Uncovering the functional organization of molecular interaction networks using network embeddings based on graphlet topology

[eng] For this purpose, Spatial Analysis of Functional Enrichment (SAFE) framework was proposed to uncover functional regions in a network by embedding it in 2-dimensions (2D) using the Spring embedding algorithm. However, biological networks often have a heterogeneous degree distribution, i.e., nodes in the network have varying numbers of neighbours. In this case, the Spring embedding sometimes provides uninformative, densely packed embeddings best described as a ‘hairball’. On the other hand, hyperbolic embeddings, such as the Coalescent embedding, maps a network onto a disk, so that nodes of high topological importance (i.e., of high node degree) are placed closer to the center of such disk. Additionally, these embedding methods only capture node connectivity information (i.e., which nodes are connected) but does not consider network structure (i.e., wiring or topology), which captures complementary information. The state-of-the-art methods to capture network structure are based on graphlets, which are small, connected, non-isomorphic, induced sub-graphs (e.g., triangles, paths). To better capture the functional organization of networks with heterogeneous degree distributions, taking into account different types of graphlet-based wiring patterns, in this work we introduce the graphlet-based Spring (GraSpring) and the graphlet-based Coalescent (GraCoal) embeddings. Furthermore, we extend the popular SAFE framework to take as input these two newly proposed embedding methods and we use SAFE to evaluate their performance on three types of molecular interaction networks (genetic interaction, protein-protein interaction and co-expression) of various model organisms. We show that the performance in terms of functional information uncovered by each of the embedding algorithms varies depending on the type of network considered and also the model organism considered. For instance, we show that GraCoals better capture the functional and spatial organization of the genetic interaction networks of four species (fruit fly, budding yeast, fission yeast and E. coli ). Moreover, we discover that GraCoals capture different topology-function relationships depending on the species. We show that triangle-based GraCoals capture functional redundancy in GI networks of species whose genome is characterised by high counts of duplicated genes

Cognitive status and referential acts in functional discourse grammar

In Functional Discourse Grammar, both Ascription and Reference are characterized as actional processes and are captured at the Interpersonal Level of linguistic description. Additionally, the temporal sequencing of Discourse Acts seems relevant to establishing dependency relations among them. However, the remainder of the levels of representation in the theory contain static descriptions of linguistic structures and not of processes. In this paper, I will argue that this is the result of an inherent contradiction between FDG?s characterization as a static grammar and the dynamicity of verbal interaction, which is best solved if the theory commits itself to the procedural nature of the Interpersonal Level. In order to do so, the different categories that have been identified in the literature on the cognitive status of referents should find relevance in the grammar. Elaborating upon García Velasco (2014), I will show that the temporal dimension of the text creating activity and referent accessibility, are relevant for a full account of constituent preposing in Spanish

The Ambrysus Stal (Heteroptera : Naucoridae) of Mexico : revision of Ambrysus (Syncollus) La Rivers and species groups of Ambrysus (Ambrysus)

Aquatic insects in the family Naucoridae are commonly known as creeping water bugs or saucer bugs. The New World genus Ambrysus (Heteroptera: Naucoridae) includes two subgenera in Mexico: Ambrysus (Syncollus) La Rivers and Ambrysus (Ambrysus) Stal. Syncollus includes nine species with mostly Neotropical distributions. The subgenus Syncollus was reviewed and the status of the Mexican fauna was evaluated. Six species of this group are present in Mexico; three of them were described as new in this study. In the subgenus Ambrysus, the A. hybridus Montandon species complex was revised and includes nine species distributed in North America. One of the Mexican species was resurrected as a valid species and two other were considered the same as a third species that was not well known prior to this work. The Ambrysus guttatipennis Stal species complex also was revised and includes eleven species distributed in North America. Six species of this group from Mexico were described as new

Living Together: The Economics of Cohabitation

Analyzes trends among unmarried couples ages 30 to 44 living together by education. Compares median household income, poverty rate, composition of household income, and number of children with those of married couples and those without partners

From texting to Internet Language. Analysis of contemporary language evolution. The case of YouTube

Han pasado miles de años y el lenguaje sigue evolucionando. Las nuevas tecnologías han contribuido masivamente a la expansión, tanto en uso como en cantidad, del lengauge de internet que tiene como objetivo principal la economía del lenguaje. Tomando como base los mensajes de texto vía teléfono móvil y teniendo en cuenta sus características, este trabajo tratará de explicar cómo el lenguage de internet está cambiando la manera de comunicarse usando las nuevas tecnologías. El material de trabajo consistirá en comentarios de YouTube, a través de los cuales extraeremos el vocabulario no reglado del inglés y clasificaremos las palabras en distintas categorías para estudiar su funcionalidad. Se tratarán, asimismo, hipótesis en relación a las causas fonéticas y explicaciones históricas añadiendo de este modo un posible razonamiento al por qué los usuarios crean determinadas abreviaturas o variantes de palabras consciente o inconscientemente. También se establecerá una diferenciación entre los usos identificados en 2008 y 2015 para futuras hipótesis.Departamento de Filología InglesaGrado en Estudios Inglese

Surface and smectic layering transitions in binary mixtures of parallel hard rods

The surface phase behavior of binary mixtures of colloidal hard rods in contact with a solid substrate (hard wall) is studied, with special emphasis on the region of the phase diagram that includes the smectic A phase. The colloidal rods are modelled as hard cylinders of the same diameter and different lengths, in the approximation of perfect alignment. A fundamental--measure density functional is used to obtain equilibrium density profiles and thermodynamic properties such as surface tensions and adsorption coefficients. The bulk phase diagram exhibits nematic-smectic and smectic-smectic demixing, with smectic phases having different compositions; in some cases they are microfractionated. The calculated surface phase diagram of the wall-nematic interface shows a very rich phase behavior, including layering transitions and complete wetting at high pressures, whereby an infinitely thick smectic film grows at the wall via an infinite sequence of stepwise first--order layering transitions. For lower pressures complete wetting also obtains, but here the smectic film grows in a continuous fashion. Finally, at very low pressures, the wall-nematic interface exhibits critical adsorption by the smectic phase, due to the second-order character of the bulk nematic-smectic transition.Comment: 13 pages, 13 figures. Accepted for publication in Physical Review

Hilbert schemes of 8 points

The Hilbert scheme H^d_n of n points in A^d contains an irreducible component R^d_n which generically represents n distinct points in A^d. We show that when n is at most 8, the Hilbert scheme H^d_n is reducible if and only if n = 8 and d >= 4. In the simplest case of reducibility, the component R^4_8 \subset H^4_8 is defined by a single explicit equation which serves as a criterion for deciding whether a given ideal is a limit of distinct points. To understand the components of the Hilbert scheme, we study the closed subschemes of H_n^d which parametrize those ideals which are homogeneous and have a fixed Hilbert function. These subschemes are a special case of multigraded Hilbert schemes, and we describe their components when the colength is at most 8. In particular, we show that the scheme corresponding to the Hilbert function (1,3,2,1) is the minimal reducible example.Comment: 28 pages; Rewrote introduction and reorganized parts of the paper, some minor errors have been fixe