Interface Fantasies and Futures: Designing Human-Computer Relations in the Shadow of Memex

This dissertation is about how designers, experimental writers, and innovative thinkers have imagined both computer interfaces and the human/machine relations that might emerge through engagement with different kinds of interfaces. Although futuristic thinking about digital media and their interfaces has changed over time, we can isolate some constants that have persisted through almost all mainstream practices of interface design, particularly in American culture. Drawing from a historical trajectory that I associate with Vannevar Bush and his speculative invention, which he called “memex” in a 1945 essay, I name these constants sterilization and compartmentalization. They are two tendencies or values that I identify in mid-20th-century dreams of mastering information spaces by mastering their interfaces. My project shows how individuals and groups have reinforced or resisted these values in the engineering and design of computer interfaces, both speculative and real. The urge to sterilize and compartmentalize computers has directly and indirectly shaped what we expect and demand from our computers (and the things we make with them) today, and these values trace the horizon of what human-computer relations could be possible in the future

Value, transparency, and inclusion:A values-based study of patient involvement in musculoskeletal research

BACKGROUND: Patient and public involvement work (PPI) is essential to good research practice. Existing research indicates that PPI offers benefits to research design, conduct, communication, and implementation of findings. Understanding how PPI works and its value helps to provide information about best practice and highlight areas for further development. This study used a values-based approach to reporting PPI at a Research Unit focused on musculoskeletal conditions within a UK medical school. METHODS: The study was conducted between October 2019 and January 2020 using Gradinger’s value system framework as a theoretical basis. The framework comprises three value systems each containing five clusters. All PPI members and researchers who had attended PPI groups were invited to participate. Participants completed a structured questionnaire based on the value system framework; PPI members also provided further information through telephone interviews. Data were deductively analysed using a framework approach with data mapped onto value systems. RESULTS: Twelve PPI members and 17 researchers took part. Views about PPI activity mapped onto all three value systems. PPI members felt empowered to provide their views, and that their opinions were valued by researchers. It was important to PPI members that they were able to ‘give back’ and to do something positive with their experiences. Researchers would have liked the groups to be more representative of the wider population, patients highlighted that groups could include more younger members. Researchers recognised the value of PPI, and the study highlighted areas where researchers members might benefit from further awareness. CONCLUSIONS: Three areas for development were identified: (i) facilitating researcher engagement in training about the value and importance of PPI in research; (ii) support for researchers to reflect on the role that PPI plays in transparency of healthcare research; (iii) work to further explore and address aspects of diversity and inclusion in PPI

PIK3CA-associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution

Mosaicism is increasingly recognized as a cause of developmental disorders with the advent of next-generation sequencing (NGS). Mosaic mutations of PIK3CA have been associated with the widest spectrum of phenotypes associated with overgrowth and vascular malformations. We performed targeted NGS using 2 independent deep-coverage methods that utilize molecular inversion probes and amplicon sequencing in a cohort of 241 samples from 181 individuals with brain and/or body overgrowth. We identified PIK3CA mutations in 60 individuals. Several other individuals (n = 12) were identified separately to have mutations in PIK3CA by clinical targetedpanel testing (n = 6), whole-exome sequencing (n = 5), or Sanger sequencing (n = 1). Based on the clinical and molecular features, this cohort segregated into three distinct groups: (a) severe focal overgrowth due to low-level but highly activating (hotspot) mutations, (b) predominantly brain overgrowth and less severe somatic overgrowth due to less-activating mutations, and (c) intermediate phenotypes (capillary malformations with overgrowth) with intermediately activating mutations. Sixteen of 29 PIK3CA mutations were novel. We also identified constitutional PIK3CA mutations in 10 patients. Our molecular data, combined with review of the literature, show that PIK3CA-related overgrowth disorders comprise a discontinuous spectrum of disorders that correlate with the severity and distribution of mutations

Ten-year mortality, disease progression, and treatment-related side effects in men with localised prostate cancer from the ProtecT randomised controlled trial according to treatment received

Background The ProtecT trial reported intention-to-treat analysis of men with localised prostate cancer randomly allocated to active monitoring (AM), radical prostatectomy, and external beam radiotherapy. Objective To report outcomes according to treatment received in men in randomised and treatment choice cohorts. Design, setting, and participants This study focuses on secondary care. Men with clinically localised prostate cancer at one of nine UK centres were invited to participate in the treatment trial comparing AM, radical prostatectomy, and radiotherapy. Intervention Two cohorts included 1643 men who agreed to be randomised and 997 who declined randomisation and chose treatment. Outcome measurements and statistical analysis Analysis was carried out to assess mortality, metastasis and progression and health-related quality of life impacts on urinary, bowel, and sexual function using patient-reported outcome measures. Analysis was based on comparisons between groups defined by treatment received for both randomised and treatment choice cohorts in turn, with pooled estimates of intervention effect obtained using meta-analysis. Differences were estimated with adjustment for known prognostic factors using propensity scores. Results and limitations According to treatment received, more men receiving AM died of PCa (AM 1.85%, surgery 0.67%, radiotherapy 0.73%), whilst this difference remained consistent with chance in the randomised cohort (p = 0.08); stronger evidence was found in the exploratory analyses (randomised plus choice cohort) when AM was compared with the combined radical treatment group (p = 0.003). There was also strong evidence that metastasis (AM 5.6%, surgery 2.4%, radiotherapy 2.7%) and disease progression (AM 20.35%, surgery 5.87%, radiotherapy 6.62%) were more common in the AM group. Compared with AM, there were higher risks of sexual dysfunction (95% at 6 mo) and urinary incontinence (55% at 6 mo) after surgery, and of sexual dysfunction (88% at 6 mo) and bowel dysfunction (5% at 6 mo) after radiotherapy. The key limitations are the potential for bias when comparing groups defined by treatment received and changes in the protocol for AM during the lengthy follow-up required in trials of screen-detected PCa. Conclusions Analyses according to treatment received showed increased rates of disease-related events and lower rates of patient-reported harms in men managed by AM compared with men managed by radical treatment, and stronger evidence of greater PCa mortality in the AM group. Patient summary More than 95 out of every 100 men with low or intermediate risk localised prostate cancer do not die of prostate cancer within 10 yr, irrespective of whether treatment is by means of monitoring, surgery, or radiotherapy. Side effects on sexual and bladder function are better after active monitoring, but the risks of spreading of prostate cancer are more common

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery