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EQ3/6 model results for Randolph-Flagg et al., "Phosphate availability and implications for life on ocean worlds," Nature Communications, 2023
<p>These output files are provided as pickle format at (10.5281/zenodo.7683874) and readable using standard open-source data processing software (<em>e.g.</em>, <a href="https://www.python.org/">https://www.python.org/</a>). The authors declare that the data supporting the findings of this study are available within the paper and supporting information files.</p> <p>Thermodynamic calculations were performed with the program EQ3/6, a thoroughly vetted and commonly used aqueous geochemistry code that computes the equilibrium distribution of dissolved and solid phase species based on a specified initial composition and reaction conditions. For detailed description of please see Randolph-Flagg et al., Nature Communications, 2023.</p>
Morphometric Trends and Implications for the formation of Araneiform Clusters Supplementary Table
<p>Table of araneiform morphometric measurements used to produce plots in Figure 3 of manuscript.</p>
Magnesium isotopic fractionation during serpentinization: Implications for arc and oceanic Mg cycles
<p>Table 1. MgO contents and Sr-Pb-Mg isotopic compositions of the serpentinites from the Mariana forearc mud volcanoes.<br> Table S1. Major and trace elements of the serpentinites from the Mariana forearc mud volcanoes.<br> </p>
Inlist file for Optical color of Type Ib and Ic supernovae and implications for their progenitors
<p>Example inlist files for make He and CO progenitor models for the paper submitted to the AAS Journal entitled as "Optical color of Type Ib and Ic supernovae and implications for their progenitors"</p>
Data for: Effects of domestication and captive breeding on reaction to moving objects: Implications for avoidance behaviors of obstacles and predators by masu salmon Oncorhynchus masou
<p>Domestication and captive breeding can compromise obstacle- and predator-avoidance of animals in the wild. Whereas previous studies only examined these effects in combination, here we examine them individually by comparing the abilities of wild, F1 (offspring of wild parents), and captive-bred (approx. F15) masu salmon (<em>Oncorhynchus</em> <em>masou</em>) to avoid a falling object under experimental conditions. Rates of avoidance failure were low (wild, 12.5%; F1, 10.7%; captive-bred, 8%) under light conditions but increased under dark conditions (wild, 11.1%; F1, 32.1%; captive-bred, 60.0%). We attribute the elevated avoidance-failure rate among F1 fish to the lack of learning opportunities in hatchery environments, and the further elevation of avoidance-failure rate among captive-bred fish to the degradation of sensory organ function. These results imply reduced survival rates for F1 and captive-bred fish in the wild and are consistent with the low stocking efficiencies reported for captive-bred masu salmon.</p>
FIG. 3 in Swarming behaviour, catchment area and seasonal movement patterns of the Bechstein's bats: implications for conservation
FIG. 3. Examples illustrating the recovered movement patterns between maternity colonies and swarming sites. Individuals at swarming sites LA (A) and KG (B) were recovered at multiple colonies. Likewise, individuals recovered at colonies A (C) and H (D) were caught at different swarming sites on the same night. Capture site abbreviations and maternity colony IDs correspond to those used in Fig. 1 and Table 1
FIG. 2 in Swarming behaviour, catchment area and seasonal movement patterns of the Bechstein's bats: implications for conservation
FIG. 2. Map showing the minimum catchment polygon (dark grey), and maximum range circle (light grey) of the two main swarming sites (LA, KG). Country border between Belgium and the Netherlands (irregular black line), forest fragments (irregular grey patches), swarming sites (grey pentagons) and recovered roost sites (black dots) are also indicated
FIG. 1 in Swarming behaviour, catchment area and seasonal movement patterns of the Bechstein's bats: implications for conservation
FIG. 1. Map of the Belgium and adjacent countries (inset top right) indicating the location of study area. Within the study are (main figure), sampled swarming sites and recovered roost sites are indicated (grey pentagons and black circles, respectively). Forest fragments are shaded according to age (recent: light grey; ancient: dark grey). Capture site abbreviations correspond to those used in Table 1
Roy et al. 2023 Supplemental Information for "Sediment-encased pressure–temperature maturation experiments elucidate the impact of diagenesis on melanin-based fossil color and its paleobiological implications."
<p><em>Supplemental Information for</em></p> <p>Sediment-encased pressure–temperature maturation experiments elucidate the impact of diagenesis on melanin-based fossil color and its paleobiological implications.</p> <p>Arindam Roy<em><sup>*</sup></em> (<a href="https://orcid.org/0000-0002-4890-6851">https://orcid.org/0000-0002-4890-6851</a>)</p> <p>Michael Pittman<em><sup>*</sup></em> (<a href="https://orcid.org/0000-0002-6149-3078">https://orcid.org/0000-0002-6149-3078</a>)</p> <p>Thomas G. Kaye (<a href="https://orcid.org/0000-0001-7996-618X">https://orcid.org/0000-0001-7996-618X</a>)</p> <p>Evan T. Saitta (<a href="https://orcid.org/0000-0002-9306-9060">https://orcid.org/0000-0002-9306-9060</a>)</p> <p>*Corresponding author(s)</p> <p><strong>Email: </strong><a href="mailto:ar15313@bristol.ac.uk">ar15313@bristol.ac.uk</a> ; <a href="http://palaeopittman.com/2022/03/27/lab-members/mpittman@cuhk.edu.hk">mpittman@cuhk.edu.hk</a></p> <p>The Dataset contains two files, (1) Supporting Information and (2) Supporting Data PCA worksheet. </p> <p>The first contains Supplementary tables and figures (.docx file) while the structural organisation of the second (.xlsx file) is provided below:</p> <p>We received ToF-SIMS data (Samples 1–30, 36–51) pertaining to purified melanosome extracts of modern bird feathers (both fresh and capsule-matured) from Caitlin Colleary (Associate Curator of Vertebrate Paleontology, Cleveland Museum of Natural History), based on their previous work (Colleary et al. 2015). Citation below:</p> <p> </p> <p>Colleary, C., A. Dolocan, J. Gardner, S. Singh, M. Wuttke, R. Rabenstein, J. Habersetzer, S. Schaal, M. Feseha, M. Clemens, B. F. Jacobs, E. D. Currano, L. L. Jacobs, R. L. Sylvestersen, S. E. Gabbott, and J. Vinther. 2015. Chemical, experimental, and morphological evidence for diagenetically altered melanin in exceptionally preserved fossils. Proceedings of the National Academy of Sciences USA 112(41):12592-7. doi: https://doi.org/10.1073/pnas.1509831112</p> <p> </p> <p>We further augmented this data set by adding ToF-SIMS spectra from our own samples (31-34, 52-79) pertaining to sediment encased maturation experiments (190ºC to 300ºC) and fossilised feathers of paravian dinosaurs housed at the Shandong Tianyu Museum of Natural History, Linyi Shi, Shandong, China.</p> <p>We conducted Principal Components Analysis with this Data and this dataset effectively serves as a PCA worksheet. The file can be opened/edited using Microsoft 365 Excel (.xlsx) with the following organisation of sheets.</p> <p>Sheets:</p> <p><strong>|----- PCA All</strong> : contains Sample ID, treatment categories, mass by charge (m/z) ratios of 55 peaks, peak identity and raw intensity counts</p> <p><strong>|-----PCA All Normalised</strong> : same data as PCA All but peak raw intensity counts normalised.</p> <p><strong>|-----PCA All Mean Centered</strong>: same data as PCA Normalised but with peak raw intensity mean centered.</p> <p><strong>|-----PCA All Loading Matrix:</strong> Loading matrix for PCA All using all 55 peaks.</p> <p><strong>|-----PCA All Eigen Vectors: </strong>Eigen vectors for PCA All.</p> <p><strong>|-----PCA All Scores: </strong> PCA scores for all 55 peaks.</p> <p><strong>|-----PCA No Lipids RAW</strong>: same data as PCA All but without peaks suspected to arise from lipids (e.g., CxH-).</p> <p><strong>|-----PCA No Lipids Normalised:</strong> same data as PCA without Lipids RAW but with peak raw intensity counts normalised.</p> <p><strong>|-----PCA No Lipids MeanCentred:</strong> same data as PCA without Lipids Norm but with peak raw intensity counts mean centered.</p> <p><strong>|-----PCA No Lipids Loading Matrix:</strong> Loading matrix for PCA All excluding peaks of lipid origin (CxH-).</p> <p><strong>|-----PCA No Lipids Eigen Vectors: </strong>Eigen vectors for PCA No Lipids Eigen Vectors.</p> <p><strong>|-----PCA No Lipids Scores:</strong> PCA scores for all peaks excluding those of lipid origin (CxH-).</p> <p> </p> <p>The dataset has been created in Microsoft Office 365 (Excel: .xlsx file). The file can also be also be opened and edited using the following softwares.</p> <p>1. Google Sheets</p> <p>2. Apache Open Office</p> <p>3. Libre Office</p> <p>4. PAST 4 (free software for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy)."</p>
Fig 5. A in The oldest known bat skeletons and their implications for Eocene chiropteran diversification
Fig 5. A composite stratigraphic column of the Green River Formation showing the relative position of the Fossil Butte Member and stratigraphic levels where various bat fossils have been found. The Fossil Butte Member is the thinnest of the members in the Green River Formation, but was deposited when the lake was deepest, providing conditions that were optimal for exceptional preservation. Five units in the Fossil Butte Member (Sandwich Beds, 18-inch Layer, Minifish Bed, Gastropod Beds, and Upper Split-fish Bed) are actively quarried on private and stateowned land by companies collecting the abundant fossil fish to sell. Among the fish, one bat is found on average every two years. To date, all bats have come from the 18-inch Layer and Sandwich Beds. Bat specimens are coded by color: Icaronycteris gunnelli in red, I. index in orange, Onychonycteris finneyi in blue, and unidentified or indeterminate are black. More than 10 bat specimens are held in private collections (not shown here), but none are confirmed lower in the section than the two specimens of I. gunnelli. Left two columns modified after Buchheim et al, 2011 [40]. https://doi.org/10.1371/journal.pone.0283505.g005
Fig 3 in The oldest known bat skeletons and their implications for Eocene chiropteran diversification
Fig 3. Skeleton of paratype of Icaronycteris gunnelli (ROM:Palaeobiology-Vertebrate Fossils:52666). https://doi.org/10.1371/journal.pone.0283505.g003
Fig 4 in The oldest known bat skeletons and their implications for Eocene chiropteran diversification
Fig 4. Remaining deposits of Fossil Lake sediments of the Green River Formation are illustrated in gray with highly-fossiliferous, deep-water, laminated limestone deposits of Eocene Fossil Lake in southwest Wyoming and poorly-fossiliferous, shallow-water, non-laminated limestones in northeast Utah and southeast Idaho. Eleven of more than 20 fossil quarries are still active today. Three active quarries (A, B and D) and one inactive quarry (C) have produced fossil bats currently held in public institutions. All other historic and active quarry locations are marked by small black dots. American Fossil Quarry (A) yielded I. gunnelli (AMNH.FM.145747 and ROM.52666), I. index (AMNH.FM.125000 and AMNH.FM.144215), I. cf index (WDC-CGR-115) and O. finneyi (AMNH.FM.142467 and ROM.55351). Thompson Ranch north quarry (B) yielded I. index (FMNH.PM.62096 and HMNS.PV.001468). The Holland brother's quarry (C) was active for only one season in the mid-1930s and yielded I. index (YPM-PU.18150). The Smith Hollow quarry (D) yielded a poorly preserved and unidentified specimen (FOBU13777). Most bat specimens were recovered from two quarries operating continuously since the 1980s in nearshore deposits. A combination of proximity to the eastern shore and a large volume of rock excavated is the most probable explanation for the greater number of bat fossils being discovered in those locations. https://doi.org/10.1371/journal.pone.0283505.g004
Fig 2 in The oldest known bat skeletons and their implications for Eocene chiropteran diversification
Fig 2. Illustrated dentitions of Green River bats. A) Onychonycteris finneyi (ROM 55351A-B) upper P1-M3; B) Icaronycteris index (YPM-PU 18150) upper P1-M3; C) Icaronycteris gunnelli (FM.145747A) upper P1-M3; D) Icaronycteris gunnelli (FM.145747A) lower c1-m3, with reconstructed i1-i3, in labial view. Abbreviations of features discussed in the text: dc—distal cingulid; ec—ectocingulum; ef—ectoflexus; hs—hypocone shelf; lc—lingual cingulum; pbc—posterobasal cusp; prm—premetacrista; prp—preparacrista; ps—parastyle; psm—postmetacrista; psp— postparacrista; tal—talonid. https://doi.org/10.1371/journal.pone.0283505.g002
Figure 1. A in The limpet form in gastropods: evolution, distribution, and implications for the comparative study of history
Figure 1. A, external and internal views of Haliotis varia (Linnaeus, 1758) (Haliotidae), Kinabohutan, north-east Sulawesi, Indonesia; Vermeij collection. B, external and internal views of Cranopsis Dall, 1914 (Fissurellidae), off Iceberg Point, Lopez Island, Washington State, USA; Vermeij collection. C, external and internal views of Patelloidea saccharina (Linnaeus, 1758) (Lottiidae), Ngerdis Cove, Arakabesan, Palau; Vermeij collection. Note the strong radial ribs that extend beyond the shell margin. D, external and internal views of Concholepas concholepas (Lamarck, 1801) (Muricidae: Ralpaninaek), Montemar, Chile; Vermeij collection. E, external and internal views of Theodoxus vespertinus (Sowerby, 1849) (Neritidae), near the mouth of Wainiha River, Kauai, Hawaii; Vermeij collection. Note the internal septum and the wing-like sides of the limpet-like shell. F, external and internal views of Crepidula lessonii (Broderip, 1834) (Calyptraeidae), Playa Venado, Pacific coast of Panama; Vermeij collection. Note the internal septum, and the external sculpture of imbricated lamellae. G, external and internal views of Siphonaria gigas (Sowerby, 1825) (Siphonariidae), Playa de Panam� a, Pacific coast of Costa Riica; Vermeij collection. Note the convergence with Patelloida saccharina. H, external view of Delminiella soklici Kochansky-Devide & Sli� skovi� c, 1972, Vu� cipolje near Tomislavgrad, Bosnia and Herzegovina, late early Miocene. Holotype, stored in the National Museum of Bosnia and Herzegovina, Sarajevo (MG3631). Figured from Harzhauser et al. (2016), fig. 3A). Photograph provided by T. A. Neubauer. I, Valenciennius reussi (Neumayr in Neumayr & Paul, 1875), Tirol (=Konigsgnad), Romania, late Miocene (Pannonian). Specimen stored in the Natural History Museum Vienna (NHMW 1900/0009/0005). Photograph provided by T. A. Neubauer.
Wolverine denning behaviour and its implications for monitoring reproductive females
<p>Knowledge about the number of reproductive females is important for monitoring population dynamics, and can be critical for managing human-wildlife conflicts. For wolverines (<em>Gulo</em> <em>gulo</em>), counts of reproductive females is the basis for estimates of population size in Scandinavia, as well as a key measure for compensation payments to Sámi reindeer-herders in Sweden. However, documenting wolverine reproductive events in the field is challenging and requires knowledge of female denning behaviour. Furthermore, females may shift den sites, presenting difficulties in determining whether two den sites belong to the same or two neighbouring females. In this study, we used data from 18 GPS-collared wolverine females, monitored intensively during the denning season (February 15 – May 31) in 2004–2014, to provide baseline information on denning behaviour. We documented reproductive events in 32 of 54 potential denning seasons and identified a total of 245 den sites. Females used 8.8±8.5 (mean±SD) den sites per denning season (median=6, range: 1–28). The number of den site shifts, the distance between subsequent den sites, and the time and distance females spent away from a den site increased during the denning season, while distances between neighbouring females' den sites remained constant. From late April, the distance between consecutive den sites used by the same female overlapped with distances between neighbouring females' den sites, resulting in increased uncertainty regarding whether two den sites belonged to one or two females. <span>Using Bayesian modelling, we calculated probabilities that two den sites belonged to the same female or neighbouring females, conditional on the time of season and the distance between den sites. These findings will allow the monitoring program to adapt its methods for determining if multiple den sites belong to one or two reproductive events, using seasonally-dynamic threshold based on an understanding of wolverine denning behaviour.</span></p>
Identification of upper thermal thresholds during development in the endangered Nechako white sturgeon with management implications for a regulated river
<p>Climate change-induced warming effects are already evident in river ecosystems and projected increases in temperature will continue to amplify stress on fish communities. Additionally, many rivers globally are impacted by dams which have many negative effects on fishes by altering flow, blocking fish passage, and changing sediment composition. However, in some systems, dams present an opportunity to manage river temperature through regulated releases of cooler water. For example, there is a government mandate for Kenney dam operators in the Nechako River, BC Canada, to maintain river temperature below 20°C in July and August to protect migrating sockeye salmon (<em>Oncorhynchus</em> <em>nerka</em>). However, there is another endangered fish species inhabiting the same river, Nechako white sturgeon (<em>Acipenser</em> <em>transmontanus</em>), and it is unclear if these current temperature regulations, or timing of the regulations, are suitable for spawning and developing sturgeon. In this study, we aimed to identify upper thermal thresholds in white sturgeon embryos and larvae to investigate if exposure to current river temperatures are playing a role in recruitment failure. We incubated embryos and yolk-sac larvae in three environmentally relevant temperatures (14°, 18°C, and 21°C) throughout development to identify thermal thresholds across different levels of biological organization. Our results demonstrate upper thermal thresholds at 21°C across physiological measurements in embryo and yolk-sac larvae white sturgeon. Prior to hatch, both embryo survival and metabolic rate were reduced at 21°C. Following hatch, sublethal consequences continued at 21°C as larval sturgeon had decreased thermal plasticity and a dampened transcriptional response during development. In recent years, the Nechako River has reached 21°C by the end of June, and at this temperature, a decrease in sturgeon performance is evident in most of the traits measured. As such, the thermal thresholds identified here suggest current temperature regulations may not be suitable for developing white sturgeon and future recruitment.</p>
High-Pressure Single-Crystal Elasticity of Corundum: Implication for Multiple Seismic Structure of 660-km Discontinuity
<p>Here are the experimental data.</p>
Mantle xenoliths used in "High P-T sound velocities of amphiboles: Implications for low-velocity anomalies in metasomatized upper mantle"
<p>Mineral proportions in hydrous-mineral-bearing mantle xenoliths collected worldwide and their calculated sound velocities in this study. </p>
Figure 5 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 5. The lateral wall of the braincase of Pristerodon mackayi (BP/1/2642): right prootic (blue) in (A) anterior, (B) lateral, (C) posterior, (D) ventral and (E) medial views; and left opisthotic (golden) in (F) anterior, (G) lateral and (H) posterior views. afac, articulation facet concavity; ascc, attachment of the anterior semicircular canal; boa, basioccipital sutural area; bsa, parabasisphenoid sutural area; CNV, passage of the cranial nerve five (V); eoa, exoccipital sutural area; fa, facial foramen; flo, floccular fossa; fo, fenestra ovalis; jf, jugular foramen; lscc, attachment of the lateral semicircular area; lvb, opisthotic lateral vertical buttress; osu, opisthotic posterior vertical sulcus; ovmp, opisthotic ventromedial process; pa, pila antotica; pab, prootic anterior bulge; pad, pila antotica anterior depression; pdp, prootic dorsal process; prd, prootic lateral depression; pscc, attachment of the posterior semicircular canal; ptf, posttemporal fenestra; spa, supraoccipital sutural area; vea, vestibular area; ve, vestibule. The horizontal line pattern on the prootic in (B) represents the prootic depression. The diagonal square pattern in (F) represents the articular surface of the prootic. Scale bars equal 5 mm. The upper scale bar serves for (A-E) and the lower for (F-H).
Figure 11 in X-ray microcomputed and synchrotron tomographic analysis of the basicranial axis of emydopoid dicynodonts: implications for fossoriality and phylogeny
Figure 11. Illustration of a cistecephalid species and its inferred palaeobiology. Skin texture is inspired by the naked mole-rat and the foraging behaviour typical of a fossorial taxon feeding on insects. Reconstruction credits: copyright Luzia Soares (2021).
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.