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Figure 1 in Parajulid milliped studies XI: Initial assessment of the tribe Gosiulini (Diplopoda: Julida)
Figure 1. Known (solid lines) and projected (dashed lines) distribution of Gosiulini plotted against the maximal extent of the Western Inland Seaway in the Cretaceous Period, ca. 65–100 mya. The approximate distribution of Nesoressini (Shelley and Medrano 2006) is shaded in red.
Figures 2–5. Gosiulus conformatus, left anterior gonopods. 2 in Parajulid milliped studies XI: Initial assessment of the tribe Gosiulini (Diplopoda: Julida)
Figures 2–5. Gosiulus conformatus, left anterior gonopods. 2) Holotype, anterior view. 3) The same, lateral view. 4) Male from Travis Co., anterior view. 5) The same, lateral view. at, anterior gonopod telopodite; lsp, lateral syncoxal process.
Figure 6 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 6. Secondary structure models of the highly variable proximal part of helix 43 (S6, Fig. 1) in Zygaeninae. All structures are based on thermodynamic folding by minimizing the free energy and have been calculated considering the entire nucleotide sequence of helix 43. The change in the Gibb's free energy (dG) refers to the S6 structure only. Applied ambiguity code: G/A = R, C/U = Y.
Figure 3 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 3. Consensus structure and base pair probability matrix of helix E23-5 (S3, Fig. 1) in Lepidoptera. Nucleotides in circles indicate consistent and/or compensatory substitutions. The size of squares in the grid is proportional to the probability of a base pairing. Note that the species Z. centaureae, Z. laeta and Z. huguenini have been omitted from this analysis because of their deviating secondary structure (compare with Fig. 4).
Figure 2 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 2. Distribution of pairwise tree edit distances between highly variable SSU rRNA secondary structure areas (S1–S6, Fig. 1) of Zygaenoidea excluding taxa of the subgenus Mesembrynus (top) and of Zygaena species belonging to the subgenus Mesembrynus only (bottom). The extreme values in the Zygaenoidea tree edit distance distribution on the right all involve Z. excelsa, a species showing a highly derived secondary structure in the area S6 (compare with Fig. 6).
Figure 1 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 1. Secondary structure model of the SSU (18S) rRNA gene sequence of Zygaena (Mesembrynus) sarpedon lusitanica Reiss, 1936 (Lepidoptera: Zygaenidae; accession no. AJ830858) and structure variation in the helices E10-1 and E23-12 among species of the subfamily Zygaeninae. Nucleotides in the model are continuously numbered beginning at the 5′-end of the molecule; tick marks identify every tenth base. Light shading indicate helices numbered according to Wuyts et al. (2002). S1–S6 (dark shades) denote areas with variable secondary structure in the subfamily Zygaeninae. Roman numerals specify the domains I, II, III and IV. The following ambiguity code has been applied: A/C = M, C/U = Y, G/A = R.
Figure 7 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 7. Neighbour-joining tree based on structural differences in the variable areas S1–S6 (compare with Fig. 1) of the small-subunit (18S) rRNA in taxa of the genus Zygaena. The topology is rooted with Reissita simonyi and Epizygaenella caschmirensis as outgroup. Taxa of the subgenus Mesembrynus are indicated by shading. Numbers in parentheses specify the number of species in a particular group.
Figure 5 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 5. Consensus structure and base pair probability matrix of the proximal part of helix 43 (S6, Fig. 1) in Lepidoptera. Nucleotides in circles indicate consistent and/or compensatory substitutions. The size of squares in the grid is proportional to the probability of a base pairing. Note that the unpaired nucleotides C and G in the helix will most likely bind in individual structures having this specific nucleotide combination, but non-Watson–Crick pairings are too frequent in the alignment for assuming a generally nucleotide interaction at this position in the consensus structure.
Biogenesis of C. elegans spermatogenesis small RNAs is initiated by a zc3h12a like ribonuclease
<p><span>Small RNAs regulate spermatogenesis in many species, ranging from <em>Caenorhabditis elegans</em> to mammals. In <em>C. elegans</em>, two Argonaute proteins, ALG-3 and ALG-4, and their associated <em>alg-3/4</em> 26G-small RNAs are essential for spermatogenesis at 25°C and for imprinting paternal memory of germline gene expression in offspring. The <em>alg-3/4</em> 26G-small RNAs are antisense to their target mRNAs and are known to be produced by </span><span>the</span><span> RNA-dependent RNA polymerase, RRF-3. However, it remains unclear how the RNA templates for RRF-3 are generated and which cellular processes are affected by </span><em><span>alg-3/4</span></em><span> 26G-small RNAs</span><span>. Here, we demonstrate a key role for the conserved zc3h12a-ribonuclease-like NYN-domain-containing protein, NYN-3, in spermatogenesis at 25°C. Expression of NYN-3 was temporally coordinated with ALG-3, and our sequencing of both total and 2xFLAG::ALG-3-immunoprecipitated small RNAs revealed that NYN-3 is required for the biogenesis of <em>alg-3/4</em> 26G small RNAs. We further used ePAR-CLIP sequencing to identify NYN-3 binding sites on <em>alg-3/4</em>-targeted mature mRNAs; the NYN-3 binding sites were downstream of the binding sites for <em>alg-3/4</em> 26G-small RNAs. Additionally, 3'-RACE results placed the NYN-3 mRNA recognition upstream of RRF-3 binding and further revealed NYN-3 cleavage sites in <em>alg-3/4</em>-targeted mRNAs. Finally, a bioinformatics analysis was performed to parse the 26G small RNA-targeted genes into functional subclasses (e.g., signaling, chromatin defects). Collectively, these findings reveal NYN-3 as an initiator of small RNA generation that is central to the coordination of 26G small RNA-mediated gene regulation during spermatogenesis.</span></p>
Initiation of speciation across multiple dimensions in a rock-restricted, tropical lizard
<p>Population isolation and concomitant genetic divergence, resulting in strong phylogeographic structure, is a core aspect of speciation initiation. If and how speciation then proceeds and ultimately completes depends on multiple factors that mediate reproductive isolation, including divergence in genomes, ecology, and mating traits. Here we explored these multiple dimensions in two young (Plio-Pleistocene) species complexes of gekkonid lizards (<em>Heteronotia</em>) from the Kimberley–Victoria River regions of tropical Australia. Using mtDNA screening and exon capture phylogenomics, we show that the rock-restricted <em>H</em>. <em>planiceps</em> exhibits exceptional fine-scale phylogeographic structure compared to the co-distributed habitat generalist <em>H. binoei</em>. This indicates pervasive population isolation and persistence in the rock-specialist, and thus a high rate of speciation initiation across this geographically complex region, with levels of genomic divergence spanning the "grey zone" of speciation. Proximal lineages of <em>H. planiceps</em> were often separated by different rock substrates suggesting a potential role for ecological isolation; however, phylogenetic incongruence and historical introgression were inferred between one such pair. Eco-morphological divergence among lineages within both <em>H. planiceps</em> and <em>H. binoei</em> was limited, except that limestone-restricted lineages of <em>H. planiceps</em> tended to be larger than rock-generalists. By contrast, among-lineage divergence in the chemical composition of epidermal pore secretions (putative mating trait) exceeded eco-morphology in both complexes, but with less trait overlap among lineages in <em>H. planiceps</em>. This system — particularly the rock-specialist <em>H. planiceps</em> — highlights the role of multidimensional divergence during incipient speciation, with divergence in genomes, eco-morphology, and chemical signals all at play at very fine spatial scales.</p>
Data for Project 'Development and Initial Validation of the German Version of the Exergame Enjoyment Questionnaire (EEQ-G)'
<p>Data for Project 'Development and Initial Validation of the German Version of the Exergame Enjoyment Questionnaire (EEQ-G)', consisting of (1) the original and complete dataset (Data_EEQ-G_Validation_Study_for-publication.xlsx) and (2) a corresponding README file including (a) general information, (b) data and file overview, (c) sharing and access information, (d) methodological information, and (e) data-specific information.</p>
Citizen Science Initiatives in Greece
<p>This dataset contains original mapping data developed in the process of the Greek Citizen Science landscape review. In total, 20 Greek Citizen Science projects were analysed according to a common framework. During the mapping process, we weren’t always able to find information on things that interested us e.g. project impact, stakeholder engagement, the size of the volunteering force. But just because we couldn’t find something does not mean the results or activities did not happen. It goes without saying that absence of evidence is not evidence of absence. Failure to find some information on our part can be explained by the fact that we worked primarily with internet sources, so we had to make do with whatever publicly available information we could find within reasonable time.</p>
Klosterneuburg, Stiftsbibl., Cod. 48 - Ground Truth: Initial Release
<p>This is ground truth for the vast collection of sermons of Nikolaus von Dinkelsbühl (ca. 1360 to 17th March 1433), translated and reorganised by a German redactor, from the 15th century has never been edited until now. It consists of 361 folios of parchment and paper. The text speaks about various topics such as fasting and other religious practices. Being one of the leading intellectuals of his time, Nikolaus von Dinkelsbühl also contributed to the development of the University of Vienna. The manuscript was probably produced in the vicinity of Klosterneuburg in Austria and is still kept there today (Shelfmark: Cod. 48).</p> <p>Data collection and ground truth creation:</p> <p>The edition at hand was produced by an international team of researchers from various fields in the context of the Vienna HTR Winter School 2022 with the help of Transkribus Expert Client.</p> <p>We uploaded the images of the manuscript into the Transkribus platform, applied the line recognition tool and manually copied the transcribed text lines into the recognised line boxes. Various models were trained with the ground truth (20% of the entire codex) created by the team.</p> <p>Images of the Klosterneuburg, Augustiner-Chorherrenstift, Cod. 48 are available at: <a href="https://manuscripta.at/diglit/AT5000-48/0001">https://manuscripta.at/diglit/AT5000-48/0001</a></p>
Dataset for "Terrane collision-induced subduction initiation: Mode selection and implications for western Pacific subduction system"
<p>Numerical results for "<strong>Terrane collision-induced subduction initiation: Mode selection and implications for western Pacific subduction system</strong>".</p>
The LOTUS Initiative for Open Natural Products Research: wikidata query results
<p>Wikidata query results returned by the downloadLotus module of the <a href="https://github.com/lotusnprod/lotus-wikidata-interact">https://github.com/lotusnprod/lotus-wikidata-interact</a> program.</p> <p>See details of the module here <a href="https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md">https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md</a></p> <p>This dataset is constituted of 4 tables.</p> <ol> <li>compounds.tsv - chemical structures metadata (wikidataId, canonicalSmiles, isomericSmiles, inchi, inchiKey)</li> <li>references.tsv - bibliographical references metadata (wikidataId, pipe separated DOIs, titles)</li> <li>taxa.tsv - biological organisms metadata (wikidataId, pipe separated names, taxa rank)</li> <li>compound_reference_taxon.tsv - the documented structure-organism pairs</li> </ol> <p>This dataset includes not only the outputs of the LOTUS processing pipeline (available here <a href="https://doi.org/10.5281/zenodo.5665295">https://doi.org/10.5281/zenodo.5665295</a> ) but also any of wikidata chemical compounds having the found in taxon property (<a href="https://www.wikidata.org/wiki/Property:P703">https://www.wikidata.org/wiki/Property:P703</a>) and their associated organisms and documenting references.</p> <p> </p> <p><br> </p>
The LOTUS Initiative for Open Natural Products Research: frozen dataset
<p>Dataset used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
Fast Initiating Furan-Containing Hoveyda-Type Complexes: Synthesis and Applications in Metathesis Reactions
<p>Data confirming the structure of the new compounds obtained within the project, published in <em>Chemistry</em> <strong>2022</strong>, <em>4</em>(3), 786-795; <a href="https://doi.org/10.3390/chemistry4030056">https://doi.org/10.3390/chemistry4030056</a></p> <p>The research was performed within SONATA BIS project and was funded by National Science Centre, Poland, grant number DEC-2021/42/E/ST4/00187.</p> <p> </p> <p> </p>
ADCP data collected in the Southern California Bight by SWIFT drifters as part of the ONR "Langmuir Circulation Departmental Research Initiative (LC-DRI)"
<p>This is the public archive for ADCP data collected with SWIFT drifters during the 'Langmuir Circulation' Office of Naval Research Departmental Research Initiative (LC-DRI) field experiment, conducted between March 19th and April 6th, 2017 in the Southern California Bight 40 km west of Catalina Island. SWIFTs were deployed and recovered from the R/V R.G. Sproul during cruise SP1709 (Cruise DOI: 10.7284/907464). SWIFTs were deployed during storms with wind speeds up to 20 m/s and sampled strong diurnal warm layers during weaker wind periods.</p>
ETV4 mediates dosage-dependent prostate tumor initiation and cooperates with p53 loss to generate prostate cancer
<p>The mechanisms underlying ETS-driven prostate cancer initiation and progression remain poorly understood due to a lack of model systems that recapitulate this phenotype. We generated a genetically engineered mouse with prostate-specific expression of the ETS factor, ETV4, at lower and higher protein dosages through mutation of its degron. Lower-level expression of ETV4 caused mild luminal cell expansion without histologic abnormalities and higher-level expression of stabilized ETV4 caused prostatic intraepithelial neoplasia (mPIN) with 100% penetrance within 1 week. Tumor progression was limited by p53-mediated senescence and Trp53 deletion cooperated with stabilized ETV4. The neoplastic cells expressed differentiation markers such as Nkx3.1 recapitulating luminal gene expression features of untreated human prostate cancer. Single-cell and bulk RNA-sequencing showed stabilized ETV4 induced a novel luminal-derived expression cluster with signatures of the cell cycle, senescence, and epithelial to mesenchymal transition. These data suggest that ETS overexpression alone, at sufficient dosage, can initiate prostate neoplasia.</p>
Cosmological Initial Conditions (3D magnetic fields for an alfa=1.0 magnetic spectrum) for 85Mpc^3
<p>Files representing the initial conditions at z=40 for ENZO-MHD cosmological simulation of a comoving 85Mpc^3 volume, for tangled magnetic fields from an alfaB=-1.0 initial spectrum of magnetic fluctuations. The simulation has 1024^3 cells and 1024^3 DM particles. These data are in binary format and can be read by the ENZO code.</p> <p>More details of the simulations and on it cosmological parameter can be found at:</p> <ul> <li>https://ui.adsabs.harvard.edu/abs/2021Galax...9..109V/abstract</li> <li>https://ui.adsabs.harvard.edu/abs/2021MNRAS.500.5350V/abstract</li> <li>https://ui.adsabs.harvard.edu/abs/2017CQGra..34w4001V/abstract</li> </ul>
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.