Integrating musicology's heterogeneous data sources for better exploration

Musicologists have to consult an extraordinarily heterogeneous body of primary and secondary sources during all stages of their research. Many of these sources are now available online, but the historical dispersal of material across libraries and archives has now been replaced by segregation of data and metadata into a plethora of online repositories. This segregation hinders the intelligent manipulation of metadata, and means that extracting large tranches of basic factual information or running multi-part search queries is still enormously and needlessly time consuming. To counter this barrier to research, the “musicSpace” project is experimenting with integrating access to many of musicology’s leading data sources via a modern faceted browsing interface that utilises Semantic Web and Web2.0 technologies such as RDF and AJAX. This will make previously intractable search queries tractable, enable musicologists to use their time more efficiently, and aid the discovery of potentially significant information that users did not think to look for. This paper outlines our work to date

Orchestrating musical (meta)data to better address the real-world search queries of musicologists

The dispersal of musicology’s diverse array of primary and secondary sources across countless libraries and archives was once an enormous obstacle to conducting research, but this has largely been overcome by the digitisation and online publication of resources in recent years. Yet, while the research process has undoubtedly been revolutionised, the current situation is far from perfect, as the digitisation of resources has often been accompanied by their segregation—according to media type, date of publication, subject, language, copyright holder, etc.—into a myriad of discrete online repositories, often with little thought having been given to interoperability. Given that musicological research typically cuts across such artificial divisions, this segregation of data means that accessing basic factual information or running multi-part search queries remains endlessly complicated, needlessly time consuming, and sometimes impossible. This barrier to tractability is only exacerbated by the limited capabilities of currently deployed search interfaces. There is one seemingly obvious solution to this query dilemma: enable integrated real-time querying over all the available metadata from as many sources as possible, and allow users to use that metadata to guide their queries. This solution implies that all data that could feasibly be construed as useful, but which is buried in the records, is extracted in some way, and that there is an interaction approach that enables metadata to be explored effectively and allows for the formulation of rich compound queries. The musicSpace project has taken a dual approach towards realising this solution. At the back-end we are developing services to integrate and, where necessary, surface (meta)data from many of musicology’s most important online resources, including the British Library Music Collections catalogue, the British Library Sound Archive catalogue, Cecilia, Copac, Grove Music Online, Naxos Music Library, Répertoire International de Littérature Musicale (RILM), and Répertoire International des Sources Musicale (RISM) UK and Ireland. While at the front-end, in order to optimise the exploration of this integrated dataset, we are developing a modern web-based faceted browsing interface that utilises Semantic Web and Web2.0 technologies such as RDF and AJAX, and which is based on the existing ‘mSpace’ codebase. Our poster outlines the approach we have taken to importing, enriching and integrating the metadata provided by our data partners, and gives examples of the real-world musicological research questions that musicSpace has enabled

A Psychophysical Experiment Regarding Components of the Plausibility Illusion

We report on the design and results of an experiment investigating factors influencing Slater’s Plausibility Illusion (Psi) in virtual environments. Slater proposed Psi and Place Illusion (PI) as orthogonal components of virtual experience which contribute to realistic response in a VE. PI corresponds to the traditional conception of presence as “being there,” so there exists a substantial body of previous research relating to PI, but very little relating to Psi. We developed this experiment to investigate the components of plausibility illusion using subjective matching techniques similar to those used in color science. Twenty-one participants each experienced a scenario with the highest level of coherence (the extent to which a scenario matches user expectations and is internally consistent), then in eight different trials chose transitions from lower-coherence to higher-coherence scenarios with the goal of matching the level of Psi they felt in the highest-coherence scenario. At each transition, participants could change one of the following coherence characteristics: the behavior of the other virtual humans in the environment, the behavior of their own body, the physical behavior of objects, or the appearance of the environment. Participants tended to choose improvements to the virtual body before any other improvements. This indicates that having an accurate and well-behaved representation of oneself in the virtual environment is the most importa

Cell structure, stiffness and permeability of freeze-dried collagen scaffolds in dry and hydrated states.

UNLABELLED: Scaffolds for tissue engineering applications should be highly permeable to support mass transfer requirements while providing a 3-D template for the encapsulated biological cells. High porosity and cell interconnectivity result in highly compliant scaffolds. Overstraining occurs easily with such compliant materials and can produce misleading results. In this paper, the cell structure of freeze-dried collagen scaffolds, in both dry and hydrated states, was characterised using X-ray tomography and 2-photon confocal microscopy respectively. Measurements have been made of the scaffold's Young's modulus using conventional mechanical testing and a customised see-saw testing configuration. Specific permeability was measured under constant pressure gradient and compared with predictions. The collagen scaffolds investigated here have a coarse cell size (∼100-150 μm) and extensive connectivity between adjacent cells (∼10-30 μm) in both dry and hydrated states. The Young's modulus is very low, of the order of 10 kPa when dry and 1 kPa when hydrated. There is only a single previous study concerning the specific permeability of (hydrated) collagen scaffolds, despite its importance in nutrient diffusion, waste removal and cell migration. The experimentally measured value reported here (5 × 10(-)(10)m(2)) is in good agreement with predictions based on Computational Fluid Dynamics simulation and broadly consistent with the Carman-Kozeny empirical estimate. It is however about three orders of magnitude higher than the single previously-reported value and this discrepancy is attributed at least partly to the high pressure gradient imposed in the previous study. STATEMENT OF SIGNIFICANCE: The high porosity and interconnectivity of tissue engineering scaffolds result in highly compliant structures (ie large deflections under low applied loads). Characterisation is essential if these scaffolds are to be systematically optimised. Scaffold overstraining during characterisation can lead to misleading results. In this study, the stiffness (in dry and hydrated states) and specific permeability of freeze-dried collagen scaffolds have been measured using techniques customised for low stiffness structures. The scaffold cell structure is investigated using X-ray computed tomography, which has been applied previously to visualise such materials, without extracting any structural parameters or simulating fluid flow. These are carried out in this work. 2-photon confocal microscopy is used for the first time to study the structure in hydrated state.This research was supported by the European Research Council (Grant No. 240446) and the EPSRC (EP/E025862/1). Financial support for MCV and RAB has been provided via the WD Armstrong studentship and the National Institute for Health Research (NIHR), respectively.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.actbio.2016.01.04

An Instrumented Walking-Aid to Assess and Retrain Gait

An instrumented walking-aid, the iWA system, has been developed to measure kinematic and kinetic properties of walking aid (WA) use and deliver feedback to improve gait. The clinical requirements, technical specification and design of the system are developed through clinical collaboration. The development of the system is described, including hardware components and data analysis used to process the measured data for assessment. The system measurements are validated under controlled laboratory conditions. The iWA system is evaluated in a typical UK clinical environment by a participant in a rehabilitation session. The resultant data successfully capture the quality of the participant’s walking aid use and agree with clinical opinion, supporting the efficacy of this approach

Effect of Rotation on Scaffold Motion and Cell Growth in Rotating Bioreactors

Efficient use of different bioreactor designs to improve cell growth in three-dimensional scaffolds requires an understanding of their mechanism of action. To address this for rotating wall vessel bioreactors, fluid and scaffold motion were investigated experimentally at different rotation speeds and vessel fill volumes. Low cost bioreactors with single and dual axis rotation were developed to investigate the effect of these systems on human osteoblast proliferation in free floating and constrained collagen-glycosaminoglycan porous scaffolds. A range of scaffold motions (free fall, periodic oscillation, and orbital motion) were observed at the rotation speeds and vessel fluid/air ratios used, with 85% fluid fill and an outer vessel wall velocity of ∼14 mm s$^{−1}$ producing a scaffold in a free fall state. The cell proliferation results showed that after 14 and 21 days of culture, this combination of fluid fill and speed of rotation produced significantly greater cell numbers in the scaffolds than when lower or higher rotation speeds (p  0.05).This research was supported by the European Research Council (Grant No. 240446) and the EPSRC (EP/E025862/1). Financial support for M.C.V. and R.A.B. has been provided through the WD Armstrong studentship and the National Institute for Health Research, respectively

Direct determination of the air-sea CO₂ gas transfer velocity in Arctic sea-ice regions

The Arctic Ocean is an important sink for atmospheric CO₂. The impact of decreasing sea-ice extent and expanding marginal ice zones on Arctic air-sea CO₂ exchange depends on the rate of gas transfer in the presence of sea ice. Sea ice acts to limit air-sea gas exchange by reducing contact between air and water, but is also hypothesised to enhance gas transfer rates across surrounding open water surfaces through physical processes such as increased surface-ocean turbulence from ice-water shear and ice-edge form drag. Here we present the first direct determination of the CO₂ air-sea gas transfer velocity in a wide range of Arctic sea-ice conditions. We show that the gas transfer velocity increases near-linearly with decreasing sea-ice concentration. We also show that previous modeling approaches overestimate gas transfer rates in sea-ice regions

Facilitating return to work through early specialist health-based interventions (FRESH): protocol for a feasibility randomised controlled trial

Background Over one million people sustain traumatic brain injury each year in the UK and more than 10 % of these are moderate or severe injuries, resulting in cognitive and psychological problems that affect the ability to work. Returning to work is a primary rehabilitation goal but fewer than half of traumatic brain injury survivors achieve this. Work is a recognised health service outcome, yet UK service provision varies widely and there is little robust evidence to inform rehabilitation practice. A single-centre cohort comparison suggested better work outcomes may be achieved through early occupational therapy targeted at job retention. This study aims to determine whether this intervention can be delivered in three new trauma centres and to conduct a feasibility, randomised controlled trial to determine whether its effects and cost effectiveness can be measured to inform a definitive trial. Methods/design Mixed methods study, including feasibility randomised controlled trial, embedded qualitative studies and feasibility economic evaluation will recruit 102 people with traumatic brain injury and their nominated carers from three English UK National Health Service (NHS) trauma centres. Participants will be randomised to receive either usual NHS rehabilitation or usual rehabilitation plus early specialist traumatic brain injury vocational rehabilitation delivered by an occupational therapist. The primary objective is to assess the feasibility of conducting a definitive trial; secondary objectives include measurement of protocol integrity (inclusion/exclusion criteria, intervention adherence, reasons for non-adherence) recruitment rate, the proportion of eligible patients recruited, reasons for non-recruitment, spectrum of TBI severity, proportion of and reasons for loss to follow-up, completeness of data collection, gains in face-to-face Vs postal data collection and the most appropriate methods of measuring primary outcomes (return to work, retention) to determine the sample size for a larger trial. Discussion To our knowledge, this is the first feasibility randomised controlled trial of a vocational rehabilitation health intervention specific to traumatic brain injury. The results will inform the design of a definitive trial

The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs