Master of Science

thesisIn recent years, the release of carbon dioxide into the atmosphere has been a growing concern. In order to mitigate this problem, technological options to help stabilize the CO2 concentrations have been studied by scientists all over the world. One of the more promising solutions, called geological sequestration, is comprised of pumping captured CO2 underground and storing it in deep saline aquifers. However, long-term storage CO2 raises concerns, the most prominent being the effect of the carbon dioxide if it were to escape. Batch reactors were set up to determine the effect of carbon dioxide on the aerobic bacterium Nitrosospria multiformis and the anaerobic archaeon Methanobacterium subterraneum. The N. multiformis was grown over a period of 5 days. Live and dead cells were enumerated using a BacLight kit and an epiflourescence microscope. The M. subterraneum was grown over a period of 6 days and enumerated using Flow-FISH (Flourescent In Situ Hybridization) with a MB1174 probe and DAPI. It was determined that both autotrophic growths were supported by carbon dioxide gas. The aerobic autotrophic bacterium N. multiformis had more growth when supplied with bicarbonate as a carbon source, but the CO2 had no inhibitory effects. The anaerobic archaeon M. Subterraneum growth was stimulated by the addition of CO2 gas. Optimization of this protocol would give more accurate results, but since little research has been conducted on the effect of geologic carbon sequestration on deep subsurface microbiology, this study laid down an important foundation for future research

The Science Performance of JWST as Characterized in Commissioning

This paper characterizes the actual science performance of the James Webb Space Telescope (JWST), as determined from the six month commissioning period. We summarize the performance of the spacecraft, telescope, science instruments, and ground system, with an emphasis on differences from pre-launch expectations. Commissioning has made clear that JWST is fully capable of achieving the discoveries for which it was built. Moreover, almost across the board, the science performance of JWST is better than expected; in most cases, JWST will go deeper faster than expected. The telescope and instrument suite have demonstrated the sensitivity, stability, image quality, and spectral range that are necessary to transform our understanding of the cosmos through observations spanning from near-earth asteroids to the most distant galaxies.Comment: 5th version as accepted to PASP; 31 pages, 18 figures; https://iopscience.iop.org/article/10.1088/1538-3873/acb29

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Central places in a rural archaeological landscape

Archaeological survey in western Ireland has identified the existence of clusters of activity within the mapped landscapes of the 5th to 12th centuries A.D. Exploring this further, it is possible to identify elements characteristic of such clusters, and discuss the possible significance of such places. The basics of German geographer Walter Christaller’s Central Place Theory provide an interesting analytical tool in this regard. Although a spatial theory developed in the study of urban geography, some elements of Christaller’s work have been applied to urban archaeological landscapes in recent times. Their application in the rural ringfort landscapes of western Ireland proves an interesting exercise, one that suggests that Central Places also existed in more dispersed, rural communities in Early Medieval Ireland.Thanks are due to a number of funding bodies and archaeological professionals—the Heritage Council of Ireland funded the initial phases of survey, and the Royal Irish Academy the excavation of the sub-square cashel. Excavation at Caherconnell Cashel is made possible by the Caherconnell Archaeological Field School and the Davoren family who own the land (with early excavations undertaken in conjunction with Graham Hull and TVAS Ireland). An anonymous donation to the Department of Archaeology at NUI, Galway has allowed the final completion of the survey and the creation of some of the maps included here. Survey work was undertaken in conjunction with Liam Hickey, Nick Hogan, Cormac Bruton, Paul Naessens, and Noel McCarthy. Thanks also to manuscript editor Carleton Jones and two referees for their part in improving this paper

Using preprints in evidence synthesis: commentary on experience during the COVID-19 pandemic

Key findings: Evidence syntheses are increasingly drawing on preprint servers as a source for emergent literature on COVID-19. Our research group, has conducted a large number of rapid reviews of a broad range of public health topics related to COVID-19. We outline several considerations when including preprints in rapid reviews and lessons learned from this process.What this adds to what is known?: Including preprints in rapid reviews has implications for the rapid review process and review teams should have clear protocol regarding the selection and coverage of bibliographic databases, indication within reviews where an included study is a preprint and prespecifying any sensitivity analysis (quantitative or narrative) to assess the impact of inclusion of preprints on the overall results and conclusions.Specific challenges encountered in including preprints in rapid reviews such as those related to matching preprints to subsequent peer review publications and dealing with changes between preprints and peer review publications are presented using three exemplar review, and suggestions for study authors and review teams are provided.What is the implication and what should change now?: We suggest that preprint study authors include a statement in the final peer-reviewed version of the manuscript with the citation of the preprint version.Rapid review teams should have a clear policy around whether they will or will not check peer review status of preprints included in a rapid review, and at what point in the review process this would occur.</div

The duration of infectiousness of individuals infected with SARS-CoV-2

Objectives: To summarise the evidence on the duration of infectiousness of individuals in whom SARS-CoV-2 ribonucleic acid is detected.Methods: A rapid review was undertaken in PubMed, Europe PubMed Central and EMBASE from 1 January 2020 to 26 August 2020.Results: We identified 15 relevant studies, including 13 virus culture and 2 contact tracing studies. For 5 virus culture studies, the last day on which SARS-CoV-2 was isolated occurred within 10 days of symptom onset. For another 5 studies, SARS-CoV-2 was isolated beyond day 10 for approximately 3% of included patients. The remaining 3 virus culture studies included patients with severe or critical disease; SARS-CoV-2 was isolated up to day 32 in one study. Two studies identified immunocompromised patients from whom SARS-CoV-2 was isolated for up to 20 days. Both contact tracing studies, when close contacts were first exposed greater than 5 days after symptom onset in the index case, found no evidence of laboratory-confirmed onward transmission of SARS-CoV-2.Conclusion: COVID-19 patients with mild-to-moderate illness are highly unlikely to be infectious beyond 10 days of symptoms. However, evidence from a limited number of studies indicates that patients with severe-to-critical illness or who are immunocompromised, may shed infectious virus for longer.</p

Airborne transmission of SARS-CoV-2 via aerosols

 A key consideration in the Covid-19 pandemic is the dominant modes of transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The objective of this review was to synthesise the evidence for the potential airborne transmission of SARS-CoV-2 via aerosols. Systematic literature searches were conducted in PubMed, Embase, Europe PMC and National Health Service UK evidence up to 27 July 2020. A protocol was published and Cochrane guidance for rapid review methodology was adhered to throughout. Twenty-eight studies were identified. Seven out of eight epidemiological studies suggest aerosol transmission may occur, with enclosed environments and poor ventilation noted as possible contextual factors. Ten of the 16 air sampling studies detected SARS-CoV-2 ribonucleic acid; however, only three of these studies attempted to culture the virus with one being successful in a limited number of samples. Two of four virological studies using artificially generated aerosols indicated that SARS-CoV-2 is viable in aerosols. The results of this review indicate there is inconclusive evidence regarding the viability and infectivity of SARS-CoV-2 in aerosols. Epidemiological studies suggest possible transmission, with contextual factors noted. Viral particles have been detected in air sampling studies with some evidence of clinical infectivity, and virological studies indicate these particles may represent live virus, adding further plausibility. However, there is uncertainty as to the nature and impact of aerosol transmission of SARS-CoV-2, and its relative contribution to the Covid-19 pandemic compared with other modes of transmission. </p

Effectiveness of face masks worn in community settings at reducing the transmission of SARS-CoV-2: a rapid review [version 1; peer review: 1 approved with reservations]

Background: The use of face masks is part of a suite of infection prevention and control measures intended to limit the transmission of respiratory viral diseases. The use of face masks by the general public has been subject to ongoing debate, with limited direct evidence on the effectiveness of face masks in the community during the COVID-19 pandemic. The aim of this review was to synthesise direct evidence on the effectiveness of wearing face masks at reducing the transmission of SARS-CoV-2 in community settings. Methods: A rapid review was conducted. PubMed, Embase, NHS Evidence and Europe PMC were searched systematically from 1 January to 27 August 2020. Clinical trials, cohort, case control, and cross-sectional studies were included if they reported on the effectiveness of face masks in community settings at reducing the transmission of SARS-CoV-2. Studies were critically appraised and synthesised narratively. Results:  Seven observational studies were identified, including one study set in households and six in community settings, that reported on the effectiveness of wearing face masks compared with not wearing face masks at reducing the transmission of SARS-CoV-2. Results suggested that face masks reduce the risk of SARS-CoV-2 infection; however, all studies were at high risk of bias and the quality of the evidence was low. Conclusions: This is to date the most comprehensive review of direct evidence on the effectiveness of wearing face masks in the community during the COVID-19 pandemic. There is limited, low certainty direct evidence that wearing face masks reduces the risk of transmission of SARS-CoV-2 in community settings. Further high quality studies are required to confirm these findings. </p