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Fig 4 in The last giants: New evidence for giant Late Triassic (Rhaetian) ichthyosaurs from the UK

Fig 4. Invertebrate and trace fossils found on the bone surface of the BAS surangular, BRSMG Cg3178. A-B. Associated bivalves, including Atreta intrusstriata (A) and Plagiostoma giganteum (B); it is worth noting that a small group of the latter are preserved adjacent to the coronoid process, see Fig 2C. C-D. Examples of the probable scavenging marks that are also observed in the Lilstock surangular, see Lomax et al. 2018, Fig 4. https://doi.org/10.1371/journal.pone.0300289.g004

Fig 6 in The last giants: New evidence for giant Late Triassic (Rhaetian) ichthyosaurs from the UK

Fig 6. Histological overview of BRSMG Cg3178 (BAS surangular). A. Composite image of thin section under circular polarized light. B. Close-up of the external margin of the outer cortex, showing the presence of multiple growth marks (GMs), open vascular canals and cortical vascular canals with all degrees of maturity (simple canals, primary osteons and secondary osteons), supporting an ongoing active and continuous growth. Note the evident darker border of the lumen of a diagonal canal running from the top left toward the margin of the large nutrient canal (NC) showing further longitudinal vascularization. C. Concentric secondary osteon in the outer cortex under lambda filter. D. Close-up of the upper margin of the nutrient canal under crossed polarized (left) and circular polarized light (right). The growth marks appear as alternated tightly packed rows of brighter and darker periosteal intrinsic fibres (PIF). The same tight packing of the GMs occurs also deeper in the cortex. E. Lateral margin of the nutrient canal under circular polarized view. PIF are evident as bright yellow and blue coiled structures. The presence of simple canals alongside osteons, indicates primary deposition of bone along the margin of the large nutrient canal. F. Concentric secondary osteon in the trabecular bone under transmitted light. It is evident the high amount of osteocyte lacunae and the presence of plump irregular shaped ones in the lamellar bone. G. Trabecular bone under circular polarized view. The presence of primary matrix and concentric secondary osteons indicate that the trabeculae are secondary, produced from compact bone made cancellous. White arrows (D, E, G) point at PIF; white arrowheads point at resorption lines in concentric osteons (C, F, G); white dotted lines indicate borders of primary osteons (C, F, G); yellow arrow heads (B, D) point at rows of GMs. Abbreviations. LB, Lamellar bone; NC, Nutrient canal; OC, Open periosteal canal; PO, Primary osteon; RC, Resorption cavity; SC, Simple canal; SO, Secondary osteon. https://doi.org/10.1371/journal.pone.0300289.g006

Fig 3 in The last giants: New evidence for giant Late Triassic (Rhaetian) ichthyosaurs from the UK

Fig 3. Comparison of the holotype (BRSMG Cg3178, A and C right surangular, BAS specimen) and referred specimen (BRSMG Cg2488, B and D left surangular, Lilstock specimen) of Ichthyotitan severnensis gen. et sp. nov. To ease comparison, A and C have been reversed. A-B. Lateral view of both surangulars showing same unique shape; note the upturned, almost 90-degree angle bend and the spatulate-shaped posterior end. C-D. Medial view of both surangulars displaying same morphology posteriorly; anteriorly the Lilstock specimen (D) has been heavily eroded and distorted along its length (see Discussion in Lomax et al. 2018 for more details). Note the position of an elongated foramen on the lateral surface (A-B), identified as part of the fossa surangularis that passes through the bone into the Meckelian canal. See also the damaged (?)angular that is articulated with the surangular and defined by a continuous groove (?suture) as seen in Fig 2H. https://doi.org/10.1371/journal.pone.0300289.g003

Fig 1 in The last giants: New evidence for giant Late Triassic (Rhaetian) ichthyosaurs from the UK

Fig 1. Distribution of the Triassic rocks in the Bristol Channel–Severn Estuary area and the three key ichthyosaur localities (where specimens discussed herein were found) referred to in the text. Modified from Lomax et al. 2018 [7]. https://doi.org/10.1371/journal.pone.0300289.g001

Fig 2 in The last giants: New evidence for giant Late Triassic (Rhaetian) ichthyosaurs from the UK

Fig 2. The holotype of Ichthyotitan severnensis gen. et sp. nov., a newly collected specimen (BRSMG Cg3178) comprising a very large, but incomplete right surangular (the 'BAS Specimen'). A. All associated pieces with an approximate outline of the complete surangular, in medial view. The surangular is separated into two main parts, Part #A to the right and Part #B to the left (see text). B. A close-up of the coronoid process in lateral view, showing moderate eminence. C. Bulbous coronoid process in dorsal view with lateral displacement. D. Subcircular cross section at the level of the coronoid process (posterior view, medial to the left). E-F. Comparison of the massively developed M.A.M.E. ridge observed in BAS (E) and the Lilstock surangular (F); arrows indicate top of the ridge. G. Oblique view of the medial surface highlighting part of the overhanging shelf that encloses the Meckelian canal. H. Ventromedial view of the mid-posterior portion of the surangular showing a distinct, continuous, and straight thin groove that might be a suture and could indicate two distinct bones (perhaps including a damaged angular). https://doi.org/10.1371/journal.pone.0300289.g002

opencc-by-4.0Dec 2021View details →

UK Power Station Transformer Dissolved Gas Analysis Data (2010-2015)

This dataset includes dissolved gas analysis records from coolant oil in 13 UK power station transformers for various timespans between 2010-2015. They form the basis of the paper "Assessing the impact of weak and moderate geomagnetic storms on UK power station transformers" submitted to the AGU "Space Weather" Journal by Z.M. Lewis, J.A. Wild and M. Allcock in December 2021. Please cite Lewis et al. if using these data. The authors thank D. Barker, EDF Energy Nuclear Generation, for providing these data.   The data are presented in comma separated variable format files, as described in the readme.txt file.

opencc-by-4.0Jan 2022View details →

Terrestrial paleoclimate reconstruction of the UK Neogene (?Langhian to Piacenzian) comparing CREST, CRACLE and the Co-existence Approach

Abstract  The first detailed reconstruction of the terrestrial paleoclimate development of the UK Neogene (?Langhian to Piacenzian) is presented. The paleoclimate data are derived from the paleobotanical record using two probability-based reconstruction techniques CREST (Climate REconstruction SofTware) (Chevalier et al. 2014) and CRACLE (Climate Reconstruction Analysis using Coexistence Likelihood Estimation) (Harbert & Nixon 2015) that use Bayesian and likelihood estimation probability respectively. The results of these reconstructions are presented alongside reconstructions using the widely-applied Co-existence Approach (CA) (Utescher et al. 2014) for comparison. While all three techniques use the climate requirements of their Nearest Living Relatives as the basis of their reconstruction, they use different database observations. CREST and CRACLE use the GBIF (Global Biodiverstiy Information Facility) (GBIF, 2021) as well as WorldClim inputs for the 19 bioclimate variables used by BIOCLIM (<a href="http://www.worldclim.org/bioclim">http://www.worldclim.org/bioclim</a>). Meanwhile, the CA uses the Palaeoflora database, meaning the input for the three models is different. The reconstructions for the UK Neogene palaeoclimate come from 4 localities (12 samples total) spanning the Middle Miocene (Langhian) to Pliocene (Piacenzian): Trwyn y Parc, Anglesey (Middle Miocene), Brassington Formation, Derbyshire (Serravallian-Tortonian), Coralline Crag Formation (latest Zanclean-earliest Piacenzian) and Red Crag Formation (Piacenzian-Gelasian) of southeast England. We present CREST and CRACLE reconstructions of Mean Annual Temperature (MAT), Mean Temperature of Warmest Quarter (MTWQ), Mean Temperature of Coldest Quarter (MTCQ), Mean Annual Precipitation (MAP) and precipitation seasonality (CoV ×100). The CA does not reconstruct MTWQ, MTCQ or precipitation seasonality. Instead, the CA reconstructs Warmest Month Mean Temperature (WMMT) and Coldest Month Mean Temperature (CMMT). The proportion of rainfall falling in the wettest months of the year (RMPwet(%)) was used as a proxy for precipitation seasonality following the methodology of Jacques et al. (2011) and Utescher et al. (2015). The CREST R-code output provides 0.5 and 0.95 (2-σ) uncertainties as well as an optimum and mean for each variable. The CRACLE R-code output provides both parametric and non-parametric joint likelihoods (P-CRACLE and N-CRACLE) with 0.95 (2-σ) uncertainties and a mean that is based on P-CRACLE. The CA generates a minimum and maximum likelihood which together comprise the coexistence interval. The Neogene climate reconstruction of the UK shows a cooling trend from the Langhian to the Pliocene-Pleistocene boundary. CREST and CRACLE produce trends and values consistent with Co-existence Approach data with 0.95 uncertainties overlapping with the CA coexistence interval. File Descriptions  Table S1 displays the complete reconstruction for the UK Neogene using CREST, CRACLE and the Co-existence Approach. Table S2 displays detailed site information including: modern and paleo latitude and longitude, dating technique, modern climatology and fossil assemblage diversity (number of fossil taxa versus number of NLRs used for climate reconstruction). Modern climatology has been included to serve as a comparison to the reconstructed Neogene climate. This data has been extracted from WorldClim 2.1 (Fick & Hijmans, 2017). Data Set S1 contains the list of fossil spore and pollen taxa per site and associated Nearest Living Relatives (NLRs), where identifiable, used as the input for CREST, CRACLE and the Co-existence Approach. Relic taxa are included and highlighted in red. Data Set S2 is included to show the effect relic taxa have on paleoclimate reconstructions. The relic taxa are removed following the protocol of Utescher et al. (2014) whereby known relic taxa are removed from analyses to avoid biased reconstructions. Relic taxa removed from analyses include Cathaya, Cryptomeria, Pinus sylvestris and Sciadopitys when present. Data Set S3 is included to show the effects of removing family-level identifications in CRACLE reconstructions. Removing families is shown to generate a less informative reconstruction. Including both genera- and family-level classifications of NLR (Nearest Living Relative) is recommended, however we suggest identifying NLRs (Nearest Living Relatives) to genera-level wherever possible.

opencc-by-4.0Feb 2022View details →

A survey of access to the digital collections of 195 UK GLAMs across internal and external platforms - Appendix 1 for A Culture of Copyright: A scoping study on open access to digital cultural heritage collections in the UK

Created for the<a href="https://doi.org/10.5281/zenodo.6242611"> 'A Culture of Copyright: A scoping study on open access to digital cultural heritage collections in the UK' </a>report, this sample replicates and expands the Open galleries, libraries, archives and museums (GLAMs) Survey data extraction and methodology to include a range of GLAMs across the UK and new data points. The initial sample of 350 organisations included Independent Research Organisations (IROs) and Research Centre Institutes (RCIs), GLAMs associated with <a href="https://www.nationalcollection.org.uk/">Towards a National Collection</a> Foundation and Discovery projects, UK GLAMs in the Open GLAM Survey, and other UK GLAMs and related organisations. An initial review was performed to identify and remove organisations outside the scope of inquiry (e.g., no permanent collections). The final sample included 195 organisations. From the final sample, 24 are IROs (all RCIs were removed). Another 32 are Universities (including GLAMs within universities). This brings the total number of organisations eligible for AHRC funding to 56 (or 28.6%). The remaining 140 include public and private GLAMs at national, regional and local levels (e.g., councils, historic buildings) and research initiatives or data aggregators (e.g., Portable Antiquities Scheme, Culture Grid, Archaeology Data Service). Organisations are distributed across the UK as follows: Channel Islands (1 total); England (154 total); Isle of Man (1 total); Northern Ireland (5 total); Scotland (28 total); Wales (6 total). A survey of the copyright and open access policies of 63 GLAMs from the UK GLAM Sample is available on Zenodo at: <a href="https://doi.org/10.5281/zenodo.6242559">https://doi.org/10.5281/zenodo.6242559</a>

opencc-by-4.0Feb 2022View details →

UK-based think tanks

A database of UK-based think-tanks including: <ul> <li>Name    </li> <li>Year established    </li> <li>Year disbanded or merged    </li> <li>Main area    </li> <li>A specific education emphasis    </li> <li>Description    </li> <li>Explicit political stand    </li> <li>Focused stand    </li> <li>Source for description    </li> <li>Date accessed    </li> <li>Notes    </li> <li>Education emphasis boolean    </li> <li>Affiliation</li> </ul> The data on think tanks drew on the Wikipedia page ‘List of think tanks in the United Kingdom’ in 2014 (Wikipedia 2014), crosschecked with other online think tank lists (Harvard Kennedy School Library & Knowledge Services 2013, Telegraph 2008, Guardian 2013), and updated in 2020 (Wikipedia 2020). Websites were accessed to gain additional information about activity, area of interest, and political affiliation. If information on the exact date of foundation was unavailable, the date of its first publication was used, or in a very few cases as a final resort unconfirmed data such as the Wikipedia entry. In some cases we resorted to internet archive sites such as web.archive.org. As a result, eighteen think tanks were excluded, because they were clearly only research institutes with no extensive outreach, they did not function in the UK, or they did not provide enough information about their work. The final sample consisted of 163 think tanks.

opencc-by-4.0May 2022View details →

Inputs of the Jupyter Notebook - Cosmos-UK soil moisture

The dataset contains the inputs of the notebook "Cosmos-UK soil moisture" published in The Environmental Data Science Book. The input data refer to a subset of the public 2013-2019 COSMOS-UK dataset, daily and subhourly observations and metadata for four stations: WYTH1, WADDN, SHEEP and CHIMN. These stations represent the first sites to prototype COSMOS sensors in the UK, see further details in Evans et al. (2016) and they are situated in human-intervened areas (grassland and cropland), except for one in a woodland land cover site. Data from COSMOS-UK up to the end of 2019 are available for download from the UKCEH Environmental Information Data Centre (EIDC). The data are accompanied by documentation that describes the site-specific instrumentation, data and processing including quality control. The full dataset is available for <a href="https://doi.org/10.5285/b5c190e4-e35d-40ea-8fbe-598da03a1185">download</a> under the terms of the Open Government License. Contributions Notebook <ul> <li> Alejandro Coca-Castro (author), The Alan Turing Institute, <a href="https://github.com/acocac">@acocac</a> </li> <li> Doran Khamis (reviewer), UK Centre for Ecology & Hydrology, <a href="https://github.com/dorankhamis">@dorankhamis</a> </li> <li> Matt Fry (reviewer), UK Centre for Ecology & Hydrology, <a href="https://github.com/mattfry-ceh">@mattfry-ceh</a> </li> </ul> Dataset originator/creator <ul> <li> UK Centre for Ecology & Hydrology (creator) </li> <li> Natural Environment Research Council (support) </li> </ul> Dataset reference and documentation <ul> <li> S. Stanley, V. Antoniou, A. Askquith-Ellis, L.A. Ball, E.S. Bennett, J.R. Blake, D.B. Boorman, M. Brooks, M. Clarke, H.M. Cooper, N. Cowan, A. Cumming, J.G. Evans, P. Farrand, M. Fry, O.E. Hitt, W.D. Lord, R. Morrison, G.V. Nash, D. Rylett, P.M. Scarlett, O.D. Swain, M. Szczykulska, J.L. Thornton, E.J. Trill, A.C. Warwick, and B. Winterbourn. Daily and sub-daily hydrometeorological and soil data (2013-2019) [cosmos-uk]. 2021. URL: <a href="https://doi.org/10.5285/b5c190e4-e35d-40ea-8fbe-598da03a1185">https://doi.org/10.5285/b5c190e4-e35d-40ea-8fbe-598da03a1185</a>, <a href="https://doi.org/10.5285/b5c190e4-e35d-40ea-8fbe-598da03a1185">doi:10.5285/b5c190e4-e35d-40ea-8fbe-598da03a1185</a>. </li> </ul> Further references <ul> <li> Jonathan G. Evans, H. C. Ward, J. R. Blake, E. J. Hewitt, R. Morrison, M. Fry, L. A. Ball, L. C. Doughty, J. W. Libre, O. E. Hitt, D. Rylett, R. J. Ellis, A. C. Warwick, M. Brooks, M. A. Parkes, G. M.H. Wright, A. C. Singer, D. B. Boorman, and A. Jenkins. Soil water content in southern england derived from a cosmic-ray soil moisture observing system – cosmos-uk. Hydrological Processes, 30:4987–4999, 12 2016. <a href="https://doi.org/10.1002/hyp.10929">doi:10.1002/hyp.10929</a>. </li> <li> M. Zreda, W. J. Shuttleworth, X. Zeng, C. Zweck, D. Desilets, T. Franz, and R. Rosolem. Cosmos: the cosmic-ray soil moisture observing system. Hydrology and Earth System Sciences, 16(11):4079–4099, 2012. URL: <a href="https://hess.copernicus.org/articles/16/4079/2012/">https://hess.copernicus.org/articles/16/4079/2012/</a>, <a href="https://doi.org/10.5194/hess-16-4079-2012">doi:10.5194/hess-16-4079-2012</a>. </li> </ul>

Extended Data Fig. 2 in A crown-group cnidarian from the Ediacaran of Charnwood Forest, UK

Extended Data Fig. 2 | Constrained phylogenetic topologies. (a) 'Ctenosis' (ctenophores as sister to all other animals) constrained. (b) Living cnidarian inter-relationships constrained against recent molecular phylogenies. All fossils were allowed to fully explore treespace under both set of constraints. Auroralumina is recovered as a cnidarian in both cases. Fossil cnidarians are shown in bold and the position of Auroralumina highted with with a silhouette. Scale bar for branch lengths is in units of expected number of substitutions per site.

Extended Data Fig. 1 in A crown-group cnidarian from the Ediacaran of Charnwood Forest, UK

Extended Data Fig. 1 | Unconstrained phylogenetic topologies presented in full. (a) Excluding the fossil taxa Namacalathus and Eolympia, Antipathes and those taxa that posses uninformative character states after safe taxonomic reduction (b) including all taxa. Auroralumina is recovered as a cnidarian in both trees. Fossil cnidarians are shown in bold and the position of Auroralumina is highlighted with a silhouette. Scale bar for branch lengths is in units of expected number of substitutions per site.

Fig. 4 in A crown-group cnidarian from the Ediacaran of Charnwood Forest, UK

Fig. 4 | The Phylogenetic position of Auroralumina attenboroughii. a, Artistic reconstruction of Auroralumina. b, Bayesian phylogenetic analysis of animals (348 characters, 108 taxa, mk + gamma model) incorporating Auroralumina attenboroughii. Numbers indicate posterior probabilities and scale bar shows expected number of substitutions per site. Fossils are indicated by dagger symbols. Raw polyp width is shown on the right, with the mean size shown for the extant groups sampled (for logged polyp size graph, see Extended Data Fig. 3). Branch length shown. Maximum polyp width data also shown in Extended Data Fig. 3. NA indicates where ancestral state values were inapplicable because they were derived from characters recovered as absent.

Fig. 5 in A crown-group cnidarian from the Ediacaran of Charnwood Forest, UK

Fig. 5 | Tubular morphospace occupation across the Ediacaran–Cambrian transition. a–c, The sum of variances (a), sum of ranges (b) and the median of centroids (c) for tubular morphospace occupation. The sum of variances examines the evenness of morphospace occupation, the sum of ranges examines the extent of morphospace occupation in all computed dimensions and the median of centroids measures the clustering of taxa around a central point. Adding Auroralumina increases the sum of variances, ranges and (marginally) the median of centroids compared to Ediacaran morphospace excluding Auroralumina. The boxes represent the interquartile range, with black line showing the median. The whiskers indicate minimum (Q1 − 1.5 × IQR) and maximum (Q3 + 1.5 × IQR), excluding outliers. Outliers are shown in black squares. d, Morphospace occupation with convex hulls showing Ediacaran morphospace occupation with and without Auroralumina and Cambrian morphospace occupation. Black circles represent Ediacaran taxa and white circles represent Cambrian taxa.

Fig. 3 in A crown-group cnidarian from the Ediacaran of Charnwood Forest, UK

Fig. 3 | Details of the distal anatomy of Auroralumina attenboroughii (GSM 106119) and the mode of preservation. a, Left-hand goblet, with dense crown of overlapping tentacles and conspicuous corner sulcus (now a ridge) and band (now a trench) near the aperture rim. The margins of the fossil are well-defined and the tentacle crown texturally and topographically distinct from the smooth periderm. b, Interpretative drawing of region in a. c, Right-hand goblet, principally preserving only one face but with a second partially visible where its edge (and intervening corner sulcus) was twisted into the plane of preservation, towards the right-hand side. d, Interpretative drawing of region in c. Specimen photographed under low-angle light and interpretations based on features revealed by varying the lighting direction. Scale bar in a and c, 5 cm. e,f, Preservation of the goblet and tentacles of A. attenboroughii. e, Apical view of the two goblets showing how their different orientations at the time of burial generated different views of the tetraradial structure in the fossil in lateral aspect. Schematic goblets (labelled 1 and 2) are representative of the two goblets in Auroralumina. The interpretative drawing of Auroralumina is also shown, with goblets labelled 1 and 2 next to a conulariid cnidarian (OUMNH DU17), also inferred to have been tetraradial in life, to illustrate analogous preservation of multiple faces in lateral view. f, Hypothetical arrangement of the tentacles in oral view in vivo and probable arrangement of tentacles in lateral view at time of burial along with proposed preservational pathway of the tentacles. 1: Tentacles, mostly overlapping, buried by sediment. 2: Partial retraction and deflation postmortem. 3: Decay and casting of the resultant space by sediment from below.

Fig. 2 in A crown-group cnidarian from the Ediacaran of Charnwood Forest, UK

Fig. 2 | Details of the proximal part of the holotype specimen of Auroralumina (GSM 106119). a, Interpretative drawing of entire specimen, with area shown in b–d outlined. b, Base of the preserved specimen, showing progressive cover of the left-hand goblet towards the bifurcation point and the mostly concealed proximal part of the right-hand goblet. The margins of the fossil in the concealed area are impressed—albeit weakly—through the sediment and the area underlain by the skeleton is defined by a change in sediment texture. Fossil photographed under low-angle light. c, Interpretative overlay, generated by combining observations made under multiple lighting directions. d, Interpretative drawing from c, showing symmetrical bifurcation of the two goblets and probable broken proximal termination of the specimen. Key in d covers all annotations in this figure. Scale bar in b and c, 5 cm.

Fig. 1 in A crown-group cnidarian from the Ediacaran of Charnwood Forest, UK

Fig. 1 | Holotype specimen of Auroralumina attenboroughii. a, In context alongside rangeomorph fossils preserved in a comparable manner and distinct from the textured background substrate (GSM 105874); imaged under low-angle light. b,c, Plastotype (GSM 106119) (b) and interpretative drawing (c) showing the differentiated stalk and cup of each goblet, well-defined corner sulci (now ridges) and texturally distinct tentacles. The proximal portions of both goblets, including their mutual branching point, are concealed beneath a thin cover of sediment but are nonetheless discernible as topographically and texturally distinct tracts (dashed grey line); see Fig. 2 for more information. RTI file available76.

Extended Data Fig. 3 in A crown-group cnidarian from the Ediacaran of Charnwood Forest, UK

Extended Data Fig. 3 | Maximum polyp width in cnidarians. Maximum polyp width plotted for extant cnidarian Classes and fossil groups. Auroralumina has a much larger polyp width than any other sampled medusozoan. Maximum conulariid polyp width is also larger than any sampled living medusozoan. Source data available with manuscript.

opencc-by-4.0May 2022View details →

LD matrices from the White British cohort in the UK Biobank in Zarr format

This dataset contains the Linkage Disequilibrium (LD) matrices that were used in the analyses described in the manuscript: Fast and Accurate Bayesian Polygenic Risk Modeling with Variational Inference Shadi Zabad, Simon Gravel, Yue Li McGill University LD matrices record the SNP-by-SNP correlations in a given sample of individuals from a general population. In this case, we threshold the matrices so that we only record the correlations between SNPs that are at most 3 centi Morgan apart. These matrices record the SNP correlations in a random sample of 50,000 individuals from the White British cohort in the UK Biobank dataset. There is one matrix per autosomal chromosome (chr_1, chr_2, ..., chr_22). The matrices are stored in <a href="https://zarr.readthedocs.io/en/stable/">Zarr</a> format, a chunked on-disk array storage format that allows for multi-threaded read and write access. To access these matrices, consult the codebase of <a href="https://github.com/shz9/magenpy">magenpy</a>, our custom python package with special data structures for processing these LD matrices. UPDATE (03/09/2022): We updated the matrices to add the reference allele attribute (A2) and we also now have one tar archive per chromosome.