Reflections on QuestVis: A Visualization System for an Environmental Sustainability Model

We present lessons learned from the iterative design of QuestVis, a visualization interface for the QUEST environmental sustainability model. The QUEST model predicts the effects of policy choices in the present using scenarios of future outcomes that consist of several hundred indicators. QuestVis treats this information as a high-dimensional dataset, and shows the relationship between input choices and output indicators using linked views and a compact multilevel browser for indicator values. A first prototype also featured an overview of the space of all possible scenarios based on dimensionality reduction, but this representation was deemed to be be inappropriate for a target audience of people unfamiliar with data analysis. A second prototype with a considerably simplified and streamlined interface was created that supported comparison between multiple scenarios using a flexible approach to aggregation. However, QuestVis was not deployed because of a mismatch between the design goals of the project and the true needs of the target user community, who did not need to carry out detailed analysis of the high-dimensional dataset. We discuss this breakdown in the context of a nested model for visualization design and evaluation

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

Although considerable progress has been made in dissecting the signaling pathways involved in the innate immune response, it is now apparent that this response can no longer be productively thought of in terms of simple linear pathways. InnateDB (www.innatedb.ca) has been developed to facilitate systems-level analyses that will provide better insight into the complex networks of pathways and interactions that govern the innate immune response. InnateDB is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with centralized annotation on the broader human and mouse interactomes. To date, more than 3500 innate immunity-relevant interactions have been contextually annotated through the review of 1000 plus publications. Integrated into InnateDB are novel bioinformatics resources, including network visualization software, pathway analysis, orthologous interaction network construction and the ability to overlay user-supplied gene expression data in an intuitively displayed molecular interaction network and pathway context, which will enable biologists without a computational background to explore their data in a more systems-oriented manner

EFSA Panel on Food Contact Materials, Enzymes, Flavourings and Processing Aids (CEF); Scientific Opinion on Flavouring Group Evaluation 9, Revision 4 (FGE.09Rev4): Secondary alicyclic saturated and unsaturated alcohols, ketones and esters containing secondary alicyclic alcohols from chemical group 8 and 30, and an ester of a phenol derivative from chemical group 25

<p>The Panel on Food Contact Materials, Enzymes, Flavourings and Processing Aids of the European Food Safety Authority was requested to evaluate 21 flavouring substances in the Flavouring Group Evaluation 9, Revision 4, using the Procedure in Commission Regulation (EC) No 1565/2000. The present revision of FGE.09 includes the assessment of four additional flavouring substances, p-menthan-3-one [FL-no: 07.059], 2,6,6-trimethylcyclohex-2-en-1-one [FL-no: 07.202], l-piperitone [FL-no: 07.255] and menthol 1-and 2-propylene glycol carbonate [FL-no: 09.843]. None of the substances were considered to have genotoxic potential. The substances were evaluated through a stepwise approach (the Procedure) that integrates information on structure-activity relationships, intake from current uses, toxicological threshold of concern, and available data on metabolism and toxicity. The Panel concluded that the 20 substances [FL-no: 02.070, 02.075, 02.135, 02.167, 06.136, 07.059, 07.202, 07.203, 07.255, 09.154, 09.355, 09.520, 09.618, 09.619, 09.621, 09.843, 09.870, 09.929, 09.935 and 09.949] do not give rise to safety concerns at their levels of dietary intake, estimated on the basis of the MSDI approach. For the remaining candidate substance [FL-no: 07.207], additional toxicity data are requested (further metabolism and/or toxicity studies). Besides the safety assessment of these flavouring substances, the specifications for the materials of commerce have been considered. Specifications including complete purity criteria and identity for the materials of commerce have been provided for all candidate substances.</p&gt

Attitudes towards fibromyalgia: A survey of Canadian chiropractic, naturopathic, physical therapy and occupational therapy students

<p>Abstract</p> <p>Background</p> <p>The frequent use of chiropractic, naturopathic, and physical and occupational therapy by patients with fibromyalgia has been emphasized repeatedly, but little is known about the attitudes of these therapists towards this challenging condition.</p> <p>Methods</p> <p>We administered a cross-sectional survey to 385 senior Canadian chiropractic, naturopathic, physical and occupational therapy students in their final year of studies, that inquired about attitudes towards the diagnosis and management of fibromyalgia.</p> <p>Results</p> <p>336 students completed the survey (response rate 87%). While they disagreed about the etiology (primarily psychological 28%, physiological 23%, psychological and physiological 15%, unsure 34%), the majority (58%) reported that fibromyalgia was difficult to manage. Respondants were also conflicted in whether treatment should prioritize symptom relief (65%) or functional gains (85%), with the majority (58%) wanting to do both. The majority of respondents (57%) agreed that there was effective treatment for fibromyalgia and that they possessed the required clinical skills to manage patients (55%).</p> <p>Chiropractic students were most skeptical in regards to fibromyalgia as a useful diagnostic entity, and most likely to endorse a psychological etiology. In our regression model, only training in naturopathic medicine (unstandardized regression coefficient = 0.33; 95% confidence interval = 0.11 to 0.56) and the belief that effective therapies existed (unstandardized regression coefficient = 0.42; 95% confidence interval = 0.30 to 0.54) were associated with greater confidence in managing patients with fibromyalgia.</p> <p>Conclusion</p> <p>The majority of senior Canadian chiropractic, naturopathic, physical and occupational therapy students, and in particular those with naturopathic training, believe that effective treatment for fibromyalgia exists and that they possess the clinical skillset to effectively manage this disorder. The majority place high priority on both symptom relief and functional gains when treating fibromyalgia.</p

Functional illness in primary care: dysfunction versus disease

<p>Abstract</p> <p>Background</p> <p>The Biopsychosocial Model aims to integrate the biological, psychological and social components of illness, but integration is difficult in practice, particularly when patients consult with medically unexplained physical symptoms or functional illness.</p> <p>Discussion</p> <p>This Biopsychosocial Model was developed from General Systems Theory, which describes nature as a dynamic order of interacting parts and processes, from molecular to societal. Despite such conceptual progress, the biological, psychological, social and spiritual components of illness are seldom managed as an integrated whole in conventional medical practice. This is because the biomedical model can be easier to use, clinicians often have difficulty relinquishing a disease-centred approach to diagnosis, and either dismiss illness when pathology has been excluded, or explain all undifferentiated illness in terms of psychosocial factors. By contrast, traditional and complementary treatment systems describe reversible functional disturbances, and appear better at integrating the different components of illness. Conventional medicine retains the advantage of scientific method and an expanding evidence base, but needs to more effectively integrate psychosocial factors into assessment and management, notably of 'functional' illness. As an aid to integration, pathology characterised by structural change in tissues and organs is contrasted with dysfunction arising from disordered physiology or psychology that may occur independent of pathological change.</p> <p>Summary</p> <p>We propose a classification of illness that includes orthogonal dimensions of pathology and dysfunction to support a broadly based clinical approach to patients; adoption of which may lead to fewer inappropriate investigations and secondary care referrals and greater use of cognitive behavioural techniques, particularly when managing functional illness.</p

A test of the adaptive network explanation of functional disorders using a machine learning analysis of symptoms.

The classification and etiology of functional disorders is controversial. Evidence supports both psychological and biological (disease) models that show, respectively, that functional disorders should be classified as one (bodily distress syndrome) and many (e.g., irritable bowel syndrome (IBS), fibromyalgia syndrome (FMS), and chronic fatigue syndrome (CFS)). Two network models (symptom network and adaptive network) can explain the specificity and covariation of symptomatology, but only the adaptive network model can explain the covariation of the somatic symptoms of functional disorders. The adaptive network model is based on the premise that a network of biological mechanisms has emergent properties and can exhibit adaptation. The purpose of this study was to test the predictions that symptom similarity increases with pathology and that network connection strengths vary with pathology, as this would be consistent with the notion that functional disorder pathology arises from network adaptation. We conducted a symptom internet survey followed by machine learning analysis. Participants were 1751 people reporting IBS, FMS or CFS diagnosis who completed a 61-item symptom questionnaire. Eleven symptom clusters were identified. Differences in symptom clusters between IBS, FMS and CFS groups decreased as overall symptom frequency increased. The strength of outgoing connections between clusters varied as a function of symptom frequency and single versus multiple diagnoses. The findings suggest that the pathology of functional disorders involves an increase in the activity and causal connections between several symptom causing mechanisms. The data provide support for the proposal that the body is capable of complex adaptation and that functional disorders result when rules that normally improve adaptation create maladaptive change

Cerebral : visualizing multiple experimental conditions on a graph with biological context

Systems biologists use interaction graphs to model the behaviour of biological systems at the molecular level. In an iterative process, such biologists observe the reactions of living cells under various experimental conditions, view the results in the context of the interaction graph, and then propose changes to the graph model. These graphs represent dynamic knowledge of the biological system being studied and evolve as new insight is gained from the experimental data. While numerous graph layout and drawing packages are available, these tools did not fully meet the needs of our immunologist collaborators. In this thesis, we describe the data display needs of these immunologists and translate these needs into visual encoding decisions. These decisions led us to create Cerebral, a system that uses a biologically guided graph layout and incorporates experimental data directly into the graph display. Our graph layout algorithm uses simulated annealing with constraints, optimized with a uniform grid to have an expected runtime of o(E/V). Small multiple views of different experimental conditions and a measurement-driven parallel coordinates view enable correlations between experimental conditions to be analyzed at the same time that the measurements are viewed in the graph context. This combination of coordinated views allows the biologist to view the data from many different perspectives simultaneously. To illustrate the typical analysis tasks performed, we analyze two datasets using Cerebral. Based on feedback from our collaborators, we conclude that Cerebral is a valuable tool for analyzing experimental data in the context of an interaction graph model.Science, Faculty ofComputer Science, Department ofGraduat

BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm057 Systems biology Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation

Summary: Cerebral (Cell Region-Based Rendering And Layout) is an open-source Java plugin for the Cytoscape biomolecular interaction viewer. Given an interaction network and subcellular localization annotation, Cerebral automatically generates a view of the network in the style of traditional pathway diagrams, providing an intuitive interface for the exploration of a biological pathway or system. The molecules are separated into layers according to their subcellular localization. Potential products or outcomes of the pathway can be shown at the bottom of the view, clustered according to any molecular attribute data—protein function—for example. Cerebral scales well to networks containing thousands of nodes