NEUVis: Comparing Affective and Effective Visualisation

Data visualisations are useful for providing insight from complex scientific data. However, even with visualisation, scientific research is difficult for non-scientists to comprehend. When developed by designers in collaboration with scientists, data visualisation can be used to articulate scientific data in a way that non-experts can understand. Creating human-centred visualisations is a unique challenge, and there are no frameworks to support their design. In response, this thesis presents a practice-led study investigating design methods that can be used to develop Non-Expert User Visualisations (NEUVis), data visualisations for a general public, and the response that people have to different kinds of NEUVis. For this research, two groups of ten users participated in quantitative studies, informed by Yvonna Lincoln and Egon Guba’s method of Naturalistic Inquiry, which asked non-scientists to express their cognitive and emotional response to NEUVis using different media. The three different types of visualisations were infographics, 3D animations and an interactive installation. The installation used in the study, entitled 18S rDNA, was developed and evaluated as part of this research using John Zimmerman’s Research Through Design methodology. 18S rDNA embodies the knowledge and design methods that were developed for this research, and provided an opportunity for explication of the entire NEUVis design process. The research findings indicate that developing visualisations for the non-expert audience requires a new process, different to the way scientists visualise data. The result of this research describes how creative practitioners collaborate with primary researchers and presents a new human-centred design thinking model for NEUVis. This model includes two design tools. The first tool helps designers merge user needs with data they wish to visualise. The second tool helps designers take that merged information and begin an iterative, user-centred design process

Tangible user interface design for climate change education in interactive installation art

© 2014, ISAST. The authors discuss how tangible user interface objects can be important educational and entertainment tools in environmental education. The authors describe their interactive installation artwork Reefs on the Edge, which incorporates tangible user interface objects and combines environmental science and multiple art forms to explore coral reef ecosystems that are threatened by the effects of climate change. The authors/artists argue that the use of tangible user interface in an installation-art setting can help engage and inform the public about crucial environmental issues

Environmentalism, performance and applications: uncertainties and emancipations

This introductory article for a themed edition on environmentalism provides a particular context for those articles that follow, each of which engages with different aspects of environmentalism and performance in community-related settings. Responding to the proposition that there is a lacuna in the field of applied drama and environmentalism (Bottoms, 2010), we suggest that the more significant lack is that of ecocriticism. As the articles in this journal testify, there are many examples of applied theatre practice; what is required is sustained and rigorous critical engagement. It is to the gap of ecocriticism that we address this issue, signalling what we hope is the emergence of a critical field. One response to the multiple challenges of climate change is to more transparently locate the human animal within the environment, as one agent amongst many. Here, we seek to transparently locate the critic, intertwining the personal – ourselves, human actants – with global environmental concerns. This tactic mirrors much contemporary writing on climate change and its education, privileging personal engagement – a shift we interrogate as much as we perform. The key trope we anchor is that of uncertainty: the uncertainties that accompany stepping into a new research environment; the uncertainties arising from multiple relations (human and non-human); the uncertainties of scientific fact; the uncertainties of forecasting the future; and the uncertainties of outcomes – including those of performance practices. Having analysed a particular turn in environmental education (towards social learning) and the failure to successfully combine ‘art and reality’ in recent UK mainstream theatre events, such uncertainties lead to our suggestion for an ‘emancipated’ environmentalism. In support of this proposal, we offer up a reflection on a key weekend of performance practice that brought us to attend to the small – but not insignificant – and to consider first hand the complex relationships between environmental ‘grand narratives’ and personal experiential encounters. Locating ourselves within the field and mapping out some of the many conceptual challenges attached to it serves to introduce the territories which the following journal articles expand upon

Caspase-8 and RIP kinases regulate bacteria-induced innate immune responses and cell death

A number of pathogens cause host cell death upon infection, and Yersinia pestis, infamous for its role in large pandemics such as the Black Death in medieval Europe, induces considerable cytotoxicity. The rapid killing of macrophages induced by Y. pestis, dependent upon type III secretion system effector Yersinia outer protein J (YopJ), is minimally affected by the absence of caspase-1, caspase-11, Fas ligand, and TNF. Caspase-8 is known to mediate apoptotic death in response to infection with several viruses and to regulate programmed necrosis (necroptosis), but its role in bacterially induced cell death is poorly understood. Here we provide genetic evidence for a receptor-interacting protein (RIP) kinase-caspase-8-dependent macrophage apoptotic death pathway after infection with Y. pestis, influenced by Toll-like receptor 4-TIR-domain-containing adapter-inducing interferon-β (TLR4-TRIF). Interestingly, macrophages lacking either RIP1, or caspase-8 and RIP3, also had reduced infection-induced production of IL-1β, IL-18, TNF, and IL-6; impaired activation of the transcription factor NF-κB; and greatly compromised caspase-1 processing. Cleavage of the proform of caspase-1 is associated with triggering inflammasome activity, which leads to the maturation of IL-1β and IL-18, cytokines important to host responses against Y. pestis and many other infectious agents. Our results identify a RIP1-caspase-8/RIP3-dependent caspase-1 activation pathway after Y. pestis challenge. Mice defective in caspase-8 and RIP3 were also highly susceptible to infection and displayed reduced proinflammatory cytokines and myeloid cell death. We propose that caspase-8 and the RIP kinases are key regulators of macrophage cell death, NF-κB and inflammasome activation, and host resistance after Y. pestis infection

Speculating on biodesign in the future home

The home is a place of shelter, a place for family, and for separation from other parts of life, such as work. Global challenges, the most pressing of which are currently the COVID-19 pandemic and climate change has forced extra roles into many homes and will continue to do so in the future. Biodesign integrates living organisms into designed solutions and can offer opportunities for new kinds of technologies to facilitate a transition to the home of the future. Many families have had to learn to work alongside each other, and technology has mediated a transition from standard models of operation for industries. These are the challenges of the 21st century that mandate careful thinking around interactive systems and innovations that support new ways of living and working at home. In this workshop, we will explore opportunities for biodesign interactive systems in the future home. We will bring together a broad group of researchers in HCI, design, and biosciences to build the biodesign community and discuss speculative design futures. The outcome will generate an understanding of the role of interactive biodesign systems at home, as a place with extended functionalities

InterPro, progress and status in 2005

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)

Descent toward the icehouse: Eocene sea surface cooling inferred from GDGT distributions

The TEX86 proxy, based on the distribution of marine isoprenoidal glycerol dialkyl glycerol tetraether lipids (GDGTs), is increasingly used to reconstruct sea surface temperature (SST) during the Eocene epoch (56.0–33.9 Ma). Here we compile published TEX86 records, critically reevaluate them in light of new understandings in TEX86 palaeothermometry, and supplement them with new data in order to evaluate long-term temperature trends in the Eocene. We investigate the effect of archaea other than marine Thaumarchaeota upon TEX86 values using the branched-to-isoprenoid tetraether index (BIT), the abundance of GDGT-0 relative to crenarchaeol (%GDGT-0), and the Methane Index (MI). We also introduce a new ratio, % GDGTRS, which may help identify Red Sea-type GDGT distributions in the geological record. Using the offset between TEX86H and TEX86L(ΔH-L) and the ratio between GDGT-2 and GDGT-3 ([2]/[3]), we evaluate different TEX86 calibrations and present the first integrated SST compilation for the Eocene (55 to 34 Ma). Although the available data are still sparse some geographic trends can now be resolved. In the high latitudes (>55°), there was substantial cooling during the Eocene (~6°C). Our compiled record also indicates tropical cooling of ~2.5°C during the same interval. Using an ensemble of climate model simulations that span the Eocene, our results indicate that only a small percentage (~10%) of the reconstructed temperature change can be ascribed to ocean gateway reorganization or paleogeographic change. Collectively, this indicates that atmospheric carbon dioxide (pCO2) was the likely driver of surface water cooling during the descent toward the icehouse

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

publication en ligne. Article dans revue scientifique avec comité de lecture. nationale.National audienceThe human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology