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Figure 22 in Diversity, distribution and community composition of fish in perialpine lakes – "Projet Lac" synthesis report
Figure 22: Whole-lake average number of European perch (Perca fluviatilis) per vertical net battery compared to total phosphorus concentration in large and deep lakes (average depth> 50 m). The left panel shows the relationship for all perch caught in the lake (p-value = 0.022, R2 = 0.42). The right panel shows the relationship for only perch larger than 20 cm (length from snout to the tip of the tail; p-value = 0.003, R2 = 0.6). Note that the horizontal axis is on a log scale. Dashed red lines indicate statistically significant relationships.
Supporting data and software for: Low-temperature open-air synthesis of PVP-coated NaYF4:Yb,Er,Mn upconversion nanoparticles with strong red emission
<p>Upconversion nanoparticles (UCNPs) have unique photonic properties that make them ideally suited for many applications. They are excited by low-energy near-infrared photons and emit at higher energy (typically visible) wavebands. However, synthesis of UCNPs requires either high pressure reaction chambers or inert atmospheres. Combined with the requirements for high-temperatures (200 to 400 °C) and long reaction times (e.g. up to 24 hours), these place barriers to entry for UCNP research, in terms of both financial barriers and knowledge/"know how". These constraints may also limit the scale of UCNP production for end-user applications.</p> <p>We adapted and further developed a method for producing UCNPs with simple laboratory equipment, i.e. a hot-plate and beakers. No pressure vessel or inert atmosphere is required. The UCNPs produced have a<span> polyvinylpyrrolidone (PVP) polymer coating, with strong red emission due to Mn<sup>2+</sup> co-doping within the UCNP crystal lattice. It was found that UCNPs of composition NaYF<sub>4</sub>:Yb,Er,Mn (Yb = 20 mol %, Er = 2 mol%, Mn = 35 mol%) maximised the red emission whilst also minimising the diameter of the UCNPs to </span> 36 ± 15 nm. These combination of optical and physical properties should make these UCNPs ideal for further development and exploitation, particularly for biological applications where red emission can penetrate over a centimetre of tissue.</p> <p>This dataset and software accompanies the manuscript <em>'Low-temperature open-air synthesis of PVP-coated NaYF<sub>4:</sub>Yb,Er,Mn upconversion nanoparticles with strong red emission</em>', which was published in Royal Society Open Science on 19th January 2022. https://doi.org/10.1098/rsos.211508</p>
Database for the Geospatial Synthesis of Biogeochemical Attributions of Porphyrins to Oil Pollution in Marine Sediments of the Gulf of México
<p>This dataset is associated with the journal article "Geospatial Synthesis of Biogeochemical Attributions of Porphyrins to Oil Pollution in Marine Sediments of the Gulf of México" by Muñoz-Arriola and Macias-Zamora (2022). The porphyrin and biogeochemical data were obtained by and analyzed at the Universidad Autónoma de Baja California's Instituto de Investigaciones Oceanológicas. The samples were collected to identify the effects of natural and human-originated oil spills in the Campeche Sound, and these efforts are part of the oceanographic campaign Xaman-Ek.</p> <p> </p> <p>Associated references are:</p> <p>Munoz-Arriola, F. and V. Macias-Zamora (2022) <em>Geospatial Synthesis of Biogeochemical Attributions of Porphyrins to Oil Pollution in Marine Sediments of the Gulf of México</em>. Geosciences. https://doi.org/10.3390/ geosciences12020077.</p> <p>Macias-Zamora, J. V., J. A. Villaescusa-Celaya; A. Munoz-Barbosa; and G. Gold-Bouchot (1999). Trace metals in sediment cores from the Campeche shelf, Gulf of Mexico. Environmental Pollution. Vol 104:69-77.</p> <p> </p>
Computational synthesis of cortical dendritic morphologies
<p>Neuronal morphologies provide the foundation for the electrical behavior of neurons, the connectomes they form, and the dynamical properties of the brain. Comprehensive neuron models are essential for defining cell types, discerning their functional roles, and investigating brain disease related dendritic alterations. However, a lack of understanding of the principles underlying neuron morphologies has hindered attempts to computationally synthesize morphologies for decades. We introduce a synthesis algorithm based on a topological descriptor of neurons, which enables the rapid digital reconstruction of entire brain regions from few reference cells. This topology-guided synthesis generates dendrites that are statistically similar to biological reconstructions in terms of morpho-electrical and connectivity properties and offers a significant opportunity to investigate the links between neuronal morphology and brain function across different spatio-temporal scales. Synthesized cortical networks based on structurally altered dendrites associated with diverse brain pathologies, revealed principles linking branching properties to the structure of large-scale networks.</p> <p> </p> <p>We provide here the original biological reconstructions, the artificially generated cells and related data (electrical traces, connectivity of artificial networks) that were used for the analysis of the paper "Computational synthesis of cortical dendritic morphologies" to appear in Cell Reports.</p>
FIG. 6 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 6. — Distribution of Erymoidea during the Jurassic: A, palaeobiogeography of Middle Jurassic; B, palaeobiogeography of Late Jurassic. Colors: blue, Erymidae; orange, Enoploclytiidae. Abbreviations: En., Enoploclytia; Er., Eryma; Pal., Palaeastacus; Pu., Pustulina; S., Stenodactylina. Source of maps: Scotese 2014c.
FIG. 12 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 12. — Early Cretaceous erymoid fauna from the extreme south: A, holotype BAS KG.50.4 of Palaeastacus uranusiensis Devillez & Charbonnier, 2019, from the Aptian of Alexander Island (Antarctica); B, Specimen BAS KG.103.134 of Palaeastacus sussexiensis (Mantell, 1824), from the Aptian of Alexander Island (Antarctica); C, specimen BAS KG.11.4 of Palaeastacus terraereginae (Etheridge Jr, 1914), from the Barremian of Antarctica; D, specimens BAS KG-2-214 of Eryma sp. from the Aptian of Alexander Island (Antarctica); E-H, Australian specimens of P. terraereginae: specimen QM F3235, from the Barremian of Currane (E), specimen UQ F13417 from the Aptian of Boomers (F), specimen QM F3235 from the Barremian of Currane (G), specimen QM F3236 from the Barremian of Currane (H). Scale bars: 1 cm. Photographs: H. Blagbrough (A-D), P. Waddington (E-H).
FIG. 14 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 14. — Erymoid fauna from the Chalk Sea (Late Cretaceous): A, specimen NHMUK 5918 of Enoploclytia seitzi Glaessner, 1932, from the Cenomanian of Dover (United Kingdom); B-D, Enoploclytia leachii (Mantell, 1822), from United Kingdom: specimen NHMUK 34404 from Arundel (B), specimen BM 016987 (C), reconstruction (D); E-J, Palaeastacus sussexiensis (Mantell, 1824): specimen BM 007757, from Glynde (United Kingdom) (E), specimen NHMUK unregistered, from Maidstone (United Kingdom) (F), specimen NHMUK 59824, from Lewes (United Kingdom) (G), specimen MNHN.F.S07674, from Couvrot (France) (H), specimen BM 016988, from United Kingdom (I), reconstruction (J); K, specimen MNHN.F.A66891 of Stenodactylina cf. armata, from the Santonian of Cognac (France). Scale bars: 1 cm. Preparation: Y. Despres (H, K). Photographs: L. Cazes (H), J. Devillez (A-C, E-G, I), P. Loubry (K). Drawings: J. Devillez.
FIG. 1 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 1. — Palaeastacus terraereginae (Etheridge Jr, 1914) from Australia: A, B, holotype QM 3234 from the Barremian of the Barcoo river: general view (A), schema (B); C, D, specimen QM F3236: dorsal view (C), ventral view (D); E, F, holotype UQ F13410 of Enoploclytia tenuidigitata Woods, 1957 from the Aptian of Boomers: P1 chela (E), dorsal view of the carapace (F); G, H, specimen UQ F13417 from the Aptian of Boomer: carapace (G), schema (H). Abbreviations: a, branchiocardiac groove; b, antennal groove; b1, hepatic groove; c, postcervical groove; d, gastro-orbital groove; e1e, cervical groove; i, inferior groove; POA, post-orbital area; χ, attachment site of adductor testis muscle; ω, attachment site of mandibular muscle. Scale bars: 1 cm. Photographs: P. Waddington. Line drawings: J. Devillez.
FIG. 3 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 3. — Erymoid lobsters from the Palaeozoic and the Paleogene: A, holotype PIN 1453 of Eryma antiquum (Birshtein, 1958) from the Changhsingian of Ust-Jenisseisk (Russia); B, C, Enoploclytia gardnerae (Rathbun, 1935) from the Selandian of Coahuila (Mexico): specimen CPC 1982 (B), specimen IGM-9095 (C). Scale bars: 1 cm. Photographs: F. Schram (A), F. Vega (B, C).
FIG. 2 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 2. — Enoploclytia minor Woodward, 1900 from the Upper Cretaceous of Hornby Island (Canada): A-C, holotype GSC 5971: general view of the specimen (A), line drawing (B), counterpart (C); D, E, holotype of Eryma dawsoni GSC 5969: general view of the specimen (D), counterpart (E), line drawing (F). Abbreviations: a, branchiocardiac groove; b, antennal groove; b1, hepatic groove; c, postcervical groove; d, gastro-orbital groove; e1e, cervical groove; i, inferior groove. Scale bars: 1 cm. Photographs: M. Coyne. Line drawings: J. Devillez.
FIG. 11 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 11. — Distribution of Erymoidea during the Cretaceous: A, palaeobiogeography of the Early Cretaceous; B, palaeobiogeography of the Late Cretaceous. Colors: blue, Erymidae; orange, Enoploclytiidae. Abbreviations: En., Enoploclytia; Er., Eryma; Pal., Palaeastacus; Pu., Pustulina; S., Stenodactylina; T., Tethysastacus. Source of maps: Scotese 2014a, b.
FIG. 9 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 9. — Erymoid fauna from Madagascar: A, B, Stenodactylina granulifera (Secrétan, 1964) from the Kimmeridgian of Antsalova: holotype MNHN.F.R03975 (A), specimen MNHN.F.R.03974, holotype of Eryma madagascariensis Secrétan, 1964 (B); C, D, Stenodactylina australis (Secrétan, 1964), from the Tithonian: specimen MNHN.F.A33228 from Marolalitra (C), holotype MNHN.F.R03972 from Analavelona Massif (D); E, F, Pustulina spinulata (Secrétan, 1964), from the Valanginian-Hauterivian of Soromaraina, holotype MNHN.F.R03961 (E), paratype MNHN.F.A33189 (F); G, H, paratype MNHN.F.A33132 of Enoploclytia collignoni Secrétan, 1964, from the Campanian of Bevaho; I, holotype MNHN.F.R03913 of Stenodactylina armata (Secrétan, 1964), from the Campanian of Belo-sur-Tsiribihina. Scale bars: 1 cm. Preparation: C. Bouillet (G-H). Photographs: L. Cazes (C, G, H), C. Lemzaouda (A, B, D, E, I).
Continuous synthesis of 5-hydroxymethylfurfural from biomass in on-farm biorefinery
<p>The file contains the raw data for a paper presenting the HMF synthesis from biomass- miscanthus and chicory roots and sugars-fructose and glucose.</p>
FIG. 13 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 13. — Early Cretaceous erymoid fauna from the South-East Basin (France): A, cast MNHN.F.R10204 of the holotype of Eryma glaessneri (Van Straelen, 1936), from the Hauterivian of Escragnolles; B, C, specimens of Eryma vocontii Devillez, Charbonnier, Hyžný & Leroy, 2016 from the Albian of Rosans: holotype MNHN.F.A57457 (B), paratype MNHN.F.A57458 (C); D, original figure of Van Straelen (1923: fig. 10) of the holotype of Palaeastacus loryi (Van Straelen, 1923) from the Valanginian of Malleval; E, original figure of Van Straelen (1936: pl. 2, fig. 3) of the holotype of Pustulina victori Devillez, Charbonnier, Hyžný & Leroy, 2016, from the Berriasian of Leysse; F, holotype MNHN.F.A57459 of Pustulina colossea Devillez, Charbonnier, Hyžný & Leroy, 2016, from the Hauterivian of Castellane; G, holotype MNHN.F.A57460 of Pustulina occitana Devillez, Charbonnier, Hyžný & Leroy, 2016, from the Berriasian of Laciterne-Boisset; H, holotype OSUG.UJF-ID 11152 of Stenodactylina delphinensis (Moret, 1946), from the Berriasian of Noyarey; I, holotype MNHN.F.J03351 of Tethysastacus tithonius (Van Straelen, 1936), from the Valanginian of Laciterne-Boisset. Scale bars: 1 cm. Photographs: L. Cazes.
FIG. 4 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 4. — Erymoid lobster palaeobiodiversity: A, specific diversity for each genus during the Jurassic; B, specific diversity for each genus during the Cretaceous; C, evolution of the specific diversity during the Mesozoic for each genus across the globe (left) and in Europe (right). These graphs do not include those species that are exclusively found in the Solnhofen Lagerstätten.
FIG. 10 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 10. — Erymoid fauna from the Kimmeridgian-Tithonian "Plattenkalk" of Bavaria (Germany): A, specimen MFN 2236 P1383/3 MB.A.2891 of Eryma modestiforme (Schlotheim, 1822) from Solnhofen; B, holotype SMNS 3682 of Eryma major Oppel, 1861, from Nusplingen; C, holotype SMNS 24227 of Eryma westphali Schweigert, Dietl & RÖper, 2000, from Nusplingen; D, holotype BSPG AS VII 186 of Eryma veltheimii (Münster, 1839), from Kehlheim; E, specimen SMNS 64681 of Eryma punctatum Oppel, 1861, from Nusplingen; F, specimen SMNS 64521 of Palaeastacus fuciformis (Schlotheim, 1822), from Zandt; G, holotype BSPG 1993 XXVIII 200 of Palaeastacus rothgaengerae Schweigert & RÖper, 2001, from Brunn; H, holotype SMNS 70507 of Stenodactylina geigerae Schweigert & Härer, 2020, from Marxheim; I, holotype SMNS 64872 of Stenodactylina devillezi Schweigert & Härer, 2020, from Nusplingen; J, specimen SMNS 64319 of Pustulina suevica Quenstedt, 1857, from Nusplingen; K, specimen BSPG AS I 619 of Pustulina minuta (Schlotheim, 1822), from Solnhofen. Scale bars: 1 cm. Photographs: J. Devillez (A-F, J-K), G. Schweigert (G-I).
FIG. 7 in A synthesis of the evolutionary history of erymoid lobsters (Crustacea, Decapoda, Erymoidea)
FIG. 7. — African, Middle East and Far East erymoid lobsters, excepting E. moriedaorum: A, specimen MFN 2236 P1383/2 MB.A.1537 of Eryma ventrosum (Meyer, 1835), from the Upper Jurassic of Tanzania;B, original figure of FÖrster & Seyed-Emami (1982: fig. 3) of the specimen of Eryma compressum Eudes-Deslongchamps, 1842, from the Aalenian of the Imamzadeh Hashim Pass northeast of Teheran (Iran); C, holotype WMNH-Ge-1140320056 of Eryma nippon Karasawa, Ohara & Kato, 2008 from the Barremian of Suhara (Japan); D, specimen MSNM i 12292 of Pustulina cretacea (Roger, 1946), from the Cenomanian of Hakel (Lebanon); E, holotype MNHN.F.B18902 of Eryma oscari Charbonnier, Audo, Garassino & Hyžný, 2017, from the Cenomanian of Hadjoula (Lebanon). Scale bars: 1 cm. Photographs: J. Devillez (A), H. Karasawa (C), G. Teruzzi (D), D. Audo (E).
Cross-biome synthesis of source versus sink limits to tree growth
<p>Uncertainties surrounding tree carbon allocation to growth are a major limitation to projections of forest carbon sequestration and response to climate change. The prevalence and extent to which carbon assimilation (source) or cambial activity (sink) mediate wood production are fundamentally important and remain elusive. We quantified source-sink relations across biomes by combining eddy-covariance gross primary production with extensive on-site and regional tree ring observations. We found widespread temporal decoupling between carbon assimilation and tree growth, underpinned by contrasting climatic sensitivities of these two processes. Substantial differences in assimilation-growth decoupling between angiosperms and gymnosperms were determined, as well as stronger decoupling with canopy closure, aridity, and decreasing temperatures. Our results reveal pervasive sink control over tree growth that is likely to be increasingly prominent under global climate change.</p>
Three‐level hybrid modeling for systematic optimization of biocatalytic synthesis: α‐glucosyl glycerol production by enzymatic trans‐glycosylation from sucrose
<p>We provide here the underlying data of the publication "Three‐level hybrid modeling for systematic optimization of biocatalytic synthesis: α‐glucosyl glycerol production by enzymatic trans‐glycosylation from sucrose". Please find the abstract below.</p> <p>Mechanism-based kinetic models are rigorous tools to analyze enzymatic reactions, but their extension to actual conditions of the biocatalytic synthesis can be difficult. Here, we demonstrate (mechanistic-empirical) hybrid modeling for systematic optimization of the sucrose phosphorylase-catalyzed glycosylation of glycerol from sucrose, to synthesize the cosmetic ingredient α-glucosyl glycerol (GG). The empirical model part was developed to capture nonspecific effects of high sucrose concentrations (up to 1.5 M) on microscopic steps of the enzymatic trans-glycosylation mechanism. Based on verified predictions of the enzyme performance under initial rate conditions (Level 1), the hybrid model was expanded by microscopic terms of the reverse reaction to account for the full-time course of GG synthesis (Level 2). Lastly (Level 3), the application of the hybrid model for comprehensive window-of-operation analysis and constrained optimization of the GG production (~250 g/L) was demonstrated. Using two candidate sucrose phosphorylases (from <em>Leuconostoc mesenteroides</em> and <em>Bifidobacterium adolescentis</em>), we reveal the hybrid model as a powerful tool of “process decision making” to guide rational selection of the best-suited enzyme catalyst. Our study exemplifies a closing of the gap between enzyme kinetic models considered for mechanistic research and applicable in technologically relevant reaction conditions; and it highlights the important benefit thus realizable for biocatalytic process development.</p>
Compound Data for Robust Processes for Polymer Modification and Pharmaceutical Synthesis
<p>Compound structural (IUPAC name, InChI, InChI Key, SMILES, .mol, .sdf) and spectral (NMR, MS) data included for compounds reported in the associated doctoral thesis. NMR data collected on Bruker Avance 400, 500, or 600 MHz spectrometers. Compound structure data were generated by ChemDraw v.20 (PerkinElmer). More details about the preparation and characterization of these compounds can be found in the associated thesis.</p>
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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.