MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants

Recent times have seen an enormous growth of "omics" data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms. Besides the identification of missing genes in pathways, these methods also typically enable the discovery of biological regulators (i.e., transcription factors or signaling genes). A previously built guilt-by-association method is MORPH, which was proven to be an efficient algorithm that performs particularly well in identifying and prioritizing missing genes in plant metabolic pathways. Here, we present MorphDB, a resource where MORPH-based candidate genes for large-scale functional annotations (Gene Ontology, MapMan bins) are integrated across multiple plant species. Besides a gene centric query utility, we present a comparative network approach that enables researchers to efficiently browse MORPH predictions across functional gene sets and species, facilitating efficient gene discovery and candidate gene prioritization. MorphDB is available at http://bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/. We also provide a toolkit, named "MORPH bulk" (https://github.com/arzwa/morph-bulk), for running MORPH in bulk mode on novel data sets, enabling researchers to apply MORPH to their own species of interest

Diversity of culturable moderately halophilic and halotolerant bacteria in a marsh and two salterns a protected ecosystem of Lower Loukkos (Morocco)

To study the biodiversity of halophilic bacteria in a protected wetland located in Loukkos (Northwest, Morocco), a total of 124 strains were recovered from sediment samples from a marsh and salterns. 120 isolates (98%) were found to be moderately halophilic bacteria; growing in salt ranges of 0.5 to 20%. Of 124 isolates, 102 were Gram-positive while 22 were Gram negative. All isolates were identified based on 16S rRNA gene phylogenetic analysis and characterized phenotypically and by screening for extracellular hydrolytic enzymes. The Gram-positive isolates were dominated by the genus Bacillus (89%) and the others were assigned to Jeotgalibacillus, Planococcus, Staphylococcus and Thalassobacillus. The Gram negative isolates were dominated by the genus Vibrio (41%) and the others were assigned to Halomonas, Psychrobacter, Marinobacterium, Pseudoalteromonas, Salinivibrio and Photobacterium. The growth of strains obtained under different physico-chemical conditions and the screening for hydrolytic enzymes showed a high diversity even within the same species

A Diagrammatic Axiomatisation of Fermionic Quantum Circuits

We introduce the fermionic ZW calculus, a string-diagrammatic language for fermionic quantum computing (FQC). After defining a fermionic circuit model, we present the basic components of the calculus, together with their interpretation, and show how the main physical gates of interest in FQC can be represented in the language. We then list our axioms, and derive some additional equations. We prove that the axioms provide a complete equational axiomatisation of the monoidal category whose objects are quantum systems of finitely many local fermionic modes, with operations that preserve or reverse the parity (number of particles mod 2) of states, and the tensor product, corresponding to the composition of two systems, as monoidal product. We achieve this through a procedure that rewrites any diagram in a normal form. We conclude by showing, as an example, how the statistics of a fermionic Mach-Zehnder interferometer can be calculated in the diagrammatic language

The FCTOOLS User Manual (Version 1.0)

We describe a set of modular extensions to our Auto/Graph verification toolset for networks of communicating processes. These software additions operate from a common file exchange format for automata and networks, called {\sc fc2}. Tool functionalities comprise graphical depiction of objects, global model construction from hierarchical descriptions, various types of model reductions and of verification of simple modal properties by observers, counterexample production and visualisation. We illustrate typical verification sessions conducted on usual academic examples: dining philosophers, mutual exclusion algorithms and round-robin schedulers. Based on previous experience of drastic state explosion problems we aim here at efficiency in implementation. We use both explicit representation techniques and implicit techniques such as {\sc BDD}s, with functional overlap at places

Vínculos de apego en niños víctimas de la violencia intrafamiliar

The objective of this investigation was to describe attachment relation that children who are victims of active or passive domestic violence establish with the people around them. The study was done with a sample of 27 children between the ages of 9 and 12, who live in sectors of levels 1 and 2 in Barranquilla. The Grounded Theory method of Glasser & Strauss (1967) was chosen for this investigation, and it was useful for establishing postures from the children’s interpretations of their attachment relation with their parents, caregivers or other people of their environment. Following these guidelines, a semi-structured interview was designed. It contained four categories of analysis: Confidence, Comprehension of Feelings, Intimacy and Availability. The results determined, in first instance, the active presence of different people and contexts in the life of these children that go beyond the nuclear family. These subsidiary figures, like grandparents, uncles, cousins, brothers or sisters who play parental roles, friends, neighbors, and teachers, among others, are perceived as people who help them create a self-image, offer affection and confidence and look out for them. They help to mitigate the basic deficiencies of an inadequate relationship with parents. It was also found that children who were victims of active domestic violence perceive a greater rejection from their main caregivers than victims of passive domestic violence. This fact is related to a greater search for acceptance and demonstration of their worthiness from other figures, such as their friends or other adultsEl objetivo de esta investigación fue describir los vínculos de apego que establecen los niños víctimas de la violencia intrafamiliar activa y pasiva con las personas de su ambiente más próximo. El estudio se realizó con una muestra de 27 niños, entre 9 y 12 años de edad, que viven en sectores socioeconómicamente en desventaja de la ciudad de Barranquilla (Colombia). El método fue el de la Teoría Fundada o Grounded Theory de Glasser & Strauss (1967), el cual contribuyó a generar posturas a partir de la interpretación que los niños tenían de los vínculos de apego que establecen con sus padres o cuidadores y otras personas de su entorno. Se diseñó una entrevista semi-estructurada, que contempló cuatro categorías de análisis: Confianza, Comprensión de Sentimientos, Intimidad y Disponibilidad. Los resultados permitieron determinar, en primer lugar, la presencia activa de diferentes personas y contextos en la vida de estos niños trascendiendo el ámbito de la familia nuclear. Estas figuras subsidiarias, abuelos, tíos, primos, hermanos (cumpliendo roles parentales), amigos, vecinos y profesores, entre otros, son percibidos como personas que contribuyen a la construcción de una imagen de sí mismos, les brindan afecto, confianza y se preocupan por ellos, ayudando a mitigar así las carencias de base que encuentran en una relación inadecuada con los padres. También se encontró que los niños víctimas de la violencia activa perciben mayor inaceptación por parte de sus cuidadores principales que los víctimas de la violencia intrafamiliar pasiva, hecho que se relaciona con una marcada búsqueda de reafirmación de su valía en otras figuras, sean estos sus amigos u otros adultos