Exploring the Transcriptome of Atlantic Salmon (Salmo salar) Skin, a Major Defense Organ

The skin of fish is the first line of defense against pathogens and parasites. The skin transcriptome of the Atlantic salmon is poorly characterized, and currently only 2,089 expressed sequence tags (ESTs) out of a total of half a million sequences are generated from skin-derived cDNA libraries. The primary aim of this study was to enhance the transcriptomic knowledge of salmon skin by using next-generation sequencing (NGS) technology, namely the Roche-454 platform. An equimolar mixture of high-quality RNA from skin and epidermal samples of salmon reared in either freshwater or seawater was used for 454-sequencing. This technique yielded over 600,000 reads, which were assembled into 34,696 isotigs using Newbler. Of these isotigs, 12 % had not been sequenced in Atlantic salmon, hence representing previously unreported salmon mRNAs that can potentially be skin-specific. Many full-length genes have been acquired, representing numerous biological processes. Mucin proteins are the main structural component of mucus and we examined in greater detail the sequences we obtained for these genes. Several isotigs exhibited homology to mammalian mucins (MUC2, MUC5AC and MUC5B). Mucin mRNAs are generally > 10 kbp and contain large repetitive units, which pose a challenge towards full-length sequence discovery. To date, we have not unearthed any full-length salmon mucin genes with this dataset, but have both N- and C-terminal regions of a mucin type 5. This highlights the fact that, while NGS is indeed a formidable tool for sequence data mining of non-model species, it must be complemented with additional experimental and bioinformatic work to characterize some mRNA sequences with complex features.

The Musical Body: Devising a choreo-musical interpretation for the work Tierkreis (1974-75) by Karlheinz Stockhausen

In this chapter the authors explore a practice-led approach to understanding the role of the body in music performance.

Many writers have discussed the body in music performance, in improvised music, as well as in electronic music. In this chapter the authors offer new modalities of reflection on the musical body in the interpretation of existing contemporary repertoire. Specifically, the authors discuss a re-interpretation of German composer Karlheinz Stockhausen's musical work 'Tierkreis'. Through the development of a specifically physical approach to the performance, the authors investigate the intrinsic relationship between the body and the music and point to an under-explored modality, which is not a musical choreography, but a choreography that is shaped through the musical body itself. It is a modality in which music itself propels forward choreographic ideas, the body becoming the driving force behind musical interpretation. The authors' thinking is influenced by Susan Kozel’s understanding of performance as an ecosystem (Kozel 2007) and framed within a subjective account of musical embodiment.

By merging theory with praxis the authors offer a deeper understanding of the role of the body in music performance and consider how such contributions might lead to new and exciting interpretive frameworks for existing musical repertoires.

Pre-validation methods for developing a patient reported outcome instrument

BACKGROUND: Measures that reflect patients' assessment of their health are of increasing importance as outcome measures in randomised controlled trials. The methodological approach used in the pre-validation development of new instruments (item generation, item reduction and question formatting) should be robust and transparent. The totality of the content of existing PRO instruments for a specific condition provides a valuable resource (pool of items) that can be utilised to develop new instruments. Such 'top down' approaches are common, but the explicit pre-validation methods are often poorly reported. This paper presents a systematic and generalisable 5-step pre-validation PRO instrument methodology.

METHODS: The method is illustrated using the example of the Aberdeen Glaucoma Questionnaire (AGQ). The five steps are: 1) Generation of a pool of items; 2) Item de-duplication (three phases); 3) Item reduction (two phases); 4) Assessment of the remaining items' content coverage against a pre-existing theoretical framework appropriate to the objectives of the instrument and the target population (e.g. ICF); and 5) qualitative exploration of the target populations' views of the new instrument and the items it contains.

RESULTS: The AGQ 'item pool' contained 725 items. Three de-duplication phases resulted in reduction of 91, 225 and 48 items respectively. The item reduction phases discarded 70 items and 208 items respectively. The draft AGQ contained 83 items with good content coverage. The qualitative exploration ('think aloud' study) resulted in removal of a further 15 items and refinement to the wording of others. The resultant draft AGQ contained 68 items.

CONCLUSIONS: This study presents a novel methodology for developing a PRO instrument, based on three sources: literature reporting what is important to patient; theoretically coherent framework; and patients' experience of completing the instrument. By systematically accounting for all items dropped after the item generation phase, our method ensures that the AGQ is developed in a transparent, replicable manner and is fit for validation. We recommend this method to enhance the likelihood that new PRO instruments will be appropriate to the research context in which they are used, acceptable to research participants and likely to generate valid data.

Choosing appropriate patient-reported outcomes instrument for glaucoma research: a systematic review of vision instruments

PURPOSE: To identify vision Patient-Reported Outcomes instruments relevant to glaucoma and assess their content validity.

METHODS: MEDLINE, MEDLINE in Process, EMBASE and SCOPUS (to January 2009) were systematically searched. Observational studies or randomised controlled trials, published in English, reporting use of vision instruments in glaucoma studies involving adults were included. In addition, reference lists were scanned to identify additional studies describing development and/or validation to ascertain the final version of the instruments. Instruments' content was then mapped onto a theoretical framework, the World Health Organization International Classification of Functioning, Disability and Health. Two reviewers independently evaluated studies for inclusion and quality assessed instrument content.

RESULTS: Thirty-three instruments were identified. Instruments were categorised into thirteen vision status, two vision disability, one vision satisfaction, five glaucoma status, one glaucoma medication related to health status, five glaucoma medication side effects and six glaucoma medication satisfaction measures according to each instruments' content. The National Eye Institute Visual Function Questionnaire-25, Impact of Vision Impairment and Treatment Satisfaction Survey-Intraocular Pressure had the highest number of positive ratings in the content validity assessment.

CONCLUSION: This study provides a descriptive catalogue of vision-specific PRO instruments, to inform the choice of an appropriate measure of patient-reported outcomes in a glaucoma context.

Development of a Portable Tissue Micro Array Instrument

Tissue micro array (TMA) is based on the idea of applying miniaturization and a high throughput approach to hybridization-based analyses of tissues. It facilitates biomedical research on a large scale in a single experiment; thus representing one of the most commonly used technologies in translational research. A critical analysis of the existing TMA instruments indicates that there are potential constraints in terms of portability, apart from costs and complexity. This paper will present the development of an affordable, configurable, and portable TMA instrument to allow an efficient collection of tissues, especially in instrument-to-tissue scenarios. The purely mechanical instrument requires no energy sources other than the user, is light weight, portable, and simple to use. [DOI: 10.1115/1.4004922]

Fast recognition of musical sounds based on timbre

Human listeners seem to have an impressive ability to recognize a wide variety of natural sounds. However, there is surprisingly little quantitative evidence to characterize this fundamental ability. Here the speed and accuracy of musical-sound recognition were measured psychophysically with a rich but acoustically balanced stimulus set. The set comprised recordings of notes from musical instruments and sung vowels. In a first experiment, reaction times were collected for three target categories: voice, percussion, and strings. In a go/no-go task, listeners reacted as quickly as possible to members of a target category while withholding responses to distractors (a diverse set of musical instruments). Results showed near-perfect accuracy and fast reaction times, particularly for voices. In a second experiment, voices were recognized among strings and vice-versa. Again, reaction times to voices were faster. In a third experiment, auditory chimeras were created to retain only spectral or temporal features of the voice. Chimeras were recognized accurately, but not as quickly as natural voices. Altogether, the data suggest rapid and accurate neural mechanisms for musical-sound recognition based on selectivity to complex spectro-temporal signatures of sound sources.

Designing Digital Musical Interactions in Experimental Contexts

As NIME's focus has expanded beyond the design reports which were pervasive in the early days to include studies and experiments involving music control devices, we report on a particular area of activity that has been overlooked: designs of music devices in experimental contexts. We demonstrate this is distinct from designing for artistic performances, with a unique set of novel challenges. A survey of methodological approaches to experiments in NIME reveals a tendency to rely on existing instruments or evaluations of new devices designed for broader creative application. We present two examples from our own studies that reveal the merits of designing purpose-built devices for experimental contexts.

Dialogic Instruments: Virtuosity (Re)Located in Improvised Performance

This paper introduces a series of new musical instruments that have been designed to
address questions relating to performative virtuosity in the area of ensemble-based
improvisation. The intentionally exploited inconsistent nature of these instruments
raises questions around traditional notions of instrument mastery and opens up
possible methods of recon?guring the performer-instrument relationship.

Reflecting on Tradition: Four Ulster Musical Lives

Communicating musical knowledge through gesture: Piano teachers’ gestural behaviours across different levels of student proficiency

Teachers’ communication of musical knowledge through physical gesture represents a valuable pedagogical field in need of investigation. This exploratory case study compares the gestural behaviour of three piano teachers while giving individual lessons to students who differed according to piano proficiency levels. The data was collected by video recordings of one-to-one piano lessons and gestures were categorized using two gesture classifications: the spontaneous co-verbal gesture classification (McNeill, 1992; 2005) and spontaneous co-musical gesture classification (Simones, Schroeder & Rodger, 2013). Poisson regression analysis and qualitative observation suggest a relationship between teachers’ didactic intentions and the types of gesture they produced while teaching, as shown by differences in gestural category frequency between teaching students of higher and lower levels of proficiency. Such reported agreement between teachers’ gestural approach in relation to student proficiency levels indicates a teachers’ gestural scaffolding approach whereby teachers adapted gestural communicative channels to suit students’ specific conceptual skill levels.

Risk of myeloid neoplasms after solid organ transplantation

Solid organ transplant recipients have elevated cancer risks, owing in part to pharmacologic immunosuppression. However, little is known about risks for hematologic malignancies of myeloid origin. We linked the US Scientific Registry of Transplant Recipients with 15 population-based cancer registries to ascertain cancer occurrence among 207 859 solid organ transplants (1987–2009). Solid organ transplant recipients had a significantly elevated risk for myeloid neoplasms, with standardized incidence ratios (SIRs) of 4.6 (95% confidence interval 3.8–5.6; N=101) for myelodysplastic syndromes (MDS), 2.7 (2.2–3.2; N=125) for acute myeloid leukemia (AML), 2.3 (1.6–3.2; N=36) for chronic myeloid leukemia and 7.2 (5.4–9.3; N=57) for polycythemia vera. SIRs were highest among younger individuals and varied by time since transplantation and organ type (Poisson regression P<0.05 for all comparisons). Azathioprine for initial maintenance immunosuppression increased risk for MDS (P=0.0002) and AML (2–5 years after transplantation, P=0.0163). Overall survival following AML/MDS among transplant recipients was inferior to that of similar patients reported to US cancer registries (log-rank P<0.0001). Our novel finding of increased risks for specific myeloid neoplasms after solid organ transplantation supports a role for immune dysfunction in myeloid neoplasm etiology. The increased risks and inferior survival should heighten clinician awareness of myeloid neoplasms during follow-up of transplant recipients.

Evaluation of an in situ spatial resolution instrument for fixed beds through the assessment of the invasiveness of probes and a comparison with a micro-kinetic model

This paper reports the detailed description and validation of a fully automated, computer controlled analytical method to spatially probe the gas composition and thermal characteristics in packed bed systems. This method has been designed to limit the invasiveness of the probe, a characteristic assessed using CFD. The thermocouple is aligned with the sampling holes to enable simultaneous recording of the gas composition and temperature profiles. This analysis technique has been validated by studying CO oxidation over a 1% Pt/Al2O3 catalyst. The resultant profiles have been compared with a micro-kinetic model, to further assess the strength of the technique.