PyPlutchik: Visualising and comparing emotion-annotated corpora

The increasing availability of textual corpora and data fetched from social networks is fuelling a huge production of works based on the model proposed by psychologist Robert Plutchik, often referred simply as the “Plutchik Wheel”. Related researches range from annotation tasks description to emotions detection tools. Visualisation of such emotions is traditionally carried out using the most popular layouts, as bar plots or tables, which are however sub-optimal. The classic representation of the Plutchik’s wheel follows the principles of proximity and opposition between pairs of emotions: spatial proximity in this model is also a semantic proximity, as adjacent emotions elicit a complex emotion (a primary dyad) when triggered together; spatial opposition is a semantic opposition as well, as positive emotions are opposite to negative emotions. The most common layouts fail to preserve both features, not to mention the need of visually allowing comparisons between different corpora in a blink of an eye, that is hard with basic design solutions. We introduce PyPlutchik the Pyplutchik package is available as a Github repository (http://github.com/alfonsosemeraro/pyplutchik) or through the installation commands pip or conda. For any enquiry about usage or installation feel free to contact the corresponding author, a Python module specifically designed for the visualisation of Plutchik’s emotions in texts or in corpora. PyPlutchik draws the Plutchik’s flower with each emotion petal sized after how much that emotion is detected or annotated in the corpus, also representing three degrees of intensity for each of them. Notably, PyPlutchik allows users to display also primary, secondary, tertiary and opposite dyads in a compact, intuitive way. We substantiate our claim that PyPlutchik outperforms other classic visualisations when displaying Plutchik emotions and we showcase a few examples that display our module’s most compelling features

Characterisation of AMS H35 HV-CMOS monolithic active pixel sensor prototypes for HEP applications

Monolithic active pixel sensors produced in High Voltage CMOS (HV-CMOS) technology are being considered for High Energy Physics applications due to the ease of production and the reduced costs. Such technology is especially appealing when large areas to be covered and material budget are concerned. This is the case of the outermost pixel layers of the future ATLAS tracking detector for the HL-LHC. For experiments at hadron colliders, radiation hardness is a key requirement which is not fulfilled by standard CMOS sensor designs that collect charge by diffusion. This issue has been addressed by depleted active pixel sensors in which electronics are embedded into a large deep implantation ensuring uniform charge collection by drift. Very first small prototypes of hybrid depleted active pixel sensors have already shown a radiation hardness compatible with the ATLAS requirements. Nevertheless, to compete with the present hybrid solutions a further reduction in costs achievable by a fully monolithic design is desirable. The H35DEMO is a large electrode full reticle demonstrator chip produced in AMS 350 nm HV-CMOS technology by the collaboration of Karlsruher Institut f\"ur Technologie (KIT), Institut de F\'isica d'Altes Energies (IFAE), University of Liverpool and University of Geneva. It includes two large monolithic pixel matrices which can be operated standalone. One of these two matrices has been characterised at beam test before and after irradiation with protons and neutrons. Results demonstrated the feasibility of producing radiation hard large area fully monolithic pixel sensors in HV-CMOS technology. H35DEMO chips with a substrate resistivity of 200$\Omega$ cm irradiated with neutrons showed a radiation hardness up to a fluence of $10^{15}$n$_{eq}$cm$^{-2}$ with a hit efficiency of about 99% and a noise occupancy lower than $10^{-6}$ hits in a LHC bunch crossing of 25ns at 150V

Isolamento e caracterização de bactérias endofíticas não patogênicas em milho.

bitstream/item/58846/1/Pesq.And.-31-1.pd

ncRNA orthologies in the vertebrate lineage.

Annotation of orthologous and paralogous genes is necessary for many aspects of evolutionary analysis. Methods to infer these homology relationships have traditionally focused on protein-coding genes and evolutionary models used by these methods normally assume the positions in the protein evolve independently. However, as our appreciation for the roles of non-coding RNA genes has increased, consistently annotated sets of orthologous and paralogous ncRNA genes are increasingly needed. At the same time, methods such as PHASE or RAxML have implemented substitution models that consider pairs of sites to enable proper modelling of the loops and other features of RNA secondary structure. Here, we present a comprehensive analysis pipeline for the automatic detection of orthologues and paralogues for ncRNA genes. We focus on gene families represented in Rfam and for which a specific covariance model is provided. For each family ncRNA genes found in all Ensembl species are aligned using Infernal, and several trees are built using different substitution models. In parallel, a genomic alignment that includes the ncRNA genes and their flanking sequence regions is built with PRANK. This alignment is used to create two additional phylogenetic trees using the neighbour-joining (NJ) and maximum-likelihood (ML) methods. The trees arising from both the ncRNA and genomic alignments are merged using TreeBeST, which reconciles them with the species tree in order to identify speciation and duplication events. The final tree is used to infer the orthologues and paralogues following Fitch's definition. We also determine gene gain and loss events for each family using CAFE. All data are accessible through the Ensembl Comparative Genomics ('Compara') API, on our FTP site and are fully integrated in the Ensembl genome browser, where they can be accessed in a user-friendly manner.Database URL: http://www.ensembl.org

Caracterização morfológica e estimativa da distância genética de acessos de pimenta do banco ativo de germoplasma de Capsicum da Embrapa Clima Temperado.

bitstream/item/112062/1/boletim178-web.pd

Influence of continuous and intermittent water regimes on methane emissions from irrigated rice crops in southeast Brazil.

Irrigated rice crops in Brazil correspond to 35% of the total rice area and the preferred irrigation method is continuous flooding. In this study two water management systems ? continuous and intermittent flooding ? were monitored for the purpose of comparing their methane emission potential. Intermittent flooding was characterized by alternating flooding and draining periods during the rice cropping cycle. In both systems nitrogen fertilizers were applied twice (NPK and urea alone). Methane fluxes were determined using a closed chamber method (boxes 60x60 cm), and analyzed by GC-FID. Samples were collected from 4 boxes (2 boxes for each water management system) twice a week, for a weekly total of 46 samples. Measurements of air and soil temperature, soil and water pH, redox potential, plant biomass were done. After 104 days the accumulated fluxes resulted in a mean methane emission of 21.1 9 g CH4 m-2 d-1 under the continuous flooding regime and 23.9 g CH4 m-2 d-1 under the intermittent flooding regime. After the two N fertilizer application, methane fluxes decreased in all boxes, with a more marked reduction occurring in the intermittent regime stands. Total accumulated methane emissions, as well as grain yield, were evaluated for each water management system at the end of the cropping season, showing 13% higher productivity in the field under intermittent flooding system. The objectives of the present study were (i) to improve methane emission estimates and compare the emission potential of traditionally managed crop systems and (ii) to study the possibility of minimizing water consumption and the influence on the methane fluxes without deleterious effects to the crop