A Wireless Future: performance art, interaction and the brain-computer interfaces

Although the use of Brain-Computer Interfaces (BCIs) in the arts originates in the 1960s, there is a limited number of known applications in the context of real-time audio-visual and mixed-media performances and accordingly the knowledge base of this area has not been developed sufficiently. Among the reasons are the difficulties and the unknown parameters involved in the design and implementation of the BCIs. However today, with the dissemination of the new wireless devices, the field is rapidly growing and changing. In this frame, we examine a selection of representative works and artists, in comparison to the current scientific evidence. We identify important performative and neuroscientific aspects, issues and challenges. A model of possible interactions between the performers and the audience is discussed and future trends regarding liveness and interconnectivity are suggested

HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing-0

<p><b>Copyright information:</b></p><p>Taken from "HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing"</p><p>http://www.biomedcentral.com/1471-2105/8/418</p><p>BMC Bioinformatics 2007;8():418-418.</p><p>Published online 28 Oct 2007</p><p>PMCID:PMC2200674.</p><p></p>n content of the motifs was gradually reduced by varying the number of pseudocounts and the sensitivity of the different tools was determined by calculating the fraction of correctly identified motifs. Results are from 5 averaged trials

HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing-2

<p><b>Copyright information:</b></p><p>Taken from "HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing"</p><p>http://www.biomedcentral.com/1471-2105/8/418</p><p>BMC Bioinformatics 2007;8():418-418.</p><p>Published online 28 Oct 2007</p><p>PMCID:PMC2200674.</p><p></p>n content of the motifs was gradually reduced by varying the number of pseudocounts and the sensitivity of the different tools was determined by calculating the fraction of correctly identified motifs. Results are from 5 averaged trials

Deletion and promoter hypermethylation events in genes subject to purifying selection.

<p>Boxplots show for both sets of genes with signals of purifying selection (at 50% FDR and <i>P</i>≤0.05) and the other screened genes (<i>P</i>>0.05) the proportion of samples containing homozygous deletions <b>(a),</b> hemizygous deletions <b>(b)</b>, transcription start site (TSS) hypermethylations <b>(c)</b> and gene CDS hypermethylations <b>(d)</b>.</p

A genome-wide screen unveils patterns indicative of purifying selection.

<p>A genome-wide screen was performed on 1,187 genes to detect genes subjected to purifying selection against deleterious somatic mutations. <b>(a)</b> Manhattan plot shows all genes that were selected for analysis. Genes at 50% FDR are indicated by red dots and labelled. <b>(b)</b> qq-plot shows the difference between expressed genes (as used in the analysis) and non-expressed genes. <b>(c)</b> Correlation between the purifying selection rank and dN/dS. Solid lines represent moving averages. For visualization purposes, individual dots of CNN dN/dS values are not shown. Spearman correlation coefficients are shown on top. <b>(d)</b> CGC genes are indicated by black vertical bars and shown as a function of purifying selection rank. Color bars indicate the CGC gene density. <b>(e-f)</b> Copy number-related CADD scores <b>(e)</b> and normalized CADD scores <b>(f)</b> from the observed mutations in the top-5 ranked genes. Proportions of samples harboring the deletion are indicated below each plot in panel <b>e</b>. <b>(g)</b> Top ranked GO biological processes gene set enrichment results. <b>(h)</b> Median normalized CADD scores in HeZD compared to CNN samples for the top 76 genes from the purifying selection screen. <b>(i)</b> Bar plot shows the proportion of genes with (at 50% FDR or <i>P</i>≤0.05) or without (<i>P</i>>0.05) signals of purifying selection that are active in protein complexes. <b>(j)</b> A high number of genes with signals of purifying selection is involved in RNA-related events and complexes. Horizontal lines on plots indicate median values.</p

Somatic Mutation Patterns in Hemizygous Genomic Regions Unveil Purifying Selection during Tumor Evolution

<div><p>Identification of cancer driver genes using somatic mutation patterns indicative of positive selection has become a major goal in cancer genomics. However, cancer cells additionally depend on a large number of genes involved in basic cellular processes. While such genes should in theory be subject to strong purifying (negative) selection against damaging somatic mutations, these patterns have been elusive and purifying selection remains inadequately explored in cancer. Here, we hypothesized that purifying selection should be evident in hemizygous genomic regions, where damaging mutations cannot be compensated for by healthy alleles. Using a 7,781-sample pan-cancer dataset, we first confirmed this in <i>POLR2A</i>, an essential gene where hemizygous deletions are known to confer elevated sensitivity to pharmacological suppression. We next used this principle to identify several genes and pathways that show patterns indicative of purifying selection to avoid deleterious mutations. These include the <i>POLR2A</i> interacting protein <i>INTS10</i> as well as genes involved in mRNA splicing, nonsense-mediated mRNA decay and other RNA processing pathways. Many of these genes belong to large protein complexes, and strong overlaps were observed with recent functional screens for gene essentiality in human cells. Our analysis supports that purifying selection acts to preserve the remaining function of many hemizygously deleted essential genes in tumors, indicating vulnerabilities that might be exploited by future therapeutic strategies.</p></div

Genes subject to purifying selection are identified by orthogonal methods in cell lines.

<p>Comparison of genes showing signals of purifying selection with essential genes identified by CRISPR/Cas9 and gene-trap based methods in cell lines. <b>(a)</b> Receiver Operating Characteristic (ROC) curves using <i>S</i>. <i>Cerevisiae</i> essential gene homologs as a benchmark dataset. Area under the curve (AUC) values are compared in the inset. <b>(b)</b> Enrichment results. Curves show the cumulative proportion of experimentally-derived essential genes in cell lines as a function of purifying selection-based gene rank. <b>(c)</b> Bar plots show the proportion of genes identified to be under purifying selection (at 50% FDR or <i>P</i>≤0.05) that were retrieved by orthogonal methods. <b>(d)</b> Overview of the 24 genes identified at 50% FDR in this study and their identification by orthogonal methods.</p

Theoretical concept.

<p><b>(a-b)</b> Damaging somatic mutations in HeZD but not CNN (haplosufficient) essential genes are expected to alter cell viability and to be selected against. <b>(c-d)</b> This purifying selection will not affect silent and low impact missense mutations, leading to a shift in the overall functional impact when comparing CNN to HeZD tumors.</p

The Cell Cycle Regulator CCDC6 Is a Key Target of RNA-Binding Protein EWS

<div><p>Genetic translocation of EWSR1 to ETS transcription factor coding region is considered as primary cause for Ewing sarcoma. Previous studies focused on the biology of chimeric transcription factors formed due to this translocation. However, the physiological consequences of heterozygous EWSR1 loss in these tumors have largely remained elusive. Previously, we have identified various mRNAs bound to EWS using PAR-CLIP. In this study, we demonstrate CCDC6, a known cell cycle regulator protein, as a novel target regulated by EWS. siRNA mediated down regulation of EWS caused an elevated apoptosis in cells in a CCDC6-dependant manner. This effect was rescued upon re-expression of CCDC6. This study provides evidence for a novel functional link through which wild-type EWS operates in a target-dependant manner in Ewing sarcoma.</p></div

Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure

<div><p>Alcohol use disorder is a chronic relapsing brain disorder and a global health issue. Prolonged high alcohol consumption increases the risk for dependence development, a complex state that includes progressive alterations in brain function. The molecular mechanisms behind these changes remain to be fully disclosed, but several genes show altered expression in various regions of the rat brain even after modest alcohol exposure. The present study utilizes whole-transcriptome sequencing (RNA-seq) to investigate expression changes in the brain nucleus accumbens (NAc), an area of particular interest in addictive disorders, of alcohol consuming rats. The impact on gene expression after eight weeks of moderate voluntary alcohol consumption or voluntary consumption combined with forced excessive exposure was explored in two separate experiments. The results point to a lack of strong and consistent expression alterations in the NAc after alcohol exposure, suggesting that transcriptional effects of alcohol are weak or transient, or occur primarily in brain regions other than NAc.</p></div