From logical forms to SPARQL query with GETARUNS

We present a system for Question Answering which computes a prospective answer from Logical Forms produced by a full-fledged NLP for text understanding, and then maps the result onto schemata in SPARQL to be used for accessing the Semantic Web. As an intermediate step, and whenever there are complex concepts to be mapped, the system looks for a corresponding amalgam in YAGO classes. It is just by the internal structure of the Logical Form that we are able to produce a suitable and meaningful context for concept disambiguation. Logical Forms are the final output of a complex system for text understanding - GETARUNS - which can deal with different levels of syntactic and semantic ambiguity in the generation of a final structure, by accessing computational lexical equipped with sub-categorization frames and appropriate selectional restrictions applied to the attachment of complements and adjuncts. The system also produces pronominal binding and instantiates the implicit arguments, if needed, in order to complete the required Predicate Argument structure which is licensed by the semantic component

La riscoperta del linguaggio - Conversazione con Tengan Daisuke

Five new orbitides, cyclolinopeptides <b>21</b>–<b>25</b>, were identified in flaxseed oil (<i>Linum usitatissimum</i>) extracts. Their HPLC-ESIMS quasimolecular ion peaks at <i>m</i>/<i>z</i> 1097.7 (<b>21</b>), 1115.6 (<b>22</b>), 1131.6 (<b>23</b>), 1018.6 (<b>24</b>), and 1034.6 (<b>25</b>) [M + H]⁺ corresponded to the molecular formulae C₅₉H₈₉N₁₀O₁₀, C₅₈H₈₇N₁₀O₁₀S, C₅₈H₈₇N₁₀O₁₁S, C₅₃H₈₀N₉O₉S, and C₅₃H₈₀N₉O₁₀S, respectively. Their structures were elucidated by extensive HPLC-ESIMS/MS analyses, and their presence was confirmed by precursor proteins identified in flax genomic DNA sequence data. The amino acid sequences of these orbitides were confirmed as [1–10-NαC]-GILVPPFFLI, [1–10-NαC]-GMLIPPFFVI, [1–10-NαC]-G<i>O</i>LIPPFFVI, [1–9-NαC]-GMLVFPLFI, and [1–9-NαC]-G<i>O</i>LVFPLFI for cyclolinopeptides <b>21</b>–<b>25</b>, respectively. Previously reported orbitides, [1–9-NαC]-ILVPPFFLI (<b>1</b>), [1–9-NαC]-MLIPPFFVI (<b>2</b>), [1–9-NαC]-<i>O</i>LIPPFFVI (<b>3</b>), [1–8-NαC]-MLVFPLFI (<b>7</b>), and [1–8-NαC]-<i>O</i>LVFPLFI (<b>8</b>), were also present in flaxseed oil. The precursors of orbitides <b>21</b>, <b>22</b>, and <b>24</b> also produced orbitides <b>1</b>, <b>2</b>, and <b>7</b> by alternative cyclization. Cyclolinopeptides <b>3</b>, <b>8</b>, <b>23</b>, and <b>25</b> contain MetO (<i>O</i>) and are not directly encoded, but are products of post-translational modification of the Met present in <b>2</b>, <b>7</b>, <b>22</b>, and <b>24</b>, respectively. Sufficient cyclolinopeptide <b>23</b> was isolated for characterization via 1D (¹H and ¹³C) and 2D (NOESY and HMBC) NMR spectroscopy. These compounds have been named as cyclolinopeptides U, V, W, X, and Y for <b>21</b>, <b>22</b>, <b>23</b>, <b>24</b>, and <b>25</b>, respectively

Understanding the Diversity and Distribution of Cyclotides from Plants of Varied Genetic Origin

Cyclotides are a large family of naturally occurring plant-derived macrocyclic cystine-knot peptides, with more than 400 having been identified in species from the Violaceae, Rubiaceae, Cucurbitaceae, Fabaceae, and Solanaceae families. Nevertheless, their specialized distribution within the plant kingdom remains poorly understood. In this study, the diversity of cyclotides was explored through the screening of 197 plants belonging to 43 different families. In total, 28 cyclotides were sequenced from 15 plant species, one of which belonged to the Rubiaceae and 14 to the Violaceae. Every Violaceae species screened contained cyclotides, but they were only sparsely represented in Rubiaceae and nonexistent in other families. The study thus supports the hypothesis that cyclotides are ubiquitous in the Violaceae, and it adds to the list of plants found to express kalata S and cycloviolacin O12. Finally, previous studies suggested the existence of cyclotide isoforms with either an Asn or an Asp at the C-terminal processing site of the cyclotide domain within the precursor proteins. Here we found that despite the discovery of a few cyclotides genuinely containing an Asp in loop 6 as evidenced by gene sequencing, deamidation of Asn during enzymatic digestion resulted in the artifactual presence of Asp isoforms. This result is consistent with studies suggesting that peptides can undergo deamidation after being subjected to external factors, including pH, temperature, and enzymatic digestion