Identification of the prebiotic translation apparatus within the contemporary ribosome

A structural element that could have existed independently in the prebiotic era was identified at the active site of the contemporary ribosome. It is suggested to have functioned as a proto-ribosome catalyzing peptide bond formation and non-coded elongation in the same manner that contemporary ribosomes exert positional catalysis, namely by accommodating the reactants in stereochemistry favourable for inline nucleophilic attack. This simple apparatus is a dimer of self-folding RNA units that could have assembled spontaneously into a symmetrical pocket-like structure, sufficiently efficient to be preserved throughout evolution as the active site of modern ribosomes, thus presenting a conceivable starting point for translation.Here we discuss the proto-ribosome emergence hypothesis and show that the tendency for dimerization, a prerequisite for obtaining the catalytic centre, is linked to the fold of its two components, indicating functional selection at the molecular level in the prebiotic era and supporting the existence of dimeric proto-ribosome

Induction of Word and Phrase Alignments for Automatic Document Summarization

Current research in automatic single document summarization is dominated by two effective, yet naive approaches: summarization by sentence extraction, and headline generation via bag-of-words models. While successful in some tasks, neither of these models is able to adequately capture the large set of linguistic devices utilized by humans when they produce summaries. One possible explanation for the widespread use of these models is that good techniques have been developed to extract appropriate training data for them from existing document/abstract and document/headline corpora. We believe that future progress in automatic summarization will be driven both by the development of more sophisticated, linguistically informed models, as well as a more effective leveraging of document/abstract corpora. In order to open the doors to simultaneously achieving both of these goals, we have developed techniques for automatically producing word-to-word and phrase-to-phrase alignments between documents and their human-written abstracts. These alignments make explicit the correspondences that exist in such document/abstract pairs, and create a potentially rich data source from which complex summarization algorithms may learn. This paper describes experiments we have carried out to analyze the ability of humans to perform such alignments, and based on these analyses, we describe experiments for creating them automatically. Our model for the alignment task is based on an extension of the standard hidden Markov model, and learns to create alignments in a completely unsupervised fashion. We describe our model in detail and present experimental results that show that our model is able to learn to reliably identify word- and phrase-level alignments in a corpus of pairs

Linked open government data: lessons from Data.gov.uk

The movement to publish government data is an opportunity to populate the linked data Web with data of good provenance. The benefits range from transparency to public service improvement, citizen engagement to the creation of social and economic value. There are many challenges to be met before the vision is implemented, and this paper describes the efforts of the EnAKTing project to extract value from data.gov.uk, through the stages of locating data sources, integrating data into the linked data Web, and browsing and querying it

Collective cell durotaxis emerges from long-range intercellular force transmission

The ability of cells to follow gradients of extracellular matrix stiffness—durotaxis—has been implicated in development, fibrosis, and cancer. Here, we found multicellular clusters that exhibited durotaxis even if isolated constituent cells did not. This emergent mode of directed collective cell migration applied to a variety of epithelial cell types, required the action of myosin motors, and originated from supracellular transmission of contractile physical forces. To explain the observed phenomenology, we developed a generalized clutch model in which local stick-slip dynamics of cell-matrix adhesions was integrated to the tissue level through cell-cell junctions. Collective durotaxis is far more efficient than single-cell durotaxis; it thus emerges as a robust mechanism to direct cell migration during development, wound healing, and collective cancer cell invasion.Peer ReviewedPostprint (author's final draft

Comparison of SYSTRAN and Google Translate for English→ Portuguese

Two machine translation (MT) systems, a statistical MT (SMT) system and a hybrid system (rule-based and SMT) were tested in order to compare various MT performances. The source language was English (EN) and the target language Portuguese (PT). The SMT tool gave much fewer errors than the hybrid system. Major problem areas of both systems concerned the transfer of verb systems from source to target language, and of the hybrid system the word-to-word translation, since its resources are mainly dictionaries and not corpora.Dos sistemes de traducció automàtica (MT), un sistema estadístic (SMT) i un sistema híbrid (sistema basat en regles i SMT) es van posar a prova per tal de comparar divereses resultats en MT. La llengua d'orígen era l'anglès (EN) i a llengua de destí el portuguès (PT). L'eina SMT va donar força menys errors que el sistema híbrid. La major part dels problemes d'ambdes eines se centraven en el sistema de transferència del verb de la llengua origen a la llengua destí, i en el cas del sistema híbrid en la traducció paraula a paraula, ja que els seus recursos són sobretot diccionaris i no pas corpus.Se pusieron a prueba dos sistemas de traducción automática (MT), uno de de ellos estadístico (SMT) y el otro híbrido (basado en reglas y SMT) a fin de comparar diversos resultados en MT. La lengua de origen era el inglés (EN) y la lengua de destino el portugués (PT). La herramienta SMT generó bastantes menos errores que el sistema híbrido. La mayor parte de los problemas de ambos instrumentos se centraron en el método de transferencia del verbo de la lengua origen a la lengua destino, y en el caso del sistema híbrido, en la traducción palabra a palabra, ya que sus recursos son sobre todo diccionarios y no corpus

Mesoderm migration in Drosophila is a multi-step process requiring FGF signaling and integrin activity

Migration is a complex, dynamic process that has largely been studied using qualitative or static approaches. As technology has improved, we can now take quantitative approaches towards understanding cell migration using in vivo imaging and tracking analyses. In this manner, we have established a four-step model of mesoderm migration during Drosophila gastrulation: (I) mesodermal tube formation, (II) collapse of the mesoderm, (III) dorsal migration and spreading and (IV) monolayer formation. Our data provide evidence that these steps are temporally distinct and that each might require different chemical inputs. To support this, we analyzed the role of fibroblast growth factor (FGF) signaling, in particular the function of two Drosophila FGF ligands, Pyramus and Thisbe, during mesoderm migration. We determined that FGF signaling through both ligands controls movements in the radial direction. Thisbe is required for the initial collapse of the mesoderm onto the ectoderm, whereas both Pyramus and Thisbe are required for monolayer formation. In addition, we uncovered that the GTPase Rap1 regulates radial movement of cells and localization of the beta-integrin subunit, Myospheroid, which is also required for monolayer formation. Our analyses suggest that distinct signals influence particular movements, as we found that FGF signaling is involved in controlling collapse and monolayer formation but not dorsal movement, whereas integrins are required to support monolayer formation only and not earlier movements. Our work demonstrates that complex cell migration is not necessarily a fluid process, but suggests instead that different types of movements are directed by distinct inputs in a stepwise manner