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Rediscovery Datasets: Connecting Duplicate Reports of LibreOffice and Gentoo
<p>We present two defect rediscovery datasets mined from Bugzilla (supplementary to previously published datasets: Zenodo, http://doi.org/10.5281/zenodo.400614). These datasets capture data for two groups of open source software projects: LibreOffice and Gentoo. The datasets contain information about the inter-relationships among duplicate defects.<br> </p> <p><strong>File Descriptions</strong></p> <ul> <li>libreoffice.csv - LibreOffice Defect Rediscovery dataset</li> <li>gentoo.csv - Gentoo Defect Rediscovery dataset</li> </ul> <p> </p> <ul> <li>libreoffice.relations.csv - Inter-relations of rediscovered defects of LibreOffice</li> <li>gentoo.relations.csv - Inter-relations of rediscovered defects of Gentoo</li> </ul>
GenBank accession numbers of the four marker genes and associated voucher specimens/tissues that were used in this study. For more details see Guo et al. (2014). Sequences of species in bold are unpublished and were provided by P. Guo as personal communication in Rediscovery of Andrea's keelback, Hebius andreae (Ziegler & Le, 2006): First country record for Laos and phylogenetic placement
GenBank accession numbers of the four marker genes and associated voucher specimens/tissues that were used in this study. For more details see Guo et al. (2014). Sequences of species in bold are unpublished and were provided by P. Guo as personal communication
Fig. 5 in Rediscovery of Andrea's keelback, Hebius andreae (Ziegler & Le, 2006): First country record for Laos and phylogenetic placement
Fig. 5. Location of the Hin Nam No National Protected Area in central Laos, where the new record (star) of Hebius andreae took place, which is located opposite to the type locality in Vietnam, viz. Phong Nha – Ke Bang National Park in Vietnam.
FIG. 1 in Rediscovery of Obeliscus agassizi Pilsbry, 1906 (Gastropoda, Subulinidae, Obeliscinae), annotated checklist of species of Obeliscus Beck, 1837 and first description of the anatomy for the genus
FIG. 1. — Obeliscus agassizi Pilsbry, 1906 shell and living specimen: A, SEM of apex in profile; B, same, middle region of teleoconch; C, same, last whorl, frontal view, asterisk showing epiphragm; D-F, living crawling specimen, shell length c. 6 mm; G, detail of suture of protoconch, SEM; H, detail of epiphragm insertion on body whorl. Scale bars: A-C, 1 mm; G, 0.15 mm; H, 0.1 mm.
Fig. 8 in Rediscovery of Glauconycteris superba Hayman, 1939 (Chiroptera: Vespertilionidae) after 40 years at Mbiye Island, Democratic Republic of the Congo
Fig. 8. Climate graphs for Pawa (upper left), Mbiye (upper right), Oda (lower left), and Matonguiné (lower right). Upper line of squares: mean monthly maximum temperature, lower line of squares: mean monthly minimum temperature, bars: mean monthly precipitation (plotted using DIVA-GIS, data from Hijmans et al. 2005).
Fig. 6 in Rediscovery of Glauconycteris superba Hayman, 1939 (Chiroptera: Vespertilionidae) after 40 years at Mbiye Island, Democratic Republic of the Congo
Fig. 6. Mandibles of the four known specimens of Glauconycteris superba Hayman, 1939 (upper row: dorsal view, lower row: lateral view). From left to right: holotype of G. s. sheila Hayman, 1947 (BMNH 47.10, ♀) [lateral picture flipped to fit the orientation of the other pictures], holotype of G. superba (RMCA 14765,?), new specimen from Mbiye Island (RMCA a1.097-M-3153, ♂), and the specimen from Matonguiné (RMCA 97.077-M-7719, ♂). Scale bar = 1 cm.
Fig. 7 in Rediscovery of Glauconycteris superba Hayman, 1939 (Chiroptera: Vespertilionidae) after 40 years at Mbiye Island, Democratic Republic of the Congo
Fig. 7. Distribution map of G. superba showing the four currently known records from Ivory Coast, Ghana, and DRC; red dot: Mbiye Island. Land cover data from GLC2000 (Mayaux et al. 2004).
Fig. 5 in Rediscovery of Glauconycteris superba Hayman, 1939 (Chiroptera: Vespertilionidae) after 40 years at Mbiye Island, Democratic Republic of the Congo
Fig. 5. Crania of the four known specimens of Glauconycteris superba Hayman, 1939 (left row: dorsal, middle row: ventral; right row: lateral). From top to bottom: specimen from Matonguiné (RMCA 97.077- M-7719, ♂), Mbiye Island (RMCA a1.097-M-3153, ♂), holotype of G. superba (RMCA 14765,?), and holotype of G. s. sheila Hayman, 1947 (BMNH 47.10, ♀). Scale bar = 1 cm
Fig. 3 in Rediscovery of Glauconycteris superba Hayman, 1939 (Chiroptera: Vespertilionidae) after 40 years at Mbiye Island, Democratic Republic of the Congo
Fig. 3. Pelage pattern of the four known specimens of Glauconycteris superba Hayman, 1939 (upper row: dorsal, lower row: ventral). From left to right: holotype of G. s. sheila Hayman, 1947 (BMNH 47.10), holotype of G. superba (RMCA 14765), new specimen from Mbiye Island (RMCA a1.097-M-3153), and the specimen from Matonguiné (RMCA 97.077-M-7719). Scale bar = 2 cm.
Fig. 1 in Rediscovery of Glauconycteris superba Hayman, 1939 (Chiroptera: Vespertilionidae) after 40 years at Mbiye Island, Democratic Republic of the Congo
Fig. 1. Satellite image of the study area Mbiye Island, DRC (map data © 2012 Google & GeoEye). The blue point shows the collection locality of G. superba Hayman, 1939.
Figure 6 in Rediscovery, natural history, and conservation status of Idiocranium russeli Parker, 1936 (Amphibia: Gymnophiona: Indotyphlidae)
Figure 6. Photograph showing appearance and colour variation of four Idiocranium russeli from Makamune, site 7 (locality 11, see Tables 1, 2) in life. Note the increasing demarcation of annular grooves posteriorly, colour variation among individuals, and presence of middorsal stripe. Total length of palest specimen shown here was 130 mm when freshly anaesthetized.
Rediscovery Datasets: Connecting Duplicate Reports of Apache, Eclipse, and KDE
<p>We present three defect rediscovery datasets mined from Bugzilla. The datasets capture data for three groups of open source software projects: Apache, Eclipse, and KDE. The datasets contain information about approximately 914 thousands of defect reports over a period of 18 years (1999-2017) to capture the inter-relationships among duplicate defects. </p> <p><strong>File Descriptions</strong></p> <ul> <li>apache.csv - Apache Defect Rediscovery dataset</li> <li>eclipse.csv - Eclipse Defect Rediscovery dataset</li> <li>kde.csv - KDE Defect Rediscovery dataset</li> </ul> <p> </p> <ul> <li>apache.relations.csv - Inter-relations of rediscovered defects of Apache</li> <li>eclipse.relations.csv - Inter-relations of rediscovered defects of Eclipse</li> <li>kde.relations.csv - Inter-relations of rediscovered defects of KDE</li> </ul> <p> </p> <ul> <li>create_and_populate_neo4j_objects.cypher - Populates Neo4j graphDB by importing all the data from the CSV files. Note that you have to set dbms.import.csv.legacy_quote_escaping configuration setting to false to load the CSV files as per https://neo4j.com/docs/operations-manual/current/reference/configuration-settings/#config_dbms.import.csv.legacy_quote_escaping</li> <li>create_and_populate_mysql_objects.sql - Populates MySQL RDBMS by importing all the data from the CSV files</li> <li>rediscovery_db_mysql.zip - For your convenience, we also provide full backup of the MySQL database</li> </ul> <p> </p> <ul> <li>neo4j_examples.txt - Sample Neo4j queries</li> <li>mysql_examples.txt - Sample MySQL queries</li> <li>rediscovery_eclipse_6325.png - Output of Neo4j example #1</li> </ul> <p> </p> <ul> <li>distinct_attrs.csv - Distinct values of bug_status, resolution, priority, severity for each project</li> </ul>
FIGURE 4 in Rediscovery of the bizarre Cretaceous ant Haidomyrmex Dlussky (Hymenoptera: Formicidae), with two new species
FIGURE 4. Reconstructed habitus of Haidomyrmex zigrasi, n. sp. (top), and H. scimitarus, n. sp. (middle), showing main portions of body, and habitus drawing (bottom) of H. scimitarus with appendages included.
Figures 4–5 in Rediscovery of Myrmozercon brachiatus Berlese (Acari: Mesostigmata) in south-west Iran
Figures 4–5. Photographs of Myrmozercon brachiatus (female) – 4. Dorsal idiosoma; 5. Ventral idiosoma.
Data for: The rediscovery of the putative ant social parasite Manica parasitica syn. nov. (Hymenoptera: Formicidae) reveals an unexpected endoparasite syndrome
<p>Parasitism is ubiquitous across the tree of life, comprising approximately half of all animal species. Social insect colonies attract many pathogens, endo- and ectoparasites, and are exploited by social parasites, which usurp the social environment of their hosts for survival and reproduction. Exploitation by parasites and pathogens versus social parasites may cause similar behavioral and morphological modifications. Ants possess two overlapping syndromes: the social parasite and endoparasite syndromes. Upon rediscovering two populations of the putative social parasite <em>Manica parasitica</em> in the Sierra Nevadas, we test the hypothesis that <em>M. parasitica</em> is an independently evolving social parasite species relative to its host <em>M. bradleyi</em>. We evaluate traits used to discriminate <em>M. parasitica</em> from <em>M. bradleyi</em>, and examine the morphology and behavior of <em>M. parasitica</em> in the context of ant parasitic syndromes. We find that <em>M. parasitica</em> is not a social parasite species. Instead, <em>M. parasitica </em>individuals represents cestode-infected <em>M. bradleyi </em>workers. We propose that <em>Manica parasitica</em> should be regarded as a junior synonym of <em>Manica bradleyi</em>. Our results emphasize that an integrative approach is essential for unraveling the complex life histories of social insects and their symbionts.</p>
What factors influence the rediscovery of lost tetrapod species? Appendix G: Variables tested for their influence on rediscovery
<p>For the study associated with this dataset, we created a database of lost and rediscovered tetrapod species and identified patterns in their distribution and factors influencing rediscovery. This appendix provides a list of the lost and rediscovered species and all data used to calculate 11 variables (V):</p> <ul> <li>V1: Taxonomic status - class, order, family, species name, common name;</li> <li>V2: Countries / islands occupied by each species;</li> <li>V3: The cumulative number of lost and rediscovered species - four columns, (i) last seen date, (ii) rediscovered date, (iii) for rediscovered species, the number of years lost, (iv) for lost species, the number of years lost;</li> <li>V4: Time lost (the number of years each species has been lost for);</li> <li>V5: Adult body mass (g) of each species;</li> <li>V6: Habitat breadth - the number of broad habitat types occupied by each species;</li> <li>V7: Habitat type - the broad habitat types occupied by each species;</li> <li>V8: Small island / mainland - whether a species occupies a small island (< 20,000 km<sup>2</sup>) or a mainland location (including islands > 20,000km<sup>2</sup>) (0 = mainland, 1 = small island);</li> <li>V9: Threats - the different threats associated with each species;</li> <li>V10: Human development - the highest level of human development across the range of each species, measured using the Human Development Index (HDI);</li> <li>V11: Survey effort - the level of effort invested in searching for each species (1 = low, 2 = medium, 3 = high, 4 = very high). See Supporting Information (Table S1) for the methods used to calculate this variable.</li> </ul>
What factors influence the rediscovery of lost tetrapod species? Appendix E: Lost and rediscovered species
<p>For the study associated with this dataset, we created a database of lost and rediscovered tetrapod species and identified patterns in their distribution and factors influencing rediscovery. This appendix provides a list of the lost and rediscovered tetrapod species used in the analysis. It includes data on:</p> <ul> <li>taxonomy (class, order, family, species, common name, and whether the species is a subspecies);</li> <li>location (continent, country, region);</li> <li>each species threat status (as published on the IUCN Red List of Threatened Species: <a href="https://www.iucnredlist.org/">https://www.iucnredlist.org/</a>).</li> </ul> <p>The appendix also indicates:</p> <ul> <li>whether each species was included in another list of lost tetrapod species published by the organisation Re:wild (<a href="https://www.rewild.org/">https://www.rewild.org/</a>);</li> <li>whether each species was used to construct the phylogenetic trees used for analysis.</li> </ul>
What factors influence the rediscovery of lost tetrapod species? Appendix F: Excluded species
<p>For the study associated with this dataset, we created a database of lost and rediscovered tetrapod species and identified patterns in their distribution and factors influencing rediscovery. Our lost species list included many of the species on another published list of lost species compiled by Re:wild (<a href="https://www.rewild.org/)">https://www.rewild.org/)</a> in collaboration with the International Union for Conservation of Nature (IUCN) (<a href="https://www.iucn.org/">https://www.iucn.org/</a>). However, we did not include some of the species included on the Re:wild/IUCN list. This appendix provides a list of those species. It includes the following information for each species:</p> <ul> <li> <p>taxonomy - class, order, scientific name, common name;</p> </li> <li> <p>threat status (as published on the IUCN Red List of Threatened Species);</p> </li> <li> <p>location - continent / island, range / country.</p> </li> </ul>
Fig. 3 in Rediscovery of a Deep-sea Fish Parasite Lophoura cornuta (Copepoda: Sphyriidae) in the Western North Pacific off Hokkaido, Northern Japan
Fig. 3. Lophoura cornuta, adult female, NSMT-Cr 31508. A, Habitus, ventrolateral view, ethanol-preserved specimen; B, cephalothorax and part of neck including holdfast organ, ventral view; C, D, anterior part of cephalothorax, ventrolateral and dorsolateral views, respectively. The specimen was fixed in 70% ethanol on 24 March 1983 and photographed on 9 October 2023. Abbreviations: c, cephalothorax; cp, conical protuberance; ho, holdfast organ; n, neck. Scale bars: A, 10 mm; B, 3 mm; C, D, 0.5 mm.
Fig. 2 in Rediscovery of a Deep-sea Fish Parasite Lophoura cornuta (Copepoda: Sphyriidae) in the Western North Pacific off Hokkaido, Northern Japan
Fig. 2. Lophoura cornuta, adult female, NSMT-Cr 31509. A, Habitus, ventral view; B, C, cephalothorax and part of neck including holdfast organ, ventral and dorsal views, respectively; D, cephalothorax, anterior view. The trunks on the holdfast organ are individually numbered as 1, 2, 3, or 4 (B, C). Abbreviations: cp: conical protuberance; mo: mouth opening. Scale bars: A, 10 mm; B, C, 5 mm; D, 1 mm.
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.