The area of coordinated and multiple views has been steadily developing and maturing over the past fifteen years. Some may say that it is a "solved problem', while others argue that we are only just scratching the surface of the subject. Considering merely the CMV conference series, it is clear to see that in the early years researchers were concerned with models and techniques, while in latter years authors presented more work on how to apply these ideas to different domains. It is our view that there is still much research to be done, but the subject is changing and developing as a tool for visual analytics. This paper provides the "state of the art' of CMV, it describes areas that should be developed further and looks at what the future may hold for coordinated and multiple views.

/pdf/state-of-the-art-coordinated-multiple-views-in-exploratory-2shzg0xs8s.pdf

State of the Art: Coordinated & Multiple Views in Exploratory Visualization

The Virtual-Reality Peripheral Network (VRPN) system provides a device-independent and network-transparent interface to virtual-reality peripherals. VRPN's application of factoring by function and of layering in the context of devices produces an interface that is novel and powerful. VRPN also integrates a wide range of known advanced techniques into a publicly-available system. These techniques benefit both direct VRPN users and those who implement other applications that make use of VR peripherals.

VRPN: a device-independent, network-transparent VR peripheral system

https://www.cell.com/trends/biochemical-sciences/pdf/S0968-0004(13)00131-X.pdf

Stress granules and cell signaling: more than just a passing phase?

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular 'reactive oxygen species' (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation.

/pdf/iron-behaving-badly-inappropriate-iron-chelation-as-a-major-229l082exr.pdf

Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

Regions of protein sequences with biased amino acid composition (so-called Low-Complexity Regions (LCRs)) are abundant in the protein universe. A number of studies have revealed that i) these regions show significant divergence across protein families; ii) the genetic mechanisms from which they arise lends them remarkable degrees of compositional plasticity. They have therefore proved difficult to compare using conventional sequence analysis techniques, and functions remain to be elucidated for most of them. Here we undertake a systematic investigation of LCRs in order to explore their possible functional significance, placed in the particular context of Protein-Protein Interaction (PPI) networks and Gene Ontology (GO)-term analysis. In keeping with previous results, we found that LCR-containing proteins tend to have more binding partners across different PPI networks than proteins that have no LCRs. More specifically, our study suggests i) that LCRs are preferentially positioned towards the protein sequence extremities and, in contrast with centrally-located LCRs, such terminal LCRs show a correlation between their lengths and degrees of connectivity, and ii) that centrally-located LCRs are enriched with transcription-related GO terms, while terminal LCRs are enriched with translation and stress response-related terms. Our results suggest not only that LCRs may be involved in flexible binding associated with specific functions, but also that their positions within a sequence may be important in determining both their binding properties and their biological roles.

/pdf/low-complexity-regions-within-protein-sequences-have-22jz4n4d0r.pdf

Low-complexity regions within protein sequences have position-dependent roles.

Motivation: In recent years, the gulf between the mass of accumulating-research data and the massive literature describing and analyzing those data has widened. The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged.

Results: To this end, we have developed Utopia Documents, a novel PDF reader that semantically integrates visualization and data-analysis tools with published research articles. In a successful pilot with editors of the Biochemical Journal (BJ), the system has been used to transform static document features into objects that can be linked, annotated, visualized and analyzed interactively ( http://www.biochemj.org/bj/424/3/). Utopia Documents is now used routinely by BJ editors to mark up article content prior to publication. Recent additions include integration of various text-mining and biodatabase plugins, demonstrating the system's ability to seamlessly integrate on-line content with PDF articles.

Availability: http://getutopia.com 

Contact: teresa.k.attwood@manchester.ac.uk

Utopia documents

We live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation per se, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard – too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here – a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers…

/pdf/calling-international-rescue-knowledge-lost-in-literature-4wp55sxxm6.pdf

Calling International Rescue: knowledge lost in literature and data landslide!

Network architectures for collaborative virtual reality have traditionally been dominated by client-server and peer-to-peer approaches, with peer-to-peer strategies typically being favored where minimizing latency is a priority and client-server where consistency is key. With increasingly sophisticated behavior models and the demand for better support for haptics, we argue that neither approach provides sufficient support for these scenarios nor, thus, a hybrid architecture is required. We discuss the relative performance of different distribution strategies in the face of real network conditions and illustrate the problems they face. Finally, we present an architecture that successfully meets many of these challenges and demonstrate its use in a distributed virtual prototyping application which supports simultaneous collaboration for assembly, maintenance, and training applications utilizing haptics

A network architecture supporting consistent rich behavior in collaborative interactive applications

In this paper we present work undertaken by the Advanced Interfaces Group at the University of Manchester on the design and development of a system to support large numbers of geographically distributed users in complex, large-scale virtual environments (VEs).We shown how the problem of synchronisation in the face of network limitations is being addressed by the Deva system through the exploitation of subjectivity. Further, we present a model for flexibly describing object behaviours in the VEs.Applications of the system in use are described.

James Marsh

Papers

Low-complexity regions within protein sequences have position-dependent roles.

Utopia documents

Calling International Rescue: knowledge lost in literature and data landslide!

A network architecture supporting consistent rich behavior in collaborative interactive applications

DEVA3: architecture for a large-scale distributed virtual reality system