A standard format proposal for hierarchical analyses and representations

In the realm of digital musicology, standardizations efforts to date have mostly concentrated on the representation of music. Analyses of music are increasingly being generated or communicated by digital means. We demonstrate that the same arguments for the desirability of standardization in the representation of music apply also to the representation of analyses of music: proper preservation, sharing of data, and facilitation of digital processing. We concentrate here on analyses which can be described as hierarchical and show that this covers a broad range of existing analytical formats. We propose an extension of MEI (Music Encoding Initiative) to allow the encoding of analyses unambiguously associated with and aligned to a representation of the music analysed, making use of existing mechanisms within MEI's parent TEI (Text Encoding Initiative) for the representation of trees and graphs

New Prospects for Information Theory in Arts Research

Information Theory provoked the interest of arts researchers from its inception in the mid-20th century, but failed to produce the expected impact partly because the data and computing systems required were not available. With the modern availability of data from public collections and sophisticated software, there is renewed interest in Information Theory. Successful application in the analysis of music implies potential success in other artforms also. I give an illustrative example, applying the information-theoretic similarity measure Normalized Compression Distance with the aim of ranking paintings in a large collection by their conventionality

Improving optical music recognition by combining outputs from multiple sources

Current software for Optical Music Recognition (OMR) produces outputs with too many errors that render it an unrealistic option for the production of a large corpus of symbolic music files. In this paper, we propose a system which applies image pre-processing techniques to scans of scores and combines the outputs of different commercial OMR programs when applied to images of different scores of the same piece of music. As a result of this procedure, the combined output has around 50% fewer errors when compared to the output of any one OMR program. Image pre-processing splits scores into separate movements and sections and removes ossia staves which confuse OMR software. Post-processing aligns the outputs from different OMR programs and from different sources, rejecting outputs with the most errors and using majority voting to determine the likely correct details. Our software produces output in MusicXML, concentrating on accurate pitch and rhythm and ignoring grace notes. Results of tests on the six string quartets by Mozart dedicated to Joseph Haydn and the first six piano sonatas by Mozart are presented, showing an average recognition rate of around 95%

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice