SE in ES:Opportunities for Software Engineering and Cloud Computing in Environmental Science

New and emergent computing architectures and software engineering practices provide an opportunity for environmental models to be deployed more efficiently and democratically. In this paper we aim to capture the software engineering practices of environmental scientists, highlight opportunities for software engineering and work towards developing a domain specific language for the configuration and deployment of environmental models. We hold a series of interviews with environmental scientists involved in developing and deploying computer based environmental models about the approach taken in engineering models, and describe a case study in deploying an environmental model (WRF: Weather Research & Forecasting) on a cloud architecture. From these studies we find a number of opportunities for a) software engineering methods and tools such as Domain Specific Languages to play a role in abstracting from underlying computing complexity, and for b) new architectures to increase efficiency and availability of deployment. Together, we propose they will allow scientists to concentrate on fundamental science rather than specifics of the underlying computing

GHOST Commissioning Science Results II: a very metal-poor star witnessing the early Galactic assembly

This study focuses on Pristine$\_180956.78$$-$$294759.8$ (hereafter P180956, [Fe/H] $=-1.95\pm0.02$), a star selected from the Pristine Inner Galaxy Survey (PIGS), and followed-up with the recently commissioned Gemini High-resolution Optical SpecTrograph (GHOST) at the Gemini South telescope. The GHOST spectrograph's high efficiency in the blue spectral region ($3700-4800$~\AA) enables the detection of elemental tracers of early supernovae (e.g. Al, Mn, Sr, Eu), which were not accessible in the previous analysis of P180956. The star exhibits chemical signatures resembling those found in ultra-faint dwarf systems, characterised by very low abundances of neutron-capture elements (Sr, Ba, Eu), which are uncommon among stars of comparable metallicity in the Milky Way. Our analysis suggests that P180956 bears the chemical imprints of a small number (2 or 4) of low-mass hypernovae (\sim10-15\msun), which are needed to reproduce the abundance pattern of the light-elements (e.g. [Si, Ti/Mg, Ca] $\sim0.6$), and one fast-rotating intermediate-mass supernova (\sim300\kms, \sim80-120\msun). Both types of supernovae explain the high [Sr/Ba] of P180956 ($\sim1.2$). The small pericentric (\sim0.7\kpc) and apocentric (\sim13\kpc) distances and its orbit confined to the plane (\lesssim 2\kpc), indicate that this star was likely accreted during the early Galactic assembly phase. Its chemo-dynamical properties suggest that P180956 formed in a system similar to an ultra-faint dwarf galaxy accreted either alone, as one of the low-mass building blocks of the proto-Galaxy, or as a satellite of Gaia-Sausage-Enceladus. The combination of Gemini's large aperture with GHOST's high efficiency and broad spectral coverage makes this new spectrograph one of the leading instruments for near-field cosmology investigations.Comment: Submitted to MNRAS. 8 figures, 15page

The Seventh Data Release of the Sloan Digital Sky Survey

This paper describes the Seventh Data Release of the Sloan Digital Sky Survey (SDSS), marking the completion of the original goals of the SDSS and the end of the phase known as SDSS-II. It includes 11663 deg^2 of imaging data, with most of the roughly 2000 deg^2 increment over the previous data release lying in regions of low Galactic latitude. The catalog contains five-band photometry for 357 million distinct objects. The survey also includes repeat photometry over 250 deg^2 along the Celestial Equator in the Southern Galactic Cap. A coaddition of these data goes roughly two magnitudes fainter than the main survey. The spectroscopy is now complete over a contiguous area of 7500 deg^2 in the Northern Galactic Cap, closing the gap that was present in previous data releases. There are over 1.6 million spectra in total, including 930,000 galaxies, 120,000 quasars, and 460,000 stars. The data release includes improved stellar photometry at low Galactic latitude. The astrometry has all been recalibrated with the second version of the USNO CCD Astrograph Catalog (UCAC-2), reducing the rms statistical errors at the bright end to 45 milli-arcseconds per coordinate. A systematic error in bright galaxy photometr is less severe than previously reported for the majority of galaxies. Finally, we describe a series of improvements to the spectroscopic reductions, including better flat-fielding and improved wavelength calibration at the blue end, better processing of objects with extremely strong narrow emission lines, and an improved determination of stellar metallicities. (Abridged)Comment: 20 pages, 10 embedded figures. Accepted to ApJS after minor correction

Large-Scale Cortical Functional Organization and Speech Perception across the Lifespan

Aging is accompanied by substantial changes in brain function, including functional reorganization of large-scale brain networks. Such differences in network architecture have been reported both at rest and during cognitive task performance, but an open question is whether these age-related differences show task-dependent effects or represent only task-independent changes attributable to a common factor (i.e., underlying physiological decline). To address this question, we used graph theoretic analysis to construct weighted cortical functional networks from hemodynamic (functional MRI) responses in 12 younger and 12 older adults during a speech perception task performed in both quiet and noisy listening conditions. Functional networks were constructed for each subject and listening condition based on inter-regional correlations of the fMRI signal among 66 cortical regions, and network measures of global and local efficiency were computed. Across listening conditions, older adult networks showed significantly decreased global (but not local) efficiency relative to younger adults after normalizing measures to surrogate random networks. Although listening condition produced no main effects on whole-cortex network organization, a significant age group x listening condition interaction was observed. Additionally, an exploratory analysis of regional effects uncovered age-related declines in both global and local efficiency concentrated exclusively in auditory areas (bilateral superior and middle temporal cortex), further suggestive of specificity to the speech perception tasks. Global efficiency also correlated positively with mean cortical thickness across all subjects, establishing gross cortical atrophy as a task-independent contributor to age-related differences in functional organization. Together, our findings provide evidence of age-related disruptions in cortical functional network organization during speech perception tasks, and suggest that although task-independent effects such as cortical atrophy clearly underlie age-related changes in cortical functional organization, age-related differences also demonstrate sensitivity to task domains

The Role of Digital Technologies in Responding to the Grand Challenges of the Natural Environment:The Windermere Accord

Digital technology is having a major impact on many areas of society, and there is equal opportunity for impact on science. This is particularly true in the environmental sciences as we seek to understand the complexities of the natural environment under climate change. This perspective presents the outcomes of a summit in this area, a unique cross-disciplinary gathering bringing together environmental scientists, data scientists, computer scientists, social scientists, and representatives of the creative arts. The key output of this workshop is an agreed vision in the form of a framework and associated roadmap, captured in the Windermere Accord. This accord envisions a new kind of environmental science underpinned by unprecedented amounts of data, with technological advances leading to breakthroughs in taming uncertainty and complexity, and also supporting openness, transparency, and reproducibility in science. The perspective also includes a call to build an international community working in this important area

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