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Fig. 2 in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia
Fig. 2. Molecular phylogeny of Amalda hilgendorfi (von Martens, 1897) produced by a Bayesian analysis of the Cox1 gene dataset. Outgroups and other species of Amalda have been removed from the tree. Only posterior probabilities ± 90% are shown. The unit for the scale is "substitutions/site". The geographical distribution and morphological morphs are coded for each specimen: Phil = Philippines; Sol = Solomon Islands; PNG = Papua New Guinea; sNC = South New Caledonia; nNC = North New Caledonia; CS = Coral Sea. Numbers in parentheses at the tips of the tree link the MNHN IM voucher number to the corresponding photo on the right.
Data for "Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification" (ImRex)
<p>Repository containing the different experiments described in the manuscript titled: "Current challenges for epitope-agnostic TCR interaction prediction and a new perspective derived from image classification".</p> <p>Publication DOI: TBA</p> <p>Originally appeared as a preprint on bioRxiv: <a href="https://doi.org/10.1101/2019.12.18.880146">https://doi.org/10.1101/2019.12.18.880146</a>.</p> <p>Contains:</p> <ul> <li>Trained model files (.h5)</li> <li>Associated train and validation datasets for each model.</li> <li>Learning curves and evaluation metrics.</li> <li>Log files with training and data arguments (full training scripts are available in GitHub repository).</li> <li>Comparisons between different models.</li> <li>Complete raw and processed datasets (also available in the associated GitHub repository).</li> </ul> <p><strong>Please refer to the associated GitHub repository (<a href="https://github.com/pmoris/ImRex">https://github.com/pmoris/ImRex</a>) for more information on the directory structure and contents, as well as the scripts that generated these output files.</strong></p> <p><strong>Contents:</strong></p> <ul> <li> <p><code>data.zip</code>: Contains raw and preprocessed datasets. READMEs in subdirectory describe the data sources and preprocessing steps. Please refer to the associated GitHub repository for the specific scripts that generated these files. Note that the full training and test sets (i.e. containing both positive and negative examples) are stored separately for each model/CV iteration in the <code>models</code> archives.</p> </li> <li> <p><code>models-main.zip</code>: contains the trained models and evaluation metrics for the main different experiments described in the bash and pbs scripts in <code>./src/scripts/hpc_scripts</code>. Log files for the experiments outlined here can be found in <code>./src/scripts/hpc_scripts</code>.</p> </li> <li> <p><code>models-full.zip</code>: contains models that were trained on the complete VDJdb dataset without cross-validation, filtered on human TRB data, no 10x data and restricted to 10-20 (CDR3) or 8-11 (epitope) amino acid residues, with negatives that were generated by shuffling (i.e. sampling an negative epitope for each positive CDR3 sequence). One set of models uses downsampling to reduce the most abundant epitopes down to 400 pairs each, the other one does not use any downsampling. These models were also used for evaluating on the external Adaptive dataset, as outlined in <code>./src/scripts/evaluate/evaluate_adaptive.sh</code>, and the TRA subset of sequences (<code>./src/scripts/evaluate/evaluate_tra.sh</code>).</p> </li> <li> <p><code>models-decoyfit.zip</code>: contains models that were trained on true data, but evaluated on data where epitopes were replaced by decoys.</p> </li> <li> <p><code>models-padded-epitoperatio.zip</code>: contains a quick test of trained models (padded/interaction map) that use a different type of negative shuffling, see docstrings in <code>./src/processing/negative_sampler.py</code> for more info.</p> </li> <li> <p><code>models-repeat-local.zip</code>: contains a number of repeated runs from <code>models-main</code>, used to estimate variability in model performance for multiple identical runs.</p> </li> <li> <p><code>comparisons.zip</code>: contains comparison directories, each consisting of two or more model output directories, that contrast the performance metrics of the models. These outputs were generated by using the <code>./src/scripts/evaluate/visualize.py</code> script, or by using the oneliners in <code>./src/scripts/evaluate/visualise.sh</code>, which can operate on the entire comparisons directory at once.</p> </li> </ul> <p><strong>Note that any file paths described here are in reference to the associated GitHub repository (<a href="https://github.com/pmoris/ImRex">https://github.com/pmoris/ImRex</a>).</strong></p> <p><strong>Overview of different experiments:</strong></p> <ul> <li>Two main architectures were compared: the interaction map (or <code>padded</code>) CNN and a dual input CNN based on NetTCR (<code>nettcr</code>).</li> <li>Two different cross-validation strategies were used: a 5x repeated 5-fold CV (<code>repeated5fold</code>) and an epitope-grouped CV (<code>epitope_grouped</code>).</li> <li>The different dataset subsets are labelled as follows. Check the Makefile's <code>preprocess-vdjdb-aug-2019</code> command (and the underlying script <code>./src/scripts/preprocessing/preprocess_vdjdb.py</code>) for a more thorough overview of the different filtering options. <ul> <li><code>mhci</code>: only MHCI class presented epitopes.</li> <li><code>trb</code>: only TRB CDR3 sequences.</li> <li><code>tra</code>: only TRA CDR3 sequences.</li> <li><code>tratrb</code>: both types of CDR3 sequences.</li> <li><code>down</code>: moderate downsampling of most abundant epitopes to 1000 pairs.</li> <li><code>down400</code>: strong downsampling of most abundant epitopes to 400 pairs.</li> <li><code>decoy</code>: decoy epitope data.</li> <li><code>reg001</code>: regularization factor 0.01 (only for padded/interaction type models, fixed value)</li> </ul> </li> <li>Two different methods of generating negative TCR-epitope pairs were used: shuffling of positive pairs, i.e. sampling a single epitope from the positive pairs for each CDR3 sequence (<code>shuffle</code>), and sampling CDR3s from a reference repertoire (<code>negref</code>).</li> <li>The batch size is labelled as <code>b32</code> = a batch size of 32.</li> <li>The learning rate was always 0.0001 (<code>lre4</code>) or 0.001 (<code>lre3</code>).</li> </ul> <p> </p>
Data from: Leme et al. (2020) New status for the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence. Phytotaxa (doi: 10.11646/phytotaxa.499.1.1)
<p>DNA sequence alignments as well as the input and output files which specify the different data partitioning schemes used for phylogenetic analyses in Leme et al. (2020) New status for the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence. Phytotaxa (doi: 10.11646/phytotaxa.499.1.1).</p>
Karyotypes of the water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
<p>The dataset includes original photos of mitotic and meiotic nuclei and all working karyograms used for the paper, including those not published on the plates in the paper.</p>
Supporting model data for paper: Measuring the impact of a new snow model using surface energy budget process relationships
<p>Supporting model data for paper: Measuring the impact of a new snow model using surface energy budget process relationships which has been submitted to the Journal of Advances in Modelling Earth Systems: https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020MS002144</p> <p>The experiment id h3hh corresponds to simulations with the ECMWF IFS with a single layer snow model. h3eg corresponds to the experimental 5-layer snow model.</p> <p>The timeseries are made by concatenating hourly data from day2 of forecasts initialised at 00UTC each day between Dec 1st 2013 and 1 June 2014.</p>
FIGURE 1 0 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data
FIGURE 1 0 Typical habitat of C. dule, Arquia river
FIGURE 6 C. dule n in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data
FIGURE 6 C. dule n. sp. IMCN 8941, Holotype 37.4 mm LS. Scale bar = 1 cm
FIGURE 9 C. dule n in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data
FIGURE 9 C. dule n. sp. IMCN 8929, Paratype. Live specimen. Scale bar = 1 cm
FIGURE 5 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data
FIGURE 5 Typical habitat of C. dule, Ingará River, San José Del Palmar, Chocó, Colombia
Pinyon jay (Gymnorhinus cyanocephalus) nest site selection in central New Mexico: Habitat Data to be used with AICc
<p>Pinyon Jays (<i>Gymnorhinus cyanocephalus</i>) are experiencing range wide population declines primarily in response to habitat degradation. Studies examining Pinyon Jay nest site selection in pinyon-juniper woodlands would be helpful in determining potential habitat management prescriptions. Therefore, we conducted a nest site selection study in Pinyon Jay breeding habitat in central New Mexico. We compared size and foliage characteristics of pinyon and juniper trees in 42 17.5-m radius plots around Pinyon Jay nests to 41 same-sized vegetation plots in random locations using binomial generalized linear models. The strongest model indicated that Pinyon Jays preferred nesting in areas with fewer dead juniper trees within pinyon-juniper habitats. Furthermore, Pinyon Jays built nests in pinyon and juniper trees with greater height (<i>p</i> < 0.001) and nests were built below the average tree height in the plot (<i>p </i>= 0.001). Results suggest selective cutting of dead juniper and retention of tall, live pinyon or juniper trees may be used in pinyon-juniper woodlands to improve Pinyon Jay nesting habitat in the western United States.</p>
Data from: Two New Species of Aira (Poaceae) from the Iberian Peninsula and the Balearic Islands
<p>Two new diploid species, <b><i>Aira</i> <i>minoricensis</i></b> and <b><i>Aira</i> <i>hercynica</i></b> are described and illustrated, along with chromosome counts, risk assessment, distribution and habitat, phenology, and comparisons with morphologically similar species. A comparative table and a key for the species of <i>Aira</i> for the Iberian Peninsula and the Balearic Islands are provided to assist in the identification of these overlooked species, and their relationships to other taxa are discussed.</p>
Fig. 9 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data
Fig. 9. Anaplecta bicolor Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Pronotum, dorsal view. D. Head, ventral view. E. Tegmina. F. Tegmina vein. G. Front femur, ventral view. H. Wings. I. Supra-anal plate, dorsal view. J. Subgenital plate, ventral view. K. Hook, ventral view. L. Left phallomere, ventral view. M. Right phallomere, ventral view. Scale bars: A–B, G–H = 1 mm; C–F, I–J = 0.5 mm; K–M = 0.25 mm.
Fig. 8 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data
Fig. 8. Anaplecta nigra Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Maxillary palp. F. Front femur, ventral view. G. Tegmina. H. Wings. I. Supra-anal plate, dorsal view. J. Subgenital plate, ventral view. K. Hook, ventral view. L. Left and right phallomeres, ventral view. M. L2d. Scale bars: A–D = 1 mm; E–J, M = 0.5 mm; K–L = 0.25 mm.
Fig. 2 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data
Fig. 2. Anaplecta corneola Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Tegmina. F. Tegmina vein. G. Maxillary palp. H. Front femur, ventral view. I. Wings. J. Supra-anal plate, dorsal view. K. Subgenital plate, ventral view. L. Hook, ventral view. M. Left phallomere, ventral view. N. Right phallomere, ventral view. Scale bars: A–B, E–F, I = 2 mm; C, G–H = 1 mm; D, J–K, M–N = 0.5 mm; L = 0.25 mm.
Data from: A new dissorophoid temnospondyl from the Allegheny Group (Late Westphalian, Carboniferous) of Five Points, Mahoning County, Ohio (USA)
<p>A small temnospondyl skull from the Upper Carboniferous Allegheny Group of Five Points, Ohio, is referred to a new dissorophoid, <i>Palodromeus bairdi</i> n. gen n. sp. The complete skull with mandibles is preserved in counterparts. It is characterized by (1) elongated slit-like choana, (2) postfrontal, postorbital, and supratemporal bearing a distinct ridge, and (3) reduced parietal only two-thirds the length of the frontal. Phylogenetic analysis confirms a dichotomy between amphibamiforms and olsoniforms and places <i>Palodromeus bairdi</i> at the base of the olsoniforms, revealing an early stage in the evolution of that clade.</p>
Supplementary material 2 from: Shi S, Zhang M, Xie F, Jiang J, Liu W, Li Ding1, Luan L, Wang B (2020) Multiple data revealed two new species of the Asian horned toad Megophrys Kuhl & Van Hasselt, 1822 (Anura, Megophryidae) from the eastern corner of the Himalayas. ZooKeys 977: 101-161. https://doi.org/10.3897/zookeys.977.55693
Figure S1–S5
Supplementary material 1 from: Shi S, Zhang M, Xie F, Jiang J, Liu W, Li Ding1, Luan L, Wang B (2020) Multiple data revealed two new species of the Asian horned toad Megophrys Kuhl & Van Hasselt, 1822 (Anura, Megophryidae) from the eastern corner of the Himalayas. ZooKeys 977: 101-161. https://doi.org/10.3897/zookeys.977.55693
Table S1–S5
Figure 8 from: Shi S, Zhang M, Xie F, Jiang J, Liu W, Li Ding1, Luan L, Wang B (2020) Multiple data revealed two new species of the Asian horned toad Megophrys Kuhl & Van Hasselt, 1822 (Anura, Megophryidae) from the eastern corner of the Himalayas. ZooKeys 977: 101-161. https://doi.org/10.3897/zookeys.977.55693
Figure 8 The holotype adult male CIBMT171053 of Megophrys zhoui sp. nov. in life. A dorsolateral view of body B ventral view of body C dorsolateral view of head D ventral view of hand E ventral view of foot.
Figure 7 from: Shi S, Zhang M, Xie F, Jiang J, Liu W, Li Ding1, Luan L, Wang B (2020) Multiple data revealed two new species of the Asian horned toad Megophrys Kuhl & Van Hasselt, 1822 (Anura, Megophryidae) from the eastern corner of the Himalayas. ZooKeys 977: 101-161. https://doi.org/10.3897/zookeys.977.55693
Figure 7 The adult male CIB022017061805 of M. cf. pachyproctus in life. A dorsolateral view of body B ventral view of body C dorsolateral view of head D ventral view of hand E ventral view of foot.
Figure 5 from: Shi S, Zhang M, Xie F, Jiang J, Liu W, Li Ding1, Luan L, Wang B (2020) Multiple data revealed two new species of the Asian horned toad Megophrys Kuhl & Van Hasselt, 1822 (Anura, Megophryidae) from the eastern corner of the Himalayas. ZooKeys 977: 101-161. https://doi.org/10.3897/zookeys.977.55693
Figure 5 Skull of Megophrys species in Medog. A–E dorsal views of adult male holotype NWIPB770650 of M. pachyproctus, adult male topotype CIB022017061406 of M. medogensis, adult male CIB022017061805 of M. cf. pachyproctus, adult male holotype CIBMT171053 of Megophrys zhoui sp. nov., and adult male holotype CIB201706MT02 of Megophrys yeae sp. nov., respectively F–J ventral views of the specimens, respectively. Key to skull: 1 premaxillary; 2 maxillary; 3 nasal; 4 sphenethmoid; 5 anterior fontanelle; 6 frontoparietal; 7 sagittal suture; 8 pterygoid; 9 squamosal; 10 quadratojugal; 11 prootic; 12 exoccipital; 13 vomerine ridge; 14 mandible; 15 anterior process of parasphenoid; 16 columella auris. Scale bar equal to 5 mm.
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.