A model for annotating musical versions and arrangements across multiple documents and media

We present a model for the annotation of musical works, where the annotations are created with respect to a conceptual abstraction of the music instead of directly to concrete encodings. This supports musicologists in constructing arguments about musical elements that occur in multiple digital library sources (or other web resources), that recur across a work, or that appear in different forms in different arrangements. It provides a way of discussing musical content without tying that discourse to the location, notation or medium of the content, allowing evidence from multiple libraries and in different formats to be brought together to support musicological assertions. This model is implemented in Linked Data and illustrated in a prototype application in which musicologists annotate vocal arrangements of the Allegretto from Beethoven’s Seventh Symphony from multiple sources

Supporting musicological investigations with information retrieval tools: an iterative approach to data collection

Digital musicology research often proceeds by extending and enriching its evidence base as it progresses, rather than starting with a complete corpus of data and metadata, as a consequence of an emergent research need. In this paper, we consider a research workflow which assumes an incremental approach to data gathering and annotation. We describe tooling which implements parts of this workflow, developed to support the study of nineteenth-century music arrangements, and evaluate the applicability of our approach through interviews with musicologists and music editors who have used the tools. We conclude by considering extensions of this approach and the wider implications for digital musicology and music information retrieval

Radiation‐induced osteosarcoma involving the mandible – report of a rare diagnosis

Background Radiation-induced osteosarcomas of the jaws are a rare but often fatal consequence of radiation therapy in the head and neck region. Here we present a case of radiation-induced osteosarcoma of the mandible. Case Presentation A male presented with severe trismus and marked left lingual alveolus expansion 1 year following extractions in the lower left quadrant. Four years previously, he had radical radiotherapy (70Gy) and chemotherapy for a p16-positive T1N2cM0 squamous cell carcinoma of the left tonsil with a positive left level II node. Initial bone biopsies of the left mandible showed a bony sequestrum suggestive of osteoradionecrosis with the presence of abnormal osteoid suspicious of osteosarcoma. Imaging demonstrated an abnormal exophytic bone-forming lesion in the left mandibular body and parasymphysis and ruled out a metastatic lesion. The patient underwent bilateral neck dissection, left mandibulectomy with fibula flap reconstruction and full-thickness skin graft. Conclusions Osteosarcoma should be considered if changes are seen in previously stable irradiated bone with bony destruction and a soft tissue mass. This case highlights the importance of synthesis of clinical, radiological and pathological findings in the diagnosis of such lesions, especially where the histology initially suggested a benign process

A Layered Digital Library for Cataloguing and Research: Practical Experiences with Medieval Manuscripts, from TEI to Linked Data

In this paper we report our experiences developing and applying a set of digital infrastructure elements which, in combination, realise a layered digital library (Page et al 2017) for the investigation of manuscript provenance. We describe several related technical contributions: encoding of manuscript catalogue and local authority records as TEI; using Github for version control, issue tracking, and collaboration; automated production of catalogue user interfaces derived from the TEI; an XML processing workflow identifying, extracting, and processing TEI elements for reuse in research; mapping workflow output into a CIDOC-CRM RDF export; reconciliation of RDF entities with external authorities enabling the creation and use of Linked Data bridging multiple datasets. We contextualise the co-evolution of these components and exemplify their use in studies of the provenance of medieval manuscripts. We reflect on the flexibility and extensibility provided by our layered approach, and the independent benefits for catalogers and scholars

EPEN-08. THE TREM1 POSITIVE HYPOXIC MYELOID SUBPOPULATION IN POSTERIOR FOSSA EPENDYMOMA

We have previously shown the importance of immune factors in posterior fossa ependymoma (PF EPN). Recently, we found eight transcriptionally unique subpopulations of myeloid cells infiltrating PF EPN with one population particularly enriched in PFA1 tumors. This subpopulation, denoted as hypoxia myeloid subpopulation, is defined by genes associated with angiogenesis, hypoxia response, wound healing, cell migration, neutrophil activation, and response to oxygen levels. TREM1 (Triggering receptor expressed on myeloid cells 1) was found to be expressed almost exclusively within this hypoxia myeloid subpopulation. TREM1 encodes for a receptor belonging to the immunoglobulin superfamily that is expressed on myeloid cells, and stimulates neutrophil and monocyte inflammatory responses. However, single-cell RNAseq give little data suggesting location of cells within the tumor microenvironment. We performed immunohistochemistry (IHC) on our bank of ~90 FFPE PFA EPN samples using TREM1 to characterize and identify the location of the hypoxia myeloid cells. The TREM1 positive cells have an ambiguous cytomorphology reminiscent of a monocyte with modest cytoplasm and a mono-lobated nucleus. IHC also showed that TREM1+ myeloid cells are largely localized to the interface of necrosis and viable tissue, most frequently in a perivascular and intravascular distribution. The latter finding suggests that the TREM1+ cells are derived from the bone marrow and that they may be associated with the mesenchymal tumor population (MEC), which we have previously described as being enriched in PFA1 tumors and localizing to perinecrotic zones. This is supported by parallel IHC analysis of subpopulation-specific markers in the same cohort of PFA EPN which showed the highest TREM1 correlation was with CAIX, a marker of MEC. In PFA matched primary/recurrent pairs, the proportion of TREM1+ cells were increased at recurrence in the majority of cases, suggesting an evolving interaction between this TREM1+ hypoxia myeloid subpopulation and neoplastic cells over the disease course

Beethoven in the House: Digital Studies of Domestic Music Arrangements

Performance of music in the home was the means by which most works were received before the advent of audio recordings and broadcasts, yet the notation sources that form our primary record of this culture have not been the subject of comprehensive or methodical study. Choices made by arrangers adapting music for domestic consumption – of instrumentation, abbreviation, or simplification – reflect the musical life of the 19th century, and can inform our understanding alongside contemporary accounts such as newspapers, adverts, and diaries. This position paper gives the background, motivation, and proposed approach of research currently being undertaken within the Beethoven in the House project. This will include a study of Steiner editions of Beethoven’s 7th and 8th Symphonies and Wellingtons Sieg, making a detailed comparison between arrangements, systematically identifying a core common to multiple versions, and asking if this reflects the stated values of the publisher. A second survey will look for patterns across a larger sample of lesser-known and poorly catalogued scores, collating emergent indicators of arrangers’ motivations within a narrative of the domestic market – the music industry of its day. Both studies will innovate digital methods which characterise arrangements as music encodings, including ‘sparse’ approaches to notation and annotation

Increased Matrix Metalloproteinase (MMPs) Levels Do Not Predict Disease Severity or Progression in Emphysema

Rationale: Though matrix metalloproteinases (MMPs) are critical in the pathogenesis of COPD, their utility as a disease biomarker remains uncertain. This study aimed to determine whether bronchoalveolar lavage (BALF) or plasma MMP measurements correlated with disease severity or functional decline in emphysema. Methods: Enzyme-linked immunosorbent assay and luminex assays measured MMP-1, -9, -12 and tissue inhibitor of matrix metalloproteinase-1 in the BALF and plasma of non-smokers, smokers with normal lung function and moderate-to-severe emphysema subjects. In the cohort of 101 emphysema subjects correlative analyses were done to determine if MMP or TIMP-1 levels were associated with key disease parameters or change in lung function over an 18-month time period. Main Results: Compared to non-smoking controls, MMP and TIMP-1 BALF levels were significantly elevated in the emphysema cohort. Though MMP-1 was elevated in both the normal smoker and emphysema groups, collagenase activity was only increased in the emphysema subjects. In contrast to BALF, plasma MMP-9 and TIMP-1 levels were actually decreased in the emphysema cohort compared to the control groups. Both in the BALF and plasma, MMP and TIMP-1 measurements in the emphysema subjects did not correlate with important disease parameters and were not predictive of subsequent functional decline. Conclusions: MMPs are altered in the BALF and plasma of emphysema; however, the changes in MMPs correlate poorly with parameters of disease intensity or progression. Though MMPs are pivotal in the pathogenesis of COPD, these findings suggest that measuring MMPs will have limited utility as a prognostic marker in this disease. © 2013 D'Armiento et al

Epen-22. Single-cell RNA sequencing identifies upregulation of IKZF1 in PFA2 myeloid subpopulation driving an anti-tumor phenotype

We have previously shown immune gene phenotype variations between posterior fossa ependymoma subgroups. PFA1 tumors chronically secrete IL-6, which pushes the infiltrating myeloid cells to an immune suppressive function. In contrast, PFA2 tumors have a more immune activated phenotype and have a better prognosis. The objective of this study was to use single-cell(sc) RNAseq to descriptively characterize the infiltrating myeloid cells. We analyzed approximately 8500 cells from 21 PFA patient samples and used advanced machine learning techniques to identify distinct myeloid and lymphoid subpopulations. The myeloid compartment was difficult to interrupt as the data shows a continuum of gene expression profiles exist within PFA1 and PFA2. Through lineage tracing, we were able to tease out that PFA2 myeloid cells expressed more genes associated with an anti-viral response (MHC II, TNF-a, interferon-gamma signaling); while PFA1 myeloid cells had genes associated with an immune suppressive phenotype (angiogenesis, wound healing, IL-10). Specifically, we found expression of IKZF1 was upregulated in PFA2 myeloid cells. IKZF1 regulates differentiation of myeloid cells toward M1 or M2 phenotype through upregulation of either IRF5 or IRF4 respectively. IRF5 expression correlated with IKZF1, being predominately expressed in the PFA2 myeloid cell subset. IKZF1 is also involved in T-cell activation. While we have not completed our characterization of the T-cell subpopulation, we did find significantly more T-cell infiltration in PFA2 than PFA1. Moving forward these studies will provide us with valuable information regarding the molecular switches involved in the tumor-immune microenvironment and to better develop immunotherapy for PFA ependymoma

Next Steps for Measuring Polyphony: A Prototype Editor for Encoding Mensural Music

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