The SEMAINE corpus of emotionally coloured character interactions

We have recorded a new corpus of emotionally coloured conversations. Users were recorded while holding conversations with an operator who adopts in sequence four roles designed to evoke emotional reactions. The operator and the user are seated in separate rooms; they see each other through teleprompter screens, and hear each other through speakers. To allow high quality recording, they are recorded by five high-resolution, high framerate cameras, and by four microphones. All sensor information is recorded synchronously, with an accuracy of 25 μs. In total, we have recorded 20 participants, for a total of 100 character conversational and 50 non-conversational recordings of approximately 5 minutes each. All recorded conversations have been fully transcribed and annotated for five affective dimensions and partially annotated for 27 other dimensions. The corpus has been made available to the scientific community through a web-accessible database.

Additionality of Incubator Support on Networks of University Spin-Out Firms

The formation rate of university spin-out firms has increased markedly over the past decade. While this is seen as an important channel for the commercialisation of academic research, concerns have centred around high failure rates and no-to-low growth among those which survive compared to other new technology based firms. Universities have responded to this by investing in incubators to assist spin-outs to overcome their liability of newness. Yet how effective are incubators in supporting these firms? Here we examine this in terms of the structural networks that spin-out firms form, the role of the incubator in this and the effect of this on the spin-out process.

The Belfast Storytelling Database: A spontaneous social interaction database with laughter focused annotation

To support the endeavor of creating intelligent interfaces between computers and humans the use of training materials based on realistic human-human interactions has been recognized as a crucial task. One of the effects of the creation of these databases is an increased realization of the importance of often overlooked social signals and behaviours in organizing and orchestrating our interactions. Laughter is one of these key social signals; its importance in maintaining the smooth flow of human interaction has only recently become apparent in the embodied conversational agent domain. In turn, these realizations require training data that focus on these key social signals. This paper presents a database that is well annotated and theoretically constructed with respect to understanding laughter as it is used within human social interaction. Its construction, motivation, annotation and availability are presented in detail in this paper.

Turing’s Menagerie: Talking Lions, Virtual Bats, Electric Sheep and Analogical Peacocks: Common Ground and Common Interest are Necessary Components of Engagement

This theoretical paper attempts to define some of the key components and challenges required to create embodied conversational agents that can be genuinely interesting conversational partners. Wittgenstein’s argument concerning talking lions emphasizes the importance of having a shared common ground as a basis for conversational interactions. Virtual bats suggests that–for some people at least–it is important that there be a feeling of authenticity concerning a subjectively experiencing entity that can convey what it is like to be that entity. Electric sheep reminds us of the importance of empathy in human conversational interaction and that we should provide a full communicative repertoire of both verbal and non-verbal components if we are to create genuinely engaging interactions. Also we may be making the task more difficult rather than easy if we leave out non-verbal aspects of communication. Finally, analogical peacocks highlights the importance of between minds alignment and establishes a longer term goal of being interesting, creative, and humorous if an embodied conversational is to be truly an engaging conversational partner. Some potential directions and solutions to addressing these issues are suggested.

Of no fixed form: The Irish Pavilion at Venice 2014 and beyond

This paper explores the theme of exhibiting architectural research through a particular example, the development of the Irish pavilion for the 14th architectural biennale, Venice 2014. Responding to Rem Koolhaas’s call to investigate the international absorption of modernity, the Irish pavilion became a research project that engaged with the development of the architectures of infrastructure in Ireland in the twentieth and twenty-first centuries. Central to this proposition was that infrastructure is simultaneously a technological and cultural construct, one that for Ireland occupied a critical position in the building of a new, independent post-colonial nation state, after 1921.

Presupposing infrastructure as consisting of both visible and invisible networks, the idea of a matrix become a central conceptual and visual tool in the curatorial and design process for the exhibition and pavilion. To begin with this was a two-dimensional grid used to identify and order what became described as a series of ten ‘infrastructural episodes’. These were determined chronologically across the decades between 1914 and 2014 and their spatial manifestations articulated in terms of scale: micro, meso and macro. At this point ten academics were approached as researchers. Their purpose was twofold, to establish the broader narratives around which the infrastructures developed and to scrutinise relevant archives for compelling visual material. Defining the meso scale as that of the building, the media unearthed was further filtered and edited according to a range of categories – filmic/image, territory, building detail, and model – which sought to communicate the relationship between the pieces of architecture and the larger systems to which they connect. New drawings realised by the design team further iterated these relationships, filling in gaps in the narrative by providing composite, strategic or detailed drawings.

Conceived as an open-ended and extendable matrix, the pavilion was influenced by a series of academic writings, curatorial practices, artworks and other installations including: Frederick Kiesler’s City of Space (1925), Eduardo Persico and Marcello Nizzoli’s Medaglio d’Oro room (1934), Sol Le Witt’s Incomplete Open Cubes (1974) and Rosalind Krauss’s seminal text ‘Grids’ (1979). A modular frame whose structural bays would each hold and present an ‘episode’, the pavilion became both a visual analogue of the unseen networks embodying infrastructural systems and a reflection on the predominance of framed structures within the buildings exhibited. Sharing the aspiration of adaptability of many of these schemes, its white-painted timber components are connected by easily-dismantled steel fixings. These and its modularity allow the structure to be both taken down and re-erected subsequently in different iterations. The pavilion itself is, therefore, imagined as essentially provisional and – as with infrastructure – as having no fixed form. Presenting archives and other material over time, the transparent nature of the space allowed these to overlap visually conveying the nested nature of infrastructural production. Pursuing a means to evoke the qualities of infrastructural space while conveying a historical narrative, the exhibition’s termination in the present is designed to provoke in the visitor, a perceptual extension of the matrix to engage with the future.

Fish product mislabelling: failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) fishing

Increasing consumer demand for seafood, combined with concern over the health of our oceans, has led to many initiatives aimed at tackling destructive fishing practices and promoting the sustainability of fisheries. An important global threat to sustainable fisheries is Illegal, Unreported and Unregulated (IUU) fishing, and there is now an increased emphasis on the use of trade measures to prevent IUU-sourced fish and fish products from entering the international market. Initiatives encompass new legislation in the European Union requiring the inclusion of species names on catch labels throughout the distribution chain. Such certification measures do not, however, guarantee accuracy of species designation. Using two DNA-based methods to compare species descriptions with molecular ID, we examined 386 samples of white fish, or products labelled as primarily containing white fish, from major UK supermarket chains. Species specific real-time PCR probes were used for cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) to provide a highly sensitive and species-specific test for the major species of white fish sold in the UK. Additionally, fish-specific primers were used to sequence the forensically validated barcoding gene, mitochondrial cytochrome oxidase I (COI). Overall levels of congruence between product label and genetic species identification were high, with 94.34% of samples correctly labelled, though a significant proportion in terms of potential volume, were mislabelled. Substitution was usually for a cheaper alternative and, in one case, extended to a tropical species. To our knowledge, this is the first published study encompassing a large-scale assessment of UK retailers, and if representative, indicates a potentially significant incidence of incorrect product designation.

Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F(CT) = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F(CT) range 0.275-0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.

A genomic island linked to ecotype divergence in Atlantic cod

The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome-wide or localized in 'genomic mosaics' during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or 'genomic island', as potentially associated with ecological divergence and suggest the involvement of a selective sweep. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although the underlying mechanisms are still unknown, the results suggest that 'genomic mosaics' of differentiation may even be found under high levels of gene flow and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.

SNP discovery using Next Generation Transcriptomic Sequencing in Atlantic herring (Clupea harengus)

The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.

Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic, including two temperature clines (5-12 °C) and two salinity clines (5-35‰). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic-North Sea transition area, North Sea/British Isles and North Atlantic; notably, samples exhibited divergent clustering patterns for neutral and selected loci. We found statistically strong evidence for divergent selection at 16 outlier loci on a global scale, and significant correlations with temperature and salinity at nine loci. On regional scales, we identified two outlier loci with parallel patterns across temperature clines and five loci associated with temperature in the North Sea/North Atlantic. Likewise, we found seven replicated outliers, of which five were significantly associated with low salinity across both salinity clines. Our results reveal a complex pattern of varying spatial genetic variation among outlier loci, likely reflecting adaptations to local environments. In addition to disclosing the fine scale of local adaptation in a highly vagile species, our data emphasize the need to preserve functionally important biodiversity.

Gene-associated markers provide tools for tackling illegal fishing and false eco-certification

Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.

Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake

The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).

Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring

Regulations on the exploitation of populations of commercially important fish species and the ensuing consumer interest in sustainable products have increased the need to accurately identify the population of origin of fish and fish products. Although genomics-based tools have proven highly useful, there are relatively few examples in marine fish displaying accurate origin assignment. We synthesize data for 156 single-nucleotide polymorphisms typed in 1039 herring, Clupea harengus L., spanning the Northeast Atlantic to develop a tool that allows assignment of individual herring to their regional origin. We show the method's suitability to address specific biological questions, as well as management applications. We analyse temporally replicated collections from two areas, the Skagerrak (n = 81, 84, 66) and the western Baltic (n = 52, 52). Both areas harbour heavily fished mixed-origin stocks, complicating management issues. We report novel genetic evidence that herring from the Baltic Sea contribute to catches in the North Sea, and find support that western Baltic feeding aggregations mainly constitute herring from the western Baltic with contributions from the Eastern Baltic. Our study describes a general approach and outlines a database allowing individual assignment and traceability of herring across a large part of its East Atlantic distribution.

Making Ireland Modern

Making Ireland Modern is a cross-disciplinary, inter-institutional, inter-media design and research project which emerged from an open competition (won by Boyd and McLaughlin) to commission/curate the Irish pavilion for the Venice biennale 2014. It explores the relationship between architecture, infrastructure and technology in the building of a new nation. Constructed as a demountable, open matrix of drawings, photographs, models and other artefacts, the exhibition (12 x 5 x 6 metres) presents ten infrastructural episodes – Negation, Electricity, Health, Transportation, Television, Aviation, Education, Telecommunications, Motorways, Data – spanning a period of one hundred years from 1916-2016. Exploring a range of scales from the detail design of objects to entire landscapes and other territories, Making Ireland Modern describes architecture’s role in transforming the physical and cultural identity of the new state through its intersession in the everyday lives of its population. In 2015, we were commissioned by the Arts Council of Ireland to expand and develop the pavilion for a three cities tour of Ireland as one of the five major strands of the Arts Council’s Art2016 programme of Irish State’s 1916-2016 centennial celebrations (2016).