Evolving training sets for improved transfer learning in brain computer interfaces

A new proof-of-concept method for optimising the performance of Brain Computer Interfaces (BCI) while minimising the quantity of required training data is introduced. This is achieved by using an evolutionary approach to rearrange the distribution of training instances, prior to the construction of an Ensemble Learning Generic Information (ELGI) model. The training data from a population was optimised to emphasise generality of the models derived from it, prior to a re-combination with participant-specific data via the ELGI approach, and training of classifiers. Evidence is given to support the adoption of this approach in the more difficult BCI conditions: smaller training sets, and those suffering from temporal drift. This paper serves as a case study to lay the groundwork for further exploration of this approach

An NF-κB and Slug Regulatory Loop Active in Early Vertebrate Mesoderm

BACKGROUND: In both Drosophila and the mouse, the zinc finger transcription factor Snail is required for mesoderm formation; its vertebrate paralog Slug (Snai2) appears to be required for neural crest formation in the chick and the clawed frog Xenopus laevis. Both Slug and Snail act to induce epithelial to mesenchymal transition (EMT) and to suppress apoptosis. METHODOLOGY & PRINCIPLE FINDINGS: Morpholino-based loss of function studies indicate that Slug is required for the normal expression of both mesodermal and neural crest markers in X. laevis. Both phenotypes are rescued by injection of RNA encoding the anti-apoptotic protein Bcl-xL; Bcl-xL's effects are dependent upon IκB kinase-mediated activation of the bipartite transcription factor NF-κB. NF-κB, in turn, directly up-regulates levels of Slug and Snail RNAs. Slug indirectly up-regulates levels of RNAs encoding the NF-κB subunit proteins RelA, Rel2, and Rel3, and directly down-regulates levels of the pro-apopotic Caspase-9 RNA. CONCLUSIONS/SIGNIFICANCE: These studies reveal a Slug/Snail–NF-κB regulatory circuit, analogous to that present in the early Drosophila embryo, active during mesodermal formation in Xenopus. This is a regulatory interaction of significance both in development and in the course of inflammatory and metastatic disease

The transcriptional regulator BBX24 impairs DELLA activity to promote shade avoidance in Arabidopsis thaliana

[EN] In response to canopy shade, plant vegetative structures elongate to gain access to light. However, the mechanism that allows a plastic transcriptional response to canopy shade light is not fully elucidated. Here we propose that the activity of PIF4, a key transcription factor in the shade signalling network, is modulated by the interplay between the BBX24 transcriptional regulator and DELLA proteins, which are negative regulators of the gibberellin (GA) signalling pathway. We show that GA-related targets are enriched among genes responsive to BBX24 under shade and that the shade-response defect in bbx24 mutants is rescued by a GA treatment that promotes DELLA degradation. BBX24 physically interacts with DELLA proteins and alleviates DELLA-mediated repression of PIF4 activity. The proposed molecular mechanism provides reversible regulation of the activity of a key transcription factor that may prove especially relevant under fluctuating light conditions.We thank Santiago Mora Garcia for valuable initial discussions and Peter Quail for the PIL1::LUC construct. This work was supported by grants from Agencia Nacional de Promocion Cientifica y Tecnologica, and Universidad de Buenos Aires (to J.F.B), and the Spanish Ministry of Science, BIO2010-15071 (to M.A.B.).Crocco, C.; Locascio ., AAM.; Escudero, CM.; Alabadí Diego, D.; Blazquez Rodriguez, MA.; Botto, J. (2015). The transcriptional regulator BBX24 impairs DELLA activity to promote shade avoidance in Arabidopsis thaliana. Nature Communications. 6:1-10. https://doi.org/10.1038/ncomms7202S1106Valladares, F. & Niinemets, U. Shade tolerance, a key plant feature of complex nature and consequences. Annu. Rev. Ecol. Evol. Syst. 39, 237–257 (2008).Casal, J. J. 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A comprehensive analysis of neurotrophins and neurotrophin tyrosine kinase receptors expression during development of zebrafish.

Neurotrophins (NTF) are a family of secreted nerve growth factors with affinity for tyrosine kinase (Ntrk) and p75 receptors. To fully understand the variety of developmental roles played by NTFs, it is critical to know when and where genes encoding individual ligands and receptors are transcribed. Identification of ntf and ntrk transcripts in zebrafish development remains to be fully characterized for further uncovering the potential function(s) of the NTF signal transduction pathway. Here, we conducted a systematic analysis of the expression profiles of four ntf and five ntrk genes during zebrafish development using whole-mount in situ hybridization. Our study unveils new expression domains in the developing embryo, confirms those previously known, and shows that ntf and ntrk genes have different degrees of cell- and tissue-type specificity. The unique and overlapping expression patterns here depicted indicate the coordination of the redundant and divergent functions of NTFs and represent valuable tools for deciphering the molecular pathways involved in the specification and function of embryonic cell types. This article is protected by copyright. All rights reserved

Context-specific roles of EMT programmes in cancer cell dissemination

News and Views.The role of the epithelial-to-mesenchymal transition in tumour progression remains a topic of intense debate. Now, data on the role of Zeb1 in the metastatic spread of pancreatic cancer clarify apparently conflicting views by revealing context-specific, differential use of individual epithelial-to-mesenchymal transition transcription factors in cancer cell dissemination.Peer reviewe

Genome-wide occupancy of RGA at target loci.

<p>(<i>A</i>) Genomic location of the statistically significant peaks of GFP-RGA along its target genes. (<i>B</i>) Gene ontology analysis of RGA targets, using ReviGO. (<i>C</i>) Statistically significant over-representation of <i>cis</i> elements for different transcription factor families. The <i>p</i> value for each element is indicated. Bars represent the number of genes with at least one copy of the corresponding <i>cis</i> element in the ChIP peak. Colours indicate induction (red), repression (blue), both (yellow) or no effect (gray) by DELLAs across all published transcriptomic datasets. Please note that each ChIP peak may contain more than one <i>cis</i> element, therefore the sum of all genes in the graph is much larger than the 421 genes associated to ChIP peaks.</p