Rethinking affordance

n/a – Critical survey essay retheorising the concept of 'affordance' in digital media context. Lead article in a special issue on the topic, co-edited by the authors for the journal Media Theory

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

On the Matter of the Digital in Contemporary Media Art

This dissertation brings together aesthesis, media art and theory to explore how contemporary media artists are aestheticizing, conceptualizing and grappling with “digital materiality” through their artworks and practices of making. It stems from a series of process-oriented interviews conducted with thirty-three contemporary media artists from across North America and Europe. Responding to prominent themes that emerged through a triangulated analysis of the interviews, corresponding artworks and media theory, the dissertation offers grounded accounts of five coinciding strategies that artists are enacting in an effort to make sense of the materiality of the digital. Developed over five substantive chapters, these key areas of material analysis include: the materiality of glitch; the indexical materialism of digital surfaces; the treatment of digital materiality as a matter of “resolutions”; the transpositional concretization of “formal materialism” in Post-Internet Art; and the deployment of “synesthetic catachresis” as a means of grasping at modes of materialism that remain definitionally evasive. While each chapter maps out a different perspective on materiality, the driving intention of the dissertation is to advance an overarching aesthetic approach that moves beyond hardware/software distinctions to provide needed perspective on the material dynamism of contemporary digital processes.Ph.D.2020-02-09 00:00:0

Supplementary material for "Prior Austenite Grain Measurement: A Direct Comparison of EBSD Reconstruction, Thermal Etching and Chemical Etching"

&lt;p&gt;The complete collection of measured, modelled and analysed data associated with the work "Prior Austenite Grain Measurement: A Direct Comparison of EBSD Reconstruction, Thermal Etching and Chemical Etching" and includes:&lt;/p&gt; &lt;ol&gt; &lt;li&gt;&lt;span&gt;EBSD files&lt;/span&gt;&lt;/li&gt; &lt;li&gt;&lt;span&gt;SE images&lt;/span&gt;&lt;/li&gt; &lt;li&gt;&lt;span&gt;Measured grain size lists&lt;/span&gt;&lt;/li&gt; &lt;li&gt;&lt;span&gt;EDS measurements&lt;/span&gt;&lt;/li&gt; &lt;li&gt;&lt;span&gt;Microhardness measurements&lt;/span&gt;&lt;/li&gt; &lt;li&gt;&lt;span&gt;Thermo-Calc predictions&lt;/span&gt;&lt;/li&gt; &lt;li&gt;&lt;span&gt;Supplementary Gif-1.&lt;/span&gt;&lt;/li&gt; &lt;/ol&gt

Comparative efficacy of an optimal exam between ultrasound versus abbreviated MRI for HCC screening in NAFLD cirrhosis: A prospective study

BackgroundRetrospective studies report that visualisation of the liver may be severely limited using ultrasound (US), potentially contributing to diminished sensitivity for detection of hepatocellular carcinoma (HCC) among patients with nonalcoholic fatty liver disease (NAFLD) and cirrhosis, but there are limited prospective data.AimsTo compare liver visualisation scores prospectively for US and abbreviated hepatobiliary phase (HBP) magnetic resonance imaging (AMRI) in a cohort of participants with NAFLD cirrhosis and a clinical indication for HCC surveillance.MethodsThis prospective multicenter study included 54 consecutive participants (67% women) with NAFLD cirrhosis who underwent contemporaneous US as well as HBP-AMRI with gadoxetic acid. Primary outcome was the proportion of imaging examinations with severe limitations in liver visualisation (visualisation score C) compared head-to-head between US and AMRI.ResultsThe mean (± standard deviation) age was 63.3&nbsp;years (±8.4) and body mass index was 32.0&nbsp;kg/m2 (±6.0). Nineteen participants (35%) had severe visualisation limitations on US, compared with 10 (19%) with AMRI, p&nbsp;&lt;&nbsp;0.0001. Nine (17%) participants had &lt;90% of the liver visualised on US, compared with only 1 (2%) participant with AMRI, p&nbsp;&lt;&nbsp;0.0001. Obesity was a strong and independent predictor for severe visualisation limitation on US (OR 5.1, CI 1.1-23.1, p&nbsp;=&nbsp;0.03), after adjustment for age, sex and ethnicity.ConclusionMore than one-third of participants with NAFLD cirrhosis had severe visualisation limitations on US for HCC screening, compared with one-sixth on AMRI. US adequacy should be reported in all clinical studies and when suboptimal then AMRI may be considered for HCC screening

Inhibition of p25/Cdk5 Attenuates Tauopathy in Mouse and iPSC Models of Frontotemporal Dementia

Increased p25, a proteolytic fragment of the regulatory subunit p35, is known to induce aberrant activity of cyclin-dependent kinase 5 (Cdk5), which is associated with neurodegenerative disorders, including Alzheimer’s disease. Previously, we showed that replacing endogenous p35 with the noncleavable mutant p35 (Δp35) attenuated amyloidosis and improved cognitive function in a familial Alzheimer’s disease mouse model. Here, to address the role of p25/Cdk5 in tauopathy, we generated double-transgenic mice by crossing mice overexpressing mutant human tau (P301S) with Δp35KI mice. We observed significant reduction of phosphorylated tau and its seeding activity in the brain of double transgenic mice compared with the P301S mice. Furthermore, synaptic loss and impaired LTP at hippocampal CA3 region of P301S mice were attenuated by blocking p25 generation. To further validate the role of p25/Cdk5 in tauopathy, we used frontotemporal dementia patient-derived induced pluripotent stem cells (iPSCs) carrying the Tau P301L mutation and generated P301L: Δp35KI isogenic iPSC lines using CRISPR/Cas9 genome editing. We created cerebral organoids from the isogenic iPSCs and found that blockade of p25 generation reduced levels of phosphorylated tau and increased expression of synaptophysin. Together, these data demonstrate a crucial role for p25/Cdk5 in mediating tau-associated pathology and suggest that inhibition of this kinase can remedy neurodegenerative processes in the presence of pathogenic tau mutation.National Institutes of Health (Grant R37NS051874)Robert A. and Renee E. Belfer Family FoundationNeurodegeneration Consortiu