Living Legacies: Recovering Data from 5¼” Floppy Disk Storage Media for the Commodore 64

In an attempt to investigate the challenges of recovering and preserving digital objects from legacy systems this case study focuses on working with a particular storage medium and computing hardware. This study illustrates the physical and representational challenges that result from recovering data created with a Commodore 64 computer and stored on 5¼" floppy disks. A system for classifying types of digital objects found in the sample of recovered data was developed. This study contributes to the discourse of collecting institutions engaged in digital preservation and provides examples of ad hoc solutions for working through the challenges of recovering meaningful information from legacy systems. The issues that come to light in this study can be extended beyond the context of the Commodore 64 to include other types of digital resources and computing artifacts that will potentially cross the archival threshold in the near future

College Women: Documenting the Student Experience at the Seven Sisters Colleges

White Paper prepared for the National Endowment for the Humanities Division of Preservation and Access, Humanities Collections and Reference Resources as part of a grant for the College Women: Documenting the Student Experience at the Seven Sisters College

College Women: Documenting the Student Experience at the Seven Sisters Colleges

White Paper prepared for the National Endowment for the Humanities Division of Preservation and Access, Humanities Collections and Reference Resources as part of a grant for the College Women: Documenting the Student Experience at the Seven Sisters College

Mock galaxy redshift catalogues from simulations: implications for Pan-STARRS1

We describe a method for constructing mock galaxy catalogues which are well suited for use in conjunction with large photometric surveys. We use the semi-analytic galaxy formation model of Bower et al. implemented in the Millennium simulation. We apply our method to the specific case of the surveys soon to commence with PS1, the first of 4 telescopes planned for the Pan-STARRS system. PS1 has 5 photometric bands (grizy), and will carry out an all-sky 3pi survey and a medium deep survey (MDS) over 84 sq.deg. We calculate the expected magnitude limits for extended sources in the two surveys. We find that, after 3 years, the 3pi survey will have detected over 10^8 galaxies in all 5 bands, 10 million of which will lie at redshift z>0.9, while the MDS will have detected over 10^7 galaxies with 0.5 million lying at z>2. These numbers at least double if detection in the shallowest band, y is not required. We then evaluate the accuracy of photometric redshifts estimated using an off-the-shelf photo-z code. With the grizy bands alone it is possible to achieve an accuracy in the 3pi survey of Delta z/(1+z)~0.06 for 0.25<z<0.8, which could be reduced by about 15% using near infrared photometry from the UKIDDS survey, but would increase by about 25% for the deeper sample without the y band photometry. For the MDS an accuracy of Delta z/(1+z)~0.05 is achievable for 0.02<z<1.5 using grizy. A dramatic improvement in accuracy is possible by selecting only red galaxies. In this case, Delta z/(1+z)~0.02-0.04 is achievable for ~100 million galaxies at 0.4<z<1.1 in the 3pi survey and for 30 million galaxies in the MDS at 0.4<z<2. We investigate the effect of using photo-z in the estimate of the baryonic acoustic oscillation scale. We find that PS1 will achieve a similar accuracy in this estimate as a spectroscopic survey of 20 million galaxies.Comment: 23 pages, 18 figures, accepted by MNRA

26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 - Meeting Abstracts - Antwerp, Belgium. 15–20 July 2017

This work was produced as part of the activities of FAPESP Research,\ud Disseminations and Innovation Center for Neuromathematics (grant\ud 2013/07699-0, S. Paulo Research Foundation). NLK is supported by a\ud FAPESP postdoctoral fellowship (grant 2016/03855-5). ACR is partially\ud supported by a CNPq fellowship (grant 306251/2014-0)

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P &lt; 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Archivematica outside the box: Piloting a common approach to digital preservation at the Five College Libraries

This work provides a case study detailing the work and outcomes of a digital preservation pilot project undertaken by the Five College Libraries between 2014 and 2015

Phenotype data from nodule assays

Data on leaf number, length of the longest branch, root length, and total number of nodules produced by plants grown to assay effects of mutations in candidate genes

Data from: Validating genome-wide association candidates controlling quantitative variation in nodulation

Genome-wide association (GWA) studies offer the opportunity to identify genes that contribute to naturally occurring variation in quantitative traits. However, GWA relies exclusively on statistical association, so functional validation is necessary to make strong claims about gene function. We used a combination of gene-disruption platforms (Tnt1 retrotransposons, hairpin RNA-interference constructs, and CRISPR/Cas9 nucleases) together with randomized, well-replicated experiments to evaluate the function of genes that an earlier GWA study in Medicago truncatula had identified as candidates contributing to variation in the symbiosis between legumes and rhizobia. We evaluated ten candidate genes found in six clusters of strongly associated single nucleotide polymorphisms, selected on the basis of their strength of statistical association, proximity to annotated gene models, and root or nodule expression. We found statistically significant effects on nodule production for three candidate genes, each validated in two independent mutants. Annotated functions of these three genes suggest their contributions to quantitative variation in nodule production occur through processes not previously connected to nodulation, including phosphorous supply and salicylic acid-related defense response. These results demonstrate the utility of GWA combined with reverse mutagenesis technologies to discover and validate genes contributing to naturally occurring variation in quantitative traits. The results highlight the potential for GWA to complement forward genetics in identifying the genetic basis of ecologically and economically important traits