Representing USDL for humans and tools

This chapter deals with technical aspects of how USDL service descriptions can be read from and written to different representations for use by humans and tools. A combination of techniques for representing and exchanging USDL have been drawn from Model-Driven Engineering and Semantic Web technologies. The USDL language's structural definition is specified as a MOF meta-model, but some modules were originally defined using the OWL language from the Semantic Web community and translated to the meta-model format. We begin with the important topic of serializing USDL descriptions into XML, so that they can be exchanged beween editors, repositories, and other tools. The following topic is how USDL can be made available through the Semantic Web as a network of linked data, connected via URIs. Finally, consideration is given to human-readable representations of USDL descriptions, and how they can be generated, in large part, from the contents of a stored USDL model.

Prognostic value of hTERT mRNA expression in surgical samples of lung cancer patients : the European Early Lung Cancer Project

Lung cancer is the most important cause of cancer-related mortality. Resectability and eligibility for treatment with adjuvant chemotherapy is determined by staging according to the TNM classification. Other determinants of tumour behaviour that predict disease outcome, such as molecular markers, may improve decision-making. Activation of the gene encoding human telomerase reverse transcriptase (hTERT) is implicated in the pathogenesis of lung cancer, and consequently detection of hTERT mRNA might have prognostic value for patients with early stage lung cancer. A cohort of patients who underwent a complete resection for early stage lung cancer was recruited as part of the European Early Lung Cancer (EUELC) project. In 166 patients expression of hTERT mRNA was determined in tumour tissue by quantitative real-time RT-PCR and related to that of a house-keeping gene (PBGD). Of a subgroup of 130 patients tumour-distant normal tissue was additionally available for hTERT mRNA analysis. The correlation between hTERT levels of surgical samples and disease-free survival was determined using a Fine and Gray hazard model. Although hTERT mRNA positivity in tumour tissue was significantly associated with clinical stage (Fisher's exact test p=0.016), neither hTERT mRNA detectability nor hTERT mRNA levels in tumour tissue were associated with clinical outcome. Conversely, hTERT positivity in adjacent normal samples was associated with progressive disease, 28% of patients with progressive disease versus 7.5% of disease-free patients had detectable hTERT mRNA in normal tissue [adjusted HR: 3.60 (1.64-7.94), p=0.0015]. hTERT mRNA level in tumour tissue has no prognostic value for patients with early stage lung cancer. However, detection of hTERT mRNA expression in tumour-distant normal lung tissue may indicate an increased risk of progressive disease.

Comparison of historic exploration with contemporary space policy suggests a retheorisation of settings

The 2008 NASA Astrobiology Roadmap provides one way of theorising this developing field, a way which has become the normative model for the discipline: science-and scholarship-driven funding for space. By contrast, a novel re-evaluation of funding policies is undertaken in this article to reframe astrobiology, terraforming and associated space travel and research. Textual visualisation, discourse and numeric analytical methods, and value theory are applied to historical data and contemporary sources to re-investigate significant drivers and constraints on the mechanisms of enabling space exploration. Two data sets are identified and compared: the business objectives and outcomes of major 15th-17th century European joint-stock exploration and trading companies and a case study of a current space industry entrepreneur company. Comparison of these analyses suggests that viable funding policy drivers can exist outside the normative science and scholarship-driven roadmap. The two drivers identified in this study are (1) the intrinsic value of space as a territory to be experienced and enjoyed, not just studied, and (2) the instrumental, commercial value of exploiting these experiences by developing infrastructure and retail revenues. Filtering of these results also offers an investment rationale for companies operating in, or about to enter, the space business marketplace.

Fine-needle aspiration cytology of Merkel cell carcinoma-A review of 69 cases

Background This study reviewed the clinical presentation, cytologic findings and the immunophenotype of 69 Merkel Cell Carcinoma (MCC) cases sampled by FNA. Methods Demographic and clinical data, the cytology findings and results of ancillary testing were reviewed. Results Median patient age was 78 years (37 – 104) with a 1:1.8 female to male ratio. The most common FNA sites sampled included lymph nodes in the neck, the axillary region, the inguinal region and the parotid gland. Most patients had a history of MCC (68%) &/or non-MCC malignancy (70%). The common cytologic pattern was a cellular smear with malignant cells arranged in a dispersed pattern with variable numbers of disorganised groups of cells. Cytoplasm was scant or absent and nuclei showed mild to moderate anisokaryosis, stippled chromatin, inconspicuous nucleoli and nuclear molding. Numerous apoptotic bodies were often present. Cell block samples (28 cases) were usually positive for cytokeratins in a perinuclear dot pattern, including 88% of cases with CK20 positivity. CD56 was the most sensitive (95%) neuroendocrine marker on cell blocks and was also positive with flow cytometry in 9 cases tested. Conclusions MCC is most commonly seen in FNA specimens from the head and neck of elderly patients, often with a history of previous skin lesions. Occasional cases present in younger patients and some may be mistaken for other round blue cell tumors, such as lymphoma. CD 56 may be a useful marker in cell block preparations and in flow cytometric analysis of MCC.

Telomere length in circulating leukocytes is associated with lung function and disease

Several clinical studies suggest the involvement of premature ageing processes in chronic obstructive pulmonary disease (COPD). Using an epidemiological approach, we studied whether accelerated ageing indicated by telomere length, a marker of biological age, is associated with COPD and asthma, and whether intrinsic age-related processes contribute to the interindividual variability of lung function. Our meta-analysis of 14 studies included 934 COPD cases with 15 846 controls defined according to the Global Lungs Initiative (GLI) criteria (or 1189 COPD cases according to the Global Initiative for Chronic Obstructive Lung Disease (GOLD) criteria), 2834 asthma cases with 28 195 controls, and spirometric parameters (forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC) of 12 595 individuals. Associations with telomere length were tested by linear regression, adjusting for age, sex and smoking status. We observed negative associations between telomere length and asthma (β= −0.0452, p=0.024) as well as COPD (β= −0.0982, p=0.001), with associations being stronger and more significant when using GLI criteria than those of GOLD. In both diseases, effects were stronger in females than males. The investigation of spirometric indices showed positive associations between telomere length and FEV1 (p=1.07×10−7), FVC (p=2.07×10−5), and FEV1/FVC (p=5.27×10−3). The effect was somewhat weaker in apparently healthy subjects than in COPD or asthma patients. Our results provide indirect evidence for the hypothesis that cellular senescence may contribute to the pathogenesis of COPD and asthma, and that lung function may reflect biological ageing primarily due to intrinsic processes, which are likely to be aggravated in lung diseases.

Collaborative data exploration interfaces - From participatory sensing to participatory sensemaking

As technological capabilities for capturing, aggregating, and processing large quantities of data continue to improve, the question becomes how to effectively utilise these resources. Whenever automatic methods fail, it is necessary to rely on human background knowledge, intuition, and deliberation. This creates demand for data exploration interfaces that support the analytical process, allowing users to absorb and derive knowledge from data. Such interfaces have historically been designed for experts. However, existing research has shown promise in involving a broader range of users that act as citizen scientists, placing high demands in terms of usability. Visualisation is one of the most effective analytical tools for humans to process abstract information. Our research focuses on the development of interfaces to support collaborative, community-led inquiry into data, which we refer to as Participatory Data Analytics. The development of data exploration interfaces to support independent investigations by local communities around topics of their interest presents a unique set of challenges, which we discuss in this paper. We present our preliminary work towards suitable high-level abstractions and interaction concepts to allow users to construct and tailor visualisations to their own needs.

Thinking like Disney: Supporting the Disney method using ambient feedback based on group performance

The Disney method is a collaborative creativity technique that uses three roles - dreamer, realist and critic - to facilitate the consideration of different perspectives on a topic. Especially for novices it is important to obtain guidance in applying this method. One way is providing groups with a trained moderator. However, feedback about the group’s behavior might interrupt the flow of the idea finding process. We built and evaluated a system that provides ambient feedback to a group about the distribution of their statements among the three roles. Our preliminary field study indicates that groups supported by the system contribute more and roles are used in a more balanced way while the visualization does not disrupt the group work.

The ultimate edge: The case for planning media for sustaining space communities

Governments and intergovernmental organisations have long recognised that space communities – the ultimate ‘settlements at the edge’ – will exist one day and have based their first plans for these on another region ‘at the edge’, the Antarctic. United States President Eisenhower proposed to the United Nations in 1960 that the principles of the Antarctic Treaty be applied to outer space and celestial bodies (State Department, n.d.). Three years later the UN adopted the Declaration of Legal Principles Governing the Activities of States in the Exploration and Use of Outer Space and in 1967 that became the Outer Space Treaty. According to the UN Office for Outer Space Affairs, ‘the Treaty was opened for signature by the three depository Governments (the Russian Federation, the United Kingdom and the United States of America) in January 1967, and it entered into force in October 1967’ (Office for Outer Space Affairs, n.d). The status of the treaty (at time of writing) was 89 signatories and 102 parties (Office for Disarmament Affairs, n.d.). Other related instruments include the Rescue Agreement, the Liability Convention, the Registration Convention and the Moon Agreement (Office for Outer Space Affairs, n.d.-a). Jumping to the present, a newsagency reported in July 2014 (Reuters, 2014) that the British Government had shortlisted eight aerodromes in its search for a potential base for the UK’s first spaceplane flights which Ministers want to happen by 2018 (UK Space Agency, 2014). The United States already has a spaceport, in New Mexico (Cokley, Rankin, Heinrich, & McAuliffe, 2013)...

Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index

Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and approximately 2.8 million SNPs in up to 123,865 individuals with targeted follow up of 42 SNPs in up to 125,931 additional individuals. We confirmed 14 known obesity susceptibility loci and identified 18 new loci associated with body mass index (P < 5 x 10(-)(8)), one of which includes a copy number variant near GPRC5B. Some loci (at MC4R, POMC, SH2B1 and BDNF) map near key hypothalamic regulators of energy balance, and one of these loci is near GIPR, an incretin receptor. Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation.

Evaluating viewpoint entropy for ribbon representation of protein structure

While many measures of viewpoint goodness have been proposed in computer graphics, none have been evaluated for ribbon representations of protein secondary structure. To fill this gap, we conducted a user study on Amazon’s Mechanical Turk platform, collecting human viewpoint preferences from 65 participants for 4 representative su- perfamilies of protein domains. In particular, we evaluated viewpoint entropy, which was previously shown to be a good predictor for human viewpoint preference of other, mostly non-abstract objects. In a second study, we asked 7 molecular biology experts to find the best viewpoint of the same protein domains and compared their choices with viewpoint entropy. Our results show that viewpoint entropy overall is a significant predictor of human viewpoint preference for ribbon representations of protein secondary structure. However, the accuracy is highly dependent on the complexity of the structure: while most participants agree on good viewpoints for small, non-globular structures with few secondary structure elements, viewpoint preference varies considerably for complex structures. Finally, experts tend to choose viewpoints of both low and high viewpoint entropy to emphasize different aspects of the respective structure.

DIY/DIWO media architecture: The InstaBooth

Building on previous discourse regarding the ability of media architecture to be more open and accessible for the purposes of community engagement (Caldwell & Foth, 2014), this chapter explores a particular case study that was designed, constructed and implemented with the intention of allowing city users to participate in the development and creation of media architecture, the InstaBooth. In this chapter, we first explore DIY (do it yourself) and DIWO (do it with others) phenomena to examine what motivates the DIY cultures, communities, and practices. Secondly, in this chapter, we define and discuss our implementation of a DIY / DIWO media architecture example, the InstaBooth. The InstaBooth project pro-vides an opportunity to question the effectiveness of a DIY driven media architec-ture artefact to see to what extent it impacts on the experience of its users and for what benefit.