The Fourth paradigm - data-intensive scientific discovery and open science

There is broad recognition within the scientific community that the ongoing deluge of scientific data is fundamentally transforming almost all areas of academic research. A wide variety of researchers —from scientists and engineers to social scientists and humanities researchers – now require tools, technologies, and platforms that seamlessly integrate into standard scientific methodologies and processes. “The Fourth Paradigm” refers to the data management techniques and the computational systems needed to manipulate, analyze, visualize, and manage large amounts of research data. This talk will illustrate the challenges researchers will face, the opportunities these changes will afford, and the resulting implications for data-intensive researchers. In addition, the talk will discuss the issues of open access, open data and open science and research reproducibility

e-Science and the Data Deluge : The Challenge for University Libraries

Intervention à la pré-conférence "converging and dissolving the University Library" du 34e congrès LIBER (2005) qui s\u27est tenue à le Bibliothèque universitaire de Groningue aux Pays-Bas. Enjeux et perspectives des projets de collaboration scientifique et documentaire en ligne pour les bibliothèques universitaires et les professionnels

Benchmarking and scalability of machine-learning methods for photometric redshift estimation

Obtaining accurate photometric redshift (photo-z) estimations is an important aspect of cosmology, remaining a prerequisite of many analyses. In creating novel methods to produce photo-z estimations, there has been a shift towards using machine-learning techniques. However, there has not been as much of a focus on how well different machine-learning methods scale or perform with the ever-increasing amounts of data being produced. Here, we introduce a benchmark designed to analyse the performance and scalability of different supervised machine-learning methods for photo-z estimation. Making use of the Sloan Digital Sky Survey (SDSS – DR12) data set, we analysed a variety of the most used machine-learning algorithms. By scaling the number of galaxies used to train and test the algorithms up to one million, we obtained several metrics demonstrating the algorithms’ performance and scalability for this task. Furthermore, by introducing a new optimization method, time-considered optimization, we were able to demonstrate how a small concession of error can allow for a great improvement in efficiency. From the algorithms tested, we found that the Random Forest performed best with a mean squared error, MSE = 0.0042; however, as other algorithms such as Boosted Decision Trees and k-Nearest Neighbours performed very similarly, we used our benchmarks to demonstrate how different algorithms could be superior in different scenarios. We believe that benchmarks like this will become essential with upcoming surveys, such as the Vera C. Rubin Observatory’s Legacy Survey of Space and Time (LSST), which will capture billions of galaxies requiring photometric redshifts

Converging and dissolving the University Library : pré-conférence au 34e congrès LIBER (2005)

Pré-conférence au 34e congrès LIBER qui s\u27est tenu à le Bibliothèque universitaire de Groningue aux Pays-Bas du 5 au 9 juillet 2005. Réflexions sur le devenir les bibliothèques universitaires à l\u27âge des TIC et des grands vecteurs privés d\u27information (Google, Amazon, etc.)

The Iceland Microcontinent and a continental Greenland-Iceland-Faroe Ridge

The breakup of Laurasia to form the Northeast Atlantic Realm was the culmination of a long period of tectonic unrest extending back to the Late Palaeozoic. Breakup was prolonged and complex and disintegrated an inhomogeneous collage of cratons sutured by cross-cutting orogens. Volcanic rifted margins formed, which are blanketed by lavas and underlain variously by magma-inflated, extended continental crust and mafic high-velocity lower crust of ambiguous and probably partly continental provenance. New rifts formed by diachronous propagation along old zones of weakness. North of the Greenland-Iceland-Faroe Ridge the newly forming rift propagated south along the Caledonian suture. South of the Greenland-Iceland-Faroe Ridge it propagated north through the North Atlantic Craton along an axis displaced ~ 150 km to the west of the northern rift. Both propagators stalled where the confluence of the Nagssugtoqidian and Caledonian orogens formed a transverse barrier. Thereafter, the ~ 400-km-wide latitudinal zone between the stalled rift tips extended in a distributed, unstable manner along multiple axes of extension that frequently migrated or jumped laterally with shearing occurring between them in diffuse transfer zones. This style of deformation continues to the present day. It is the surface expression of underlying magma-assisted stretching of ductile mid- and lower continental crust which comprises the Icelandic-type lower crust that underlies the Greenland-Iceland-Faroe Ridge. This, and probably also one or more full-crustal-thickness microcontinents incorporated in the Ridge, are capped by surface lavas. The Greenland-Iceland-Faroe Ridge thus has a similar structure to some zones of seaward-dipping reflectors. The contemporaneous melt layer corresponds to the 3–10 km thick Icelandic-type upper crust plus magma emplaced in the ~ 10–30-km-thick Icelandic-type lower crust. This model can account for seismic and gravity data that are inconsistent with a gabbroic composition for Icelandic-type lower crust, and petrological data that show no reasonable temperature or source composition could generate the full ~ 40-km thickness of Icelandic-type crust observed. Numerical modeling confirms that extension of the continental crust can continue for many tens of Myr by lower-crustal flow from beneath the adjacent continents. Petrological estimates of the maximum potential temperature of the source of Icelandic lavas are up to 1450 °C, no more than ~ 100 °C hotter than MORB source. The geochemistry is compatible with a source comprising hydrous peridotite/pyroxenite with a component of continental mid- and lower crust. The fusible petrology, high source volatile contents, and frequent formation of new rifts can account for the true ~ 15–20 km melt thickness at the moderate temperatures observed. A continuous swathe of magma-inflated continental material beneath the 1200-km-wide Greenland-Iceland-Faroe Ridge implies that full continental breakup has not yet occurred at this latitude. Ongoing tectonic instability on the Ridge is manifest in long-term tectonic disequilibrium on the adjacent rifted margins and on the Reykjanes Ridge, where southerly migrating propagators that initiate at Iceland are associated with diachronous swathes of unusually thick oceanic crust. Magmatic volumes in the NE Atlantic Realm have likely been overestimated and the concept of a monogenetic North Atlantic Igneous Province needs to be reappraised. A model of complex, piecemeal breakup controlled by pre-existing structures that produces anomalous volcanism at barriers to rift propagation and distributes continental material in the growing oceans fits other oceanic regions including the Davis Strait and the South Atlantic and West Indian oceans

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

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

e-Science and its implications for the library community

Explains the nature of the ‘e-Science’ revolution in 21st century scientific research and its consequences for the library community. The concepts of e-Science are illustrated by a discussion of the CombeChem, eBank and SmartTea projects. The issue of open access is then discussed with reference to arXiv, PubMed Central and EPrints. The challenges these trends present to the library community are discussed in the context of the TARDis project and the University of Southampton Research Repository. Increasingly academics will need to collaborate in multidisciplinary teams distributed across several sites in order to address the next generation of scientific problems. In addition, new highthroughput devices, high resolution surveys and sensor networks will result in an increase in scientific data collected by several orders of magnitude. To analyze, federate and mine this data will require collaboration between scientists and computer scientists; to organize, curate and preserve this data will require collaboration between scientists and librarians. A vital part of the developing research infrastructure will be digital repositories containing both publications and data. The paper provides a synthesis of e-Science concepts, the question of open access to the results of scientific research, and a changing attitude towards academic publishing and communication. The paper offers a new perspective on coming demands on the library and is of special interest to librarians with strategic tasks