhibit conflicting genealogical histories. Grasses of the Triticeae tribe provide a particularly striking example of incongruence among gene trees. Previous phylogenies, mostly inferred with one gene, are in conflict for several taxon positions. Therefore, obtaining a resolved picture of relationships among genera and species of this tribe has been a challenging task. Here, we obtain the most comprehensive molecular dataset to date in Triticeae, including one chloroplastic and 26 nuclear genes. We aim to test whether it is possible to infer phylogenetic relationships in the face of (potentially) large-scale introgressive events and/or incomplete lineage sorting; to identify parts of the evolutionary history that have not evolved in a tree-like manner; and to decipher the biological causes of genetree conflicts in this tribe. Results: We obtain resolved phylogenetic hypotheses using the supermatrix and Bayesian Concordance Factors (BCF) approaches despite numerous incongruences among gene trees. These phylogenies suggest the existence of 4-5 major clades within Triticeae, with Psathyrostachys and Hordeum being the deepest genera. In addition, we construct a multigenic network that highlights parts of the Triticeae history that have not evolved in a tree-lik

Examining the effects of social media in co-located classrooms: A case study based on SpeakUp

The broad availability of mobile computing devices has prompted the apparition of social media applications that support teaching and learning. However, so far, there is conflicting evidence as to whether the benefits such applications provide in terms of engagement and interaction, outweigh their potential cost as a source of distraction. To help in clarifying these issues, the present paper presents a case study on the impact of using SpeakUp (an app aimed at promoting student participation through anonymous chatrooms) in an authentic face-to-face learning scenario. Concretely, we focus on the connection between SpeakUp and the student engagement, distraction, social interaction, and the influence of the teachers' style. Our findings highlight that SpeakUp favored students' engagement and social interaction, but they also point towards its limitations in keeping students communicating about content relevant to the course

[Food allergy in asthma. Diagnostic significance of peripheral eosinophils].

Thirty one patients with suspicion of asthma due to food allergy (lack of correlation between allergic sensitivity and asthmatic attacks, association of clinical features suggestive of food allergy, no response to the pharmacological treatment) received an elimination diet. A second group (control group) of 51 asthmatic patients were enrolled in the study for a better evaluation of the diagnostic significance of blood eosinophil counts in food-induced asthma. 29-31 patients who took a variable oligoallergenic diet had a baseline blood eosinophilia greater than 600/mm3 (range 600-2100/mm3). Eosinophil count after an appropriate diet showed an early significant fall which preceded the improvement of symptoms. Only 10 patients had not a valuable improvement from the diet. The post diet change of spirometric values was significant. There was no significant difference between subjects with an eosinophil count greater than 1000/mm3 vs. less than 1000/mm3 with regard to both inhalant and food skin prick tests. On the other hand, the group with blood eosinophilia greater than 1000/mm3 had a significant correlation with the presence of persistent asthma (persistent alteration of forced expiratory volumes verified in asymptomatic phases of the disease) as with the anamnestic or actual report of eczema or other clinical manifestations of food allergy. Blood eosinophil count showed to be essential in the management of patients with a suspicion of asthma due to food allergy

Brief announcement: On the parallel undecided-state dynamics with two colors

The Undecided-State Dynamics is a well-known protocol that achieves Consensus in distributed systems formed by a set of n anonymous nodes interacting via a communication network. We consider this dynamics in the parallel PULL communication model on the complete graph for the binary case, i.e., when every node can either support one of two possible colors or stay in the undecided state. Previous work in this setting only considers initial color configurations with no undecided nodes and a large bias (i.e.,(n)) towards the majority color. A interesting open question here is whether this dynamics reaches consensus quickly, i.e. within a polylogarithmic number of rounds. In this paper we present an unconditional analysis of the Undecided-State Dynamics which answers to the above question in the affirmative. Our analysis shows that, starting from any initial configuration, the Undecided-State Dynamics reaches a monochromatic configuration within O(log2n) rounds, with high probability (w.h.p.). Moreover, we prove that if the initial configuration has bias Ω (â\u88\u9an log n), then the dynamics converges toward the initial majority color within O(log n) round, w.h.p. At the heart of our approach there is a new analysis of the symmetry-breaking phase that the process must perform in order to escape from (almost-)unbiased configurations. Previous symmetry-breaking analysis of consensus dynamics essentially concern sequential communication models (such as Population Protocols) and/or symmetric updated rules (such as majority rules)