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FIG. 12. — A-G in Bryozoan faunas at the Tortonian-Messinian transition. A palaeoenvironmental case study from Crete Island, eastern Mediterranean
FIG. 12. — A-G, Batopora rosula (Reuss, 1847); A, colony, basal-lateral view (arrow indicates the scar of an ovicellate zooid), FAN7: AMPG(IV) 3475a; B, colony, apical view, FAN7: AMPG(IV) 3475b; C, colony, lateral-apical view, FAN7: AMPG(IV) 3475c; D-G, juvenile forms (G, basal view), FAN18: AMPG(IV)a-d; H-I, Orbitulipora excentrica Seguenza, 1880; H, whole colony, FAN22: AMPG(IV) 3580a; I, detail view of the left part of the same colony (arrows indicate ovicellate zooids), FAN22: AMPG(IV) 3580a. Scale bars: H, 500 µm; A-C, I, 200 µm; D-G, 100 µm.
FIG. 5 in Bryozoan faunas at the Tortonian-Messinian transition. A palaeoenvironmental case study from Crete Island, eastern Mediterranean
FIG. 5. — Schematic sedimentary log of Faneromeni section with sample location and semi-quantitative abundances of bryozoan species.
FIG. 3 in Bryozoan faunas at the Tortonian-Messinian transition. A palaeoenvironmental case study from Crete Island, eastern Mediterranean
FIG. 3. — Schematic sedimentary log of Keramoutsi section with sample location and semi-quantitative abundances of bryozoan species.
Normal Retinotopy in Primary Visual Cortex in a Congenital Complete Unilateral Lesion of Lateral Geniculate Nucleus in Human: A Case Study
<p>The data set contains .nii files for each condition of retinotopic mapping in fMRI. (Meridians, Wedges and concentric rings). It also contains DTI data files with .bvec and .bval files. Psychophysics data is in two excel files for motion and orientation discrimination. </p>
LEXIS Turbomachinary use case: T106 profile test case
<p>The test case for T106 profile in a linear cascade. Cascade rigs are a way to test in a simple way various turbomachinery blades. Blades are cylindrical, which means equal 2D sections from hub to tip wall, and repeated tangentially according to the specified pitch. In this case, end walls are linear, not cylindrical and not tapered. The dataset contains an</p> <ul> <li>excel file with <ul> <li>description of the airfoil (x, y coordinates in [mm])</li> <li>geometric pitch /chord data, aspect ratio (parallel end walls)</li> <li>entry boundary conditions <ul> <li>total pressure</li> <li>total temperature</li> <li>flow angle</li> </ul> </li> <li>outlet boundary condition <ul> <li>static pressure</li> </ul> </li> <li>Reynold number (120 000)</li> <li>Velocity at the exit (Mach = 0,59</li> </ul> </li> <li>OpenFOAM input files for <ul> <li>serial run (Allrun)</li> <li>parallel run (Allrun_parallel)</li> </ul> </li> <li>PDF file with the description of the case and obtained results</li> </ul>
ams-icdd-usecases: Use cases for employing ICDD containers for infrastructure asset management
<p>This repository provides two use cases for infrastructure asset management using information containers according to the <a href="https://www.iso.org/standard/74389.html">Information Container for linked Document Delivery standard (ISO 25197)</a>. Use Case 1 demonstrates the data preparation and result collection of bridge visual inspection with requirement- and delivery container. Use Case 2 demonstrates the pavement maintenance plan based on the existing condition data. Therefore, an additional connection to a relational database in the information container is provided in Use Case 2, which is registered within the container using an extension <a href="https://icdd.vm.rub.de/ontology/icdd/ExtendedDocument/">EXDOC:Extension for document types for the ISO 21597 ICDD Part 1 Container ontology</a>.</p> <p><strong>Full Changelog</strong>: <a href="https://github.com/RUB-Informatik-im-Bauwesen/ams-icdd-usecases/commits/v0.1">https://github.com/RUB-Informatik-im-Bauwesen/ams-icdd-usecases/commits/v0.1</a></p>
GIS as a heuristic tool to interpret ancient historiography: A case study to reconstruct what could plausibly have happened according to the accounts in New Testament texts
<p>This presentation summarizes the research findings of the TiG article (doi 10.1111/tgis.12762) which examines how GIS can be used as a heuristic tool to reconstruct spatial–temporal events from narratives in order to examine whether a scenario is conceivable within the narrative world. The narrative about Paul's escape from Berea (Acts 17:14–15) is used as a case study. Several interpretive issues related to spatial and temporal questions surround these texts. In the case study, three methods are applied: (a) least-cost path analysis on elevation data to construct journeys and travel times for Roman roads; (b) network analysis to find seafaring routes valid for ancient times; and (c) the integration of spatial and temporal data in a space-time cube. Our main finding is that the method yields insights into the spatial–temporal dynamics of the narrative. This helps a modern reader to better understand the narrative conceivability of a story in the mind of a first-century reader.</p>
Dataset of Mordvin GOAL-cases
<p>This open access dataset contains examples of the goal-oriented cases illative and lative in Mordvin languages Erzya and Moksha. The dataset consists of two parts: senses of the goal-cases (files with prefix sense) and type of the landmark noun (files with prefix LM). There is currently one dataset that includes 200 analyzed examples of each case in each language (800 examples in total). All the data is analyzed according to sense and landmark type. The data is collected from MokshEr corpus maintained by University of Turku.</p> <p>Sense means the semantic content that is expressed by the goal-case in a clause. The following values are found in the data: direction, location, part, place, purpose, reason, result, staying, target, and temporal. In addition, contextual variants of the senses are shown in brackets.</p> <p>Landmark type means what kind of entity the referent of the landmark is. There are eight categories in the data: 1D object, 2D bounded landmark, 2D unbounded landmark, 3D bounded landmark, 3D unbounded landmark, abstract landmark, institution, and temporal landmark.</p> <p> </p> <p>The senses-data is annotated for following information:</p> <ol> <li>The noun or relational noun phrase inflected in goal-case.</li> <li>The predicate as inflected in the data.</li> <li>Translations of both (mainly in citation form, but in predicate sometimes with some grammatical information)</li> <li>The sense of the goal-case in the utterance.</li> <li>The prototypicality of the example as a member of its sense on a scale from 1 (non- prototypical) to 5 (prototypical) NB! This assessment is based on the authors language competence and on general semantic principles, and as such should be considered only as directive.</li> <li>The original sentence from the corpus.</li> <li>Free translation. Some of the translations are done following the lexical meanings and syntactic structures of Mordvin languages, so the English is unidiomatic from time to time.</li> <li>The file name with which the original sentence can be located in the corpus.</li> </ol> <p> </p> <p>The landmark-data is annotated for the same information, except that there is additional information of the landmark type, and the prototypicality score is a value from 1 (non-prototypical) to 4 (prototypical) showing how prototypical the referent of the landmark is in its landmark type. Score 0 means that the prototypicality scale is not applied to the landmark type in question. Unlike in sense-data, the prototypicality in the landmark-data is based on prelinguistic spatial primitives of containment and support, as well as the human ability to recognize boundaries.</p> <p>The author of this dataset is Riku Erkkilä and it is published under CC-BY-NC-ND licence. The data is originally collected in the framework of Descriptive Grammar of Mordvin project (University of Helsinki) funded by Kone Foundation. If used in a publication, please refer to this publication as well as mention the original source:</p> <ul> <li>MokshEr V.3 (2010). Corpus of Mordvin languages. University of Turku.</li> </ul> <p> </p> <p>This dataset has been used in following publications:</p>
SMW-NCZARR-Use-Case-2
<p>Input Data for Use case 2 of the Shallow Water Model to experiment with Zarr backend of the NetCDF library via its Fortran Interface.</p>
The case of 100% electrification of domestic heat in Great Britain
<p>Input data set for OPHELIA optimisation model investigating optimal heat decarbonization pathways through electrification for net zero economy in Great Britain. </p>
A case-study for improved reusability of plant phenotyping data with MIAPPE
<p>Accompanying datasets for manuscript, "A case-study for improved reusability of plant phenotyping data with MIAPPE".</p> <p>The ZIP archives in this repository contain the source files and the output files that this manuscript refers to.</p>
JACUSA2 - use cases: 1 - 3
<p><strong>Supplementary data</strong> for use cases presented in:</p> <p>RNA modification mapping with JACUSA2<br> Michael Piechotta, Qi Wang, Janine Altmüller, Christoph Dieterich<br> <a href="https://doi.org/10.1101/2021.07.02.450888">doi: https://doi.org/10.1101/2021.07.02.450888</a></p> <p> </p> <p><strong>Use case 1: m6A mapping by MazF</strong></p> <ul> <li>MazF_vs_cond2_FTO_rtarrest_plain_result.out.gz (JACUSA2 output)</li> <li>Cutoff01_MazF_vs_cond2_FTO_rtarrest_plain_result.out.gz (filtered by pvalue <=0.1)</li> <li>MazF (BAM files): <ul> <li>SRR8450805_STARmapping_uniq_rmdup.bam</li> <li>SRR8450807_STARmapping_uniq_rmdup.bam</li> <li>SRR8450809_STARmapping_uniq_rmdup.bam</li> </ul> </li> <li>FTO: (BAM files): <ul> <li>SRR8450806_STARmapping_uniq_rmdup.bam</li> <li>SRR8450808_STARmapping_uniq_rmdup.bam</li> <li>SRR8450810_STARmapping_uniq_rmdup.bam</li> </ul> </li> </ul> <p><strong>Use case 2: </strong><strong>DART-seq</strong></p> <ul> <li>APOBEC1YTH_APOBEC1YTHmut_call2_result.out.gz (JACUSA2 output)</li> <li>APOBEC1YTH (BAM files): <ul> <li>SRR9940470_STARmapping_uniq_rmdup.bam</li> <li>SRR9940471_STARmapping_uniq_rmdup.bam</li> <li>SRR9940472_STARmapping_uniq_rmdup.bam</li> </ul> </li> <li>APOBEC1YTHmut (BAM files): <ul> <li>SRR9940474_STARmapping_uniq_rmdup.bam</li> <li>SRR9940475_STARmapping_uniq_rmdup.bam</li> <li>SRR9940476_STARmapping_uniq_rmdup.bam</li> </ul> </li> </ul> <p><strong>Use case 3: Nanopore</strong></p> <ul> <li>WT_vs_KO_call2_result.out.gz & WT100_vs_WT0_call2_result.out.gz (JACUSA2 output)</li> <li>WT (BAM files): <ul> <li>HEK293T-WT-rep2.bam</li> <li>HEK293T-WT-rep3.bam</li> <li>HEK293T-WT-100-rep1.bam</li> <li>HEK293T-WT-100-rep2.bam</li> <li>HEK293T-WT-100-rep3.bam</li> </ul> </li> <li>KO (BAM files): <ul> <li>HEK293T-KO-rep2.bam</li> <li>HEK293T-KO-rep3.bam</li> <li>HEK293T-WT-0-rep1.bam</li> <li>HEK293T-WT-0-rep2.bam</li> </ul> </li> </ul> <p>[1] Zhang, Z., Chen, L.-Q., Zhao, Y.-L., Yang, C.-G., Roundtree, I.A., Zhang, Z., Ren, J., Xie, W., He, C., Luo, G.-Z.: Single-base mapping of m6a by an antibody-independent method. Science advances 5, 0250 (2019). doi:10.1126/sciadv.aax0250</p> <p>[2] Garcia-Campos, M.A., Edelheit, S., Toth, U., Safra, M., Shachar, R., Viukov, S., Winkler, R., Nir, R., Lasman, L., Brandis, A., Hanna, J.H., Rossmanith, W., Schwartz, S.: Deciphering the ”m6a code” via antibody-independent quantitative profiling. Cell 178, 731–74716 (2019). doi:10.1016/j.cell.2019.06.013</p> <p>[3] Meyer, K.D.: Dart-seq: an antibody-free method for global m6a detection. Nature methods 16, 1275–1280 (2019). doi:10.1038/s41592-019- 0570-0</p> <p>[4] Pratanwanich, P.N., Yao, F., Chen, Y., Koh, C.W.Q., Hendra, C., Poon, P., Goh, Y.T., Yap, P.M.L., Yuan, C.J., Chng, 6 made available under aCC-BY-NC-ND 4.0 International license. (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is bioRxiv preprint doi: https://doi.org/10.1101/2021.07.02.450888; this version posted July 4, 2021. The copyright holder for this preprint W.J., Ng, S., Thiery, A., Goh, W.S.S., G¨oke, J.: Detection of differential rna modifications from direct rna sequencing of human cell lines. bioRxiv (2020). doi:10.1101/2020.06.18.160010. https://www.biorxiv.org/content/early/2020/06/20/2020.06.18.160010.full.pdf</p>
DALES LES data for GABLS1 (only ninth hour), ASTEX, and slow and fast strato-cumulus cases
<p>These files contain DALES LES data for:</p> <p>GABLS1 (only ninth hour) in GABLS1_LES.dat (ascii file, explanation in header)</p> <p>ASTEX profiles in dales_profiles.nc (netcdf and information in header)</p> <p>slow and fast strato-cumulus cases in vddussen_profiles* (netcdf and information in header)</p>
Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity
<p><strong>PREMISE</strong>: The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species since they create and define ecological communities, contributing disproportionately to ecosystem function.</p> <p><strong>METHODS</strong>: We examined the distribution of genetic diversity and clones, which we defined first as unique multilocus genotypes (MLG), and then by grouping similar MLGs into multilocus lineages (MLL). We used 186 markers from inter-simple sequence repeats (ISSR) across 358 ramets from 13 patches of the foundation grass <em>Leymus chinensis</em>. We examined the relationship between genetic and clonal diversities, their variation with patch-size, and the effect of the number of markers used to evaluate genetic diversity and structure in this species.</p> <p><strong>RESULTS</strong>: Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single MLL. We confirmed this with a clustering algorithm to group related genotypes. The predominance of a single lineage within each patch could be the result of the accumulation of somatic mutations, limited dispersal, some sexual reproduction with partners mainly restricted to the same patch, or a combination of all three.</p> <p><strong>CONCLUSIONS</strong>: We found strong genetic structure among patches of <em>L. chinensis</em>. Consistent with previous work on the species, the clustering of similar genotypes within patches suggests that clonal reproduction combined with somatic mutation, limited dispersal, and some degree of sexual reproduction among neighbors causes individuals within a patch to be more closely related than among patches.</p>
Fig. 3 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 3. Phylogenetic position of Macrobiotus sp., Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
Fig. 1 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 1. Phylogenetic position of D. lindholmi and L. a. exigua, Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
EAMv1 simulation output from CondiDiag1.0 use case examples
<p>This archive contains data files from three EAMv1 simulations that demonstrate the usage of an online diagnostic tool called CondiDiag1.0. The three simulations are described in Section 6 in <a href="https://gmd.copernicus.org/preprints/gmd-2021-331/">Wan et al. (2022, GMDD)</a>. The model source code, run scripts, and post-processing scripts are available on Zenodo under the DOI <a href="https://doi.org/10.5281/zenodo.5530188">10.5281/zenodo.5530188</a>. EAMv1's master DOI is 10.11578/E3SM/dc.20180418.36, see <a href="https://www.osti.gov/doecode/biblio/10475">https://www.osti.gov/doecode/biblio/10475</a>.</p>
Fig. 5 in The Alternative Distribution Of Related Earthworms Aporrectodea Caliginosa And A. Trapezoides (Oligochaeta, Lumbricidae) In Ukraine As A Case Of Geographical Parthenogenesis
Fig. 5. Changes in the proportion of A. trapezoides in A. caliginosa s. l. sample sets depending on geographical longitude.
Fig. 3. A. caliginosa–A in The Alternative Distribution Of Related Earthworms Aporrectodea Caliginosa And A. Trapezoides (Oligochaeta, Lumbricidae) In Ukraine As A Case Of Geographical Parthenogenesis
Fig. 3. A. caliginosa–A. trapezoides specimens ratio in A. caliginosa s. l. sample sets. Black filling — A. caliginosa, cross-hatching — A. trapezoids.
Fig. 1 in A Case Study Of The Herb-Dwelling Spider Assemblages (Aranei) In A Meadow Under The Power Transmission Lines In Ukrainian Carpathians
Fig. 1. Number of individuals collected at the different distances from high voltage power line near Irliava village, August 2012 (SD — standard deviation).
ScienceDex guides
Understand access before you commit
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.