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Fig. 1 in Repatriation of knowledge about insects and types through the DORSA virtual museum (Digital Orthoptera Specimen Access)
Fig. 1: Distribution of Orthoptera type specimens (including Para- and Lectotypes) housed in German Museum collections. Note the high number of types from Africa, South East Asia and Australia, collected in the last centuries. [From Riede 2003].
Impact of Phytophthora cinnamomi on the taxonomic and functional diversity of forest plants in a mediterranean-type biodiversity hotspot
<p class="MsoNormal"><strong>Aim</strong></p> <p class="MsoNormal">Diversity-rich mediterranean-type sclerophyllous forests are home to 20% of described species on Earth. In the <em>Eucalyptus marginata</em> (jarrah) forest of southwest of Western Australia diversity is being reduced by extensive human use and the introduction of the plant pathogen <em>Phytophthora cinnamomi</em>. This study investigated the influence of <em>P. cinnamomi </em>infestation on the structure, taxonomic and functional diversity, and species composition of the forest.</p> <p class="MsoNormal"><strong>Location</strong>: Jarrah forest of southwestern Australia</p> <p class="MsoNormal"><strong>Methods</strong></p> <p class="MsoNormal">Species<strong> </strong>abundance, understorey cover and canopy cover were assessed along 22, 30-m long transects which crossed infested and non-infested zones in five reserves in the jarrah forest. A trait database was assembled for 137 plants using 13 traits related to nutrient- and carbon acquisition, disturbance tolerance and reproduction. The responses of canopy cover, understorey cover, species richness, Shannon diversity, evenness, abundance, and functional diversity for trait groups, and all groups combined were modelled against reserve and zone as fixed effects and transect and transect section as random effects. To assess the species composition, NMDS ordination based on Bray Curtis resemblance and indicator species analyses were used.</p> <p class="MsoNormal"><strong>Results</strong></p> <p class="MsoNormal">Significantly higher understorey cover, species richness, Shannon diversity and evenness were recorded in non-infested compared to infested zones, but there were no changes in the canopy cover and overall abundance. In non-infested zones, the functional diversity of nutrient acquisition and reproductive traits was higher, but the functional diversity of carbon acquisition traits was lower. No difference in functional diversity was recorded in disturbance tolerance and overall traits between the two zones. NMDS ordination and ANOSIM revealed a significant difference in the species composition between the two zones, and 11 indicator species significantly associated with infested and non-infested zones were identified.<strong> </strong></p> <p class="MsoNormal"><strong>Conclusion</strong></p> <p class="MsoNormal"><em>Phytophthora cinnamomi</em> has significantly affected the forest structure, taxonomic and functional diversity, and species composition. Contrasting responses of functional trait groups obscured overall trait responses to <em>P. cinnamomi.</em></p>
Fig. 6. A in On the date of original description and the type locality of Zygaena ampellophaga (Lepidoptera: Zygaenidae: Procridinae)
Fig. 6. A page of the original description (Bayle-Barelle, 1809a) with the type locality of Zygaena ampellophaga Bayle-Barelle, 1809.
Fig. 4. A in On the date of original description and the type locality of Zygaena ampellophaga (Lepidoptera: Zygaenidae: Procridinae)
Fig. 4. A cover of the journal with the original description (Bayle-Barelle, 1809a) of Zygaena ampellophaga Bayle-Barelle, 1809.
Fig. 1 in On the date of original description and the type locality of Zygaena ampellophaga (Lepidoptera: Zygaenidae: Procridinae)
Fig. 1. Theresimima ampellophaga (Bayle-Barelle, 1809). a, male from Crimea, Miskhor, reared from ovo, 1998, K.A. Efetov leg. (photo by K.A. Efetov);b, female from Crimea, Alushta, Luchistoe (44°43′31.44″N, 034°25′31.62″E, 358 m a.s.l.), reared from larva, 23.V.2022, O.G. Gorbunov leg. (photo by O.G. Gorbunov).
Fig. 5 in On the date of original description and the type locality of Zygaena ampellophaga (Lepidoptera: Zygaenidae: Procridinae)
Fig. 5. The first page of the original description (Bayle-Barelle, 1809a) of Zygaena ampellophaga Bayle-Barelle, 1809.
Different adaptation error types in affective computing have different effects on user experience: a Wizard-of-Oz study
<p>The record consists of one Excel file that contains individual participant data for the study "Different adaptation error types in affective computing have different effects on user experience: a Wizard-of-Oz study". The study included 97 participants who were randomly divided into five groups corresponding to five adaptation behaviors (SingleSmall, SingleModerate, ImmediateLow, ImmediateHigh, IrreversibleHigh). Each participant took part in three 11-minute intervals. Difficulty changed every 60 seconds in each 11-minute interval, and there are thus 11 difficulty values per interval. At the end of each interval, participants self-reported their experience using the NASA Task Load Index (6 items) and Intrinsic Motivation Inventory (8 items). After the third interval, participants were asked to rate how much they liked the 3 intervals on a visual analog scale that was converted to 1-100 numerical scores.</p>
RINEX files from low-cost GNSS receivers equipped with few types of low-cost and high-end antennas, Wrocław, Poland; July, 2022
<p>Daily RINEX files with multi-GNSS (GPS, GLONASS, Galileo) observations at 30 sec. interval obtained with low-cost GNSS receiver u-blox ZED-F9P and few types of low-cost and high-end antennas. Time period: 05.07.2022 - 18.07.2022.</p>
Fig. 4. A in A new species of Anaglyphula Rensch, 1932 from an island off the coast of West Indonesia, with redescription of the type species (Gastropoda: Caenogastropoda: Assimineidae)
Fig. 4. A, Putative constriction position of Anaglyphula yanseni, new species, holotype MZB.Gst. 23.829; B, Constriction of Anaglyphula cancellata Rensch, 1932, syntype NHMUK 1897.8.3.150; C, Constriction of Anaglyphula whitteni Vermeulen, 1996, paratype NHMUK 20000247. Not to scale.
Fig. 1. Anaglyphula cancellata Rensch, 1932, syntype NHMUK 1897.8.3.150. A in A new species of Anaglyphula Rensch, 1932 from an island off the coast of West Indonesia, with redescription of the type species (Gastropoda: Caenogastropoda: Assimineidae)
Fig. 1. Anaglyphula cancellata Rensch, 1932, syntype NHMUK 1897.8.3.150. A, Shell; B, Upper whorls; C, Structure on body whorl; D, Detailed structure on penultimate whorl.
Fig. 3 in A new species of Anaglyphula Rensch, 1932 from an island off the coast of West Indonesia, with redescription of the type species (Gastropoda: Caenogastropoda: Assimineidae)
Fig. 3. Anaglyphula yanseni, new species, holotype MZB.Gst. 23.829. A–B, Shell; A, Visible light camera images; B, SEM images; C, Protoconch; D, Detailed structure on upper body whorl; E, Detailed structure on lower body whorl.
Fig. 2. A in A new species of Anaglyphula Rensch, 1932 from an island off the coast of West Indonesia, with redescription of the type species (Gastropoda: Caenogastropoda: Assimineidae)
Fig. 2. A, Anaglyphula cancellata Rensch, 1932, syntype NHMUK 1897.8.3.149; B–C, Anaglyphula whitteni Vermeulen, 1996, Paratype. NHMUK 20000247; B, Shell; C, Ribbing structure details.
Fig. 5. Acmella species. A in A new species of Anaglyphula Rensch, 1932 from an island off the coast of West Indonesia, with redescription of the type species (Gastropoda: Caenogastropoda: Assimineidae)
Fig. 5. Acmella species. A, Acmella cf. tersa, NHMUK; B, Acmella moreletiana G. Nevill, 1878, NHMUK 1891.3.17.944–7; C, Acmella mellilla Godwin-Austen, 1895, NHMUK 1903.7.1.1698.
Native MS dataset for: "Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants"
<p>Native mass spectrometry dataset used in: <strong>Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants.</strong> Pavla Vankova, Juan Luis Pacheco-Garcia, Dmitry S. Loginov, Atanasio Gómez-Mulas, Alan Kádek, José Manuel Martín-Garcia, Eduardo Salido, Petr Man and Angel L. Pey. FEBS Letters (2024)</p> <p><strong>Description:</strong></p> <p>Native mass spectrometry (MS) analysis verifying the oligomeric state of alanine:glyoxylate aminotransferase (AGT) protein and its P11L and I340M (LM) polymorphism and LM G170R mutation variants in primary hyperoxaluria type I.</p> <p><strong>Sample processing:</strong></p> <p>AGT protein as well as its LM and LM G130R mutants were buffer exchanged into 150 mM aqueous ammonium acetate solution (pH 7.5, MS-grade, Sigma-Aldrich) through six cycles of tenfold dilution and re-concentration using centrifugal concentrators Vivaspin 500 (30 kDa cut-off, <em>Sartorius</em>). Desalted proteins were introduced into a Synapt G2Si mass spectrometer (Waters) via static nanoelectrospray ionization from in-house prepared gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (<em>World Precision Instruments</em>). Protein concentration in samples was determined by 280 nm absorbance measurements using DeNovix DS-11 spectrophotometer. Samples were diluted in ammonium acetate and electrosprayed at 1 and 2 µM concentration. The mass spectrometer was carefully tuned for best signal quality and intensity, while keeping ion activation and unfolding minimal. Namely, electrospray voltage was kept at 1.3 kV, source desolvation temperature 80°C, sampling cone 80 V and 10 V collision voltage with 6 ml/min flow of argon in the trap region for thermalization of ions. Quadrupole was operated in a broadband transmission mode up to 8000 m/z while the spectra were acquired in mass range 500 – 20000 m/z. Spectra were externally mass recalibrated using known masses of caesium iodide clusters.</p> <p><strong>Data processing:</strong></p> <p>Raw mass spectra were averaged over 75 scans and further processed in Waters MassLynx 4.1. The averaged spectra were exported for ZENODO deposition as plain in plain m/z vs intensity .txt files as well uploaded as part of the .raw file format of the whole analysis (including initial metadata) with scan descriptions and parameter changes described in a stand-alone .txt descriptor file.</p>
Data collection for Tsuji et al., 2023, Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center
<p>Supplementary data files associated with Tsuji et al., 2023, "Anoxygenic phototrophic <i>Chloroflexota</i> member uses a Type I reaction center". These files are used by code in a corresponding GitHub repository (<a href="https://github.com/jmtsuji/Ca-Chlorohelix-allophototropha-RCI">https://github.com/jmtsuji/Ca-Chlorohelix-allophototropha-RCI</a>) that shows how various analyses that are presented in the paper were conducted.</p><p>Files included:</p><ul><li>HPLC-based spectroscopy data ("...-HPLC-run1.tsv.gz" or "...-HPLC-run2.tsv.gz") -- hyper-spectral data files, generated by a diode array detector, that are associated with pigment analyses in the paper. See the corresponding Github repo for how these files are analyzed.</li><li>Supplementary data about "<i>Ca. </i>Chloroheliales"-associated RCI:<ul><li>I_TASSER_homology_models_full_output.tar.gz -- Gzipped tarball containing the full output from I-TASSER for homology models of key phototrophy-related genes encoded by '<i>Candidatus </i>Chlorohelix allophototropha' and '<i>Candidatus </i>Chloroheliales bin L227-5C'. After unpacking the tarball, view a summary of the I-TASSER output for each gene by clicking on the 'index.html' file in that gene's folder.</li></ul></li><li>Boreal Shield lake survey data:<ul><li>lake_survey_MAGs.tar.gz -- Gzipped tarball containing the full collection of 756 metagenome-assembled genomes (MAGs) recovered from the Boreal Shield lake survey, corresponding to those mentioned in Supplementary Data 3. The FastA nucleotide genome sequences, FastA nucleotide predicted protein-coding gene sequences, FastA amino acid predicted protein sequences, and Genome Flat Files (GFFs) for all genomes are provided in the fna, ffn, faa, and gff subdirectories, respectively.</li><li>lake_survey_MAGs_eggnog_annotations.tar.gz -- Gzipped tarball containing annotations (produced via EggNOG) for all predicted proteins among the 756 MAGs recovered from lake metagenome data. Because proteins were pre-clustered prior to annotation, a "orf2gene" file inside the tarball maps the gene clusters to the ORF IDs used for each genome.</li><li>lake_survey_MAGs_featureCounts.tsv.gz -- GZipped tab-separated table containing the mapping statistics of metatranscriptome reads on all protein-coding genes from the 756 MAGs recovered from lake metagenome data.</li><li>lake_survey_Ca_Chloroheliales_MAGs_info.tar.gz -- A subset of information from the previous three files specific to genome bins ELA319 and ELA729, which represent RCI-encoding "<i>Ca</i>. Chloroheliales" members.</li></ul></li><li>Intermediate files involved in some of the genome assembly work in this paper:<ul><li>Capt_S15_sequencer_data_raw.tar.gz -- Gzipped tarball containing the raw Illumina MiSeq output data for the '<i>Candidatus </i>Chlorohelix allophototropha' subculture 15 sequencing run. The run represents a read cloud sequencing run relying on TELL-Seq technology. Indices can be parsed directly from raw output data using the Tell-Read pipeline.</li><li>scaffold.full.fasta.gz -- the assembled scaffolds generated using Tell-Read and Tell-Link on the above raw MiSeq output data.</li><li>Ca_Chloroheliaceae_bin_L227_5C_prokka_ORFs.faa.gz -- predicted open reading frames (ORFs) from the curated genome of '<i>Candidatus </i>Chloroheliales bin L227-5C'. These ORFs were predicted using prokka and were used for some of the analyses presented in the paper. Most analyses used the annotations available on NCBI (generated by PGAP) for this strain.</li></ul></li></ul>
FIGURE 4 in Specific damage recognised on land snail shells as a tool for studying predation intensity: differences related to habitat and predator types
FIGURE 4 Variation in the minimal rate of predation recorded in six samples collected in each of five habitat types. Different letters refer to significant differences (p <0.05) among habitat types, based on a generalised linear model. The central line of each box refers to the median value, box height to the interquartile range, whiskers to the non-outlier range (i.e., 1.5 times the interquartile range at each side), and small circles to outliers.
FIGURE 5 in Specific damage recognised on land snail shells as a tool for studying predation intensity: differences related to habitat and predator types
FIGURE 5 Relative representation of individual predation types recognised in six samples collected at each of five habitat types. The height of the column represents the average value, while the lines indicate the standard deviation.
FIGURE 2 in Specific damage recognised on land snail shells as a tool for studying predation intensity: differences related to habitat and predator types
FIGURE 2 Examples of the recorded evidence of predation caused by various predators. a) shell of Cochlicopa lubrica predated on by a snail; b) characteristic damage caused by a carabid beetle, here on a shell of Discus rotundatus; c) puparium of the parasitoid dipteran fly Pherbellia limbata within a Granaria frumentum shell (the shell was crushed manually); d) external damage to a Xerolenta obvia shell caused by bird predation; e) Drilus beetle larval exuviae within an Alinda biplicata shell (the shell was crushed manually).
Processed data to accompany "Clonally heritable gene expression imparts a layer of diversity within cell types"
<p>This is the processed data underlying the paper "Clonally heritable gene expression imparts a layer of diversity within cell types" by Mold, Weissman, et al. Data has been gone through preprocessing steps, using the Python Notebooks found at <a href="https://github.com/MartyWeissman/ClonalOmics/tree/main/Data">https://github.com/MartyWeissman/ClonalOmics/tree/main/Data</a>. </p> <p>Smaller files are provided in .csv (comma-separated-value) format and larger files such as expression matrices are provided in .loom format (<a href="https://anndata.readthedocs.io/en/latest/">using the AnnData package</a>).</p> <p> </p> <p> </p>
Données brut spectres émission et excitation de différents types de plante
<p>Données brut des différents spectres d'émissions et d'excitations réalisé pour l'étude de la chlorophylle au sein de différents types de plante. </p>
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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.