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opencc-zeroAug 2024View details →

FIG. 2 in Pterygoneurum sampaianum (Guim.) Guim.: range extension to Africa, first mentions in France, confirmation of specific status and improved morphological circumscription

FIG. 2. — Pterygoneurum sampaianum (Guim.) Guim.: A, habit; B-F, urn; G, gametophytes; H, leaf; I, hair-point; J-L, marginal areolation at leaf base. Scale bars: A-C, E, F, 200 µm; D, G, H, 100 µm; I, J, L, 30 µm; K, 50 µm.

opencc-zeroAug 2024View details →

FIG. 1 in Pterygoneurum sampaianum (Guim.) Guim.: range extension to Africa, first mentions in France, confirmation of specific status and improved morphological circumscription

FIG. 1. — Pterygoneurum ovatum (Hedw.) Dixon: A, habit; B, C, urn; D, gametophyte; E, leaf; F, hair-point; G, leaf base; H, marginal areolation at leaf base. Scale bars: A, D, 200 µm; B, C, F, G, 100 µm; E, 300 µm; H, 30 µm.

Figure 4 in Range extension and re-description of Synagrops argyreus (Perciformes, Acropomatidae)

Figure 4. - Distribution of Synagrops argyreus as currently known (1, location of holotype; 2, locations of studied specimens).

Figures 5 in Range extension and re-description of Synagrops argyreus (Perciformes, Acropomatidae)

Figures 5. - Otoliths (a = inner face, b = view from ventral). A: Synagrops adeni BMNH 1939.5.24.880-891, Gulf of Aden; B: Synagrops pellucidus BMNH 1890.7.31.13-15, Bay of Bengal; C: Synagrops trispinosus USNM 407771, 16°04'N-87°14'W; D-F: Synagrops argyreus, D: LACM (coll. Fitch), Oahu, Hawaii, E: refigured from Rivaton and Bourret (1999), New Caledonia, F: ZMUC 44272, 22°19'S-43°06'E.

Figure 3 in Range extension and re-description of Synagrops argyreus (Perciformes, Acropomatidae)

Figure 3. - Preopercular lobe in three Synagrops species. A: S. argyreus, ZMMGU 15338, SL 137 mm; B: S. japonicus, IORAS uncat., SL 140 mm, cleared and stained, Madagascar Ridge; C: S. aff. philippinensis, IORAS uncat., SL 50 mm, cleared and stained, Vietnam: Nha Trang. Creasts on preopercular lobe indicated by arrows. Scale bar = 5 mm.

Figure 2 in Range extension and re-description of Synagrops argyreus (Perciformes, Acropomatidae)

Figure 2. - Posterior plate of maxillary in Synagrops argyreus, ZMMGU 15338, SL 137 mm (A) and S. pellucidus, BMNH 1890.7.31, SL 85 mm (B). Posteroventral angle of maxillary indicated by arrow. Scale bar = 5 mm.

opencc-by-4.0Oct 2023View details →

UniSpec: Deep Learning for Predicting the Full Range of Peptide Fragment Ion Series to Enhance the Proteomics Data Analysis Workflow

UniSpec is a comprehensive DL spectrum predictor that can predict the intensity of the entire HCD MS/MS fragment ion series, going beyond existing tools limited to b/y ion series.  All datasets developed for UniSpec model are shared on Zenodo as part of the UniSpec publication, "UniSpec: Deep Learning for Predicting Comprehensive Peptide Fragment Ion Series to Improve Peptide-Spectrum Matches from Shotgun Proteomics Experiments". This includes UniSpec datasets, downstream evaluation and analysis, and application case studies. 1. pre-processed training, evaluation and testing data for machine learning;          UniSpec-Datasets.7z, Readme_UniSpecDatasets.txt 2. Streamlined  input datasets based on the fragmentation dictionary;         Streamlined_inputdatasets.7z, Readme_Streamlined_inputdatasets.txt 3. Predictions on the validation and test sets;        UniSpecPred_Validation-Test.7z, Readme_Predictons_ValidationTest.txt 4. Evaluation by comparison with Prosit;       a. Predictions: prosit_and_unispec_predictions.7z, Readme_prosit_and_unispec_predictions.txt       b. Cosine similarity scores: prosit_vs_unispec_CS.7z, Readme_prosit_vs_unispec_CS.txt 5. CSS for Different HCD Fragment Ion Series;        CS_for_ion_splits.tsv 6. Application 1: PSM rescoring;       PSM rescoring_zipfiles.7z,  PSM rescoring_readme.txt 7. Application 2: In-silico spectral library search         in-silico_librarysearch.7z, in-silico_librarysearch_readme.txt

opencc-by-4.0Apr 2019View details →

Fig. 1 in Range extension of Megachile lanata (Hymenoptera: Megachilidae), a non-native sunn hemp pollinator, in Florida

Fig. 1. Distribution of Megachile lanata in Florida based on museum specimens, published literature, and online database resources. The northernmost record in Sumter County is over 260 km (about 160 mi) away from the previously published northernmost location in St. Lucie County. The line at 31°N indicates the northernmost specimen record from its native range in India, which may indicate a possible range in the US.

opencc-by-4.0Jul 2024View details →

Quasi-invariance of Tropical Meridional Surface Temperature Gradient in a Wide Range of Climates

Data generated in the study "Quasi-invariance of Tropical Meridional Surface Temperature Gradient in a Wide Range of Climates" are archived here

opencc-by-4.0Jan 2012View details →

Figure 6 in Range extension for Duttaphrynus kotagamai (Amphibia: Bufonidae) and a preliminary checklist of herpetofauna from the Uda Mäliboda Trail in Samanala Nature Reserve, Sri Lanka

Figure 6. Hydroelectric power plant (note: concrete wall built across the steam and concrete particles dump into the steam).

opencc-by-4.0Jan 2012View details →

Figure 5 in Range extension for Duttaphrynus kotagamai (Amphibia: Bufonidae) and a preliminary checklist of herpetofauna from the Uda Mäliboda Trail in Samanala Nature Reserve, Sri Lanka

Figure 5. Comparison of amphibian (left) and reptile (right) diversity of Uda Mäliboda area with rest of the Sri Lankan species (Abbreviations: NOSL – total number of species in Sri Lanka; NOU – total number of species in Uda Mäliboda; ENSL – number of endemic species to Sri Lanka; ENU – number of endemic species in Uda Mäliboda; TRSL – number of threatened species in Sri Lanka and TRU – number of threatened species in Uda Mäliboda).

Fig. 5 in A review of Neusibatrachus wilferti, an Early Cretaceous frog from the Montsec Range, northeastern Spain

Fig. 5. Comparison of the radioulna and metacarpals of Neusibatrachus wilferti Seiffert, 1972, holotype, FUB 33B (A) and Eodiscoglossus santonjae Villalta, 1956, holotype, MNCN 4723 (B). Both specimens are from the upper Berriasian–lower Valanginian of Santa Maria de Meià, Spain.

Fig. 4. Neusibatrachus wilferti Seiffert, 1972 in A review of Neusibatrachus wilferti, an Early Cretaceous frog from the Montsec Range, northeastern Spain

Fig. 4. Neusibatrachus wilferti Seiffert, 1972 from the upper Berriasian– lower Valanginian of Santa Maria de Meià, Spain, holotype (FUB 33A). A. Close−up of the left scapula, ventral aspect. B. Right scapula of the same (reversed). White arrows indicate the position of the tiny medial notch.

Fig. 6 in A review of Neusibatrachus wilferti, an Early Cretaceous frog from the Montsec Range, northeastern Spain

Fig. 6. Palaeobatrachus diluvianus (Goldfuss, 1831), KU 124939 from the upper Oligocene of Bechlejovice, Czech Republic, latex cast of the ventral aspect. Note the processes on the prootics, the ventrally grooved centra, and the protruding hypochord.

Fig. 3. A, B. Neusibatrachus wilferti Seiffert, 1972 in A review of Neusibatrachus wilferti, an Early Cretaceous frog from the Montsec Range, northeastern Spain

Fig. 3. A, B. Neusibatrachus wilferti Seiffert, 1972, holotype (FUB 33A) from the upper Berriasian–lower Valanginian of Santa Maria de Meià, Spain, details in ventral view. A. Cranial and anterior postcranial regions, a photograph (A1) and interpretive drawing (A2). B. Vertebral column, a photograph (B1) and interpretive drawing (B2). C. Rana iberica Boulenger, 1879, cleared and stained wild−caught postmetamorphic froglet (MNCN 15009), posterior presacrals and sacrum in ventral view.

Fig. 2. Neusibatrachus wilferti Seiffert, 1972 in A review of Neusibatrachus wilferti, an Early Cretaceous frog from the Montsec Range, northeastern Spain

Fig. 2. Neusibatrachus wilferti Seiffert, 1972 from the upper Berriasian– lower Valanginian of Santa Maria de Meià, Spain. Partial restoration of the skeleton in dorsal aspect.

opencc-by-4.0Sep 2024View details →

Hydrology and trophic flexibility structure alpine stream food webs in the Teton Range, Wyoming, USA

Data and code necessary to replicate the findings from the manuscript titled "Hydrology and trophic flexibility structure alpine stream food webs in the Teton Range, Wyoming, USA". Abstract: Understanding biotic interactions and how they vary across habitats is important for assessing the vulnerability of communities to climate change. Receding glaciers in high mountain areas can lead to the hydrologic homogenization of streams and reduce habitat heterogeneity, which are predicted to drive declines in regional diversity and imperil endemic species. However, little is known about food web structure in alpine stream habitats, particularly among streams fed by different hydrologic sources (e.g., glaciers or snowfields). We used gut content and stable isotope analyses to characterize food web structure of alpine macroinvertebrate communities in streams fed by glaciers, subterranean ice, and seasonal snowpack in the Teton Range, Wyoming, USA. Specifically, we sought to: (1) assess community resource use among streams fed by different hydrologic sources; (2) explore how variability in resource use relates to feeding strategies; and (3) identify which environmental variables influenced resource use within communities. Average taxa diet differed among all hydrologic sources, and food webs in subterranean ice-fed streams were largely supported by the gold alga Hydrurus. This finding bolsters a hypothesis that streams fed by subterranean ice may provide key habitat for cold-water species under climate change by maintaining a longer growing season for this high-quality food resource. While a range of environmental variables associated with hydrologic source (e.g., stream temperature) were related to diet composition, hydrologic source categories explained the most variation in diet composition models. Less variable diets within versus among streams suggests high trophic flexibility, which was further supported by high levels of omnivory. This inherent trophic flexibility may bolster alpine stream communities against future changes in resource availability as the mountain cryosphere fades. Ultimately, our results expand understanding of the habitat requirements for imperiled alpine taxa while empowering predictions of their vulnerability under climate change.

openapache2.0Sep 2024View details →

Long-range axonal projections analyses of the mouse brain

Accompanying data and analyses of the article <a href="https://doi.org/10.1101/2024.10.04.616605">"Generating brain-wide connectome using synthetic axonal morphologies"</a>. The code to reproduce the figures is available at <a href="https://github.com/Remy2506/axon_projection_figures">this repository</a>. Main contents: <ul> <li>SEU_morphs.zip, peng_2021_morphs.zip, ML_morphs.zip: input morphologies from various sources (novel morphologies collected by H. Peng, Southeast University, <a href="https://www.nature.com/articles/s41586-021-03941-1">Peng et al. 2021</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754285/">Winnubst et al. 2019</a>) after <a href="https://github.com/BlueBrain/morphology-workflows">morphology-workflows Repair</a> post-processing steps.</li> <li>atlas: atlas of the mouse brain used (enhanced version of Allen Brain CCFv3)</li> <li>out_a_p: output of the <a href="https://github.com/BlueBrain/axon-projection">axon projection</a> anaylsis and clustering on the 3601 morphologies of the dataset. <ul> <li>axon_lengths_12.csv, axon_terminals_12.csv: the lengths of axons in each subregion where they terminate, and terminals, at hierarchy level 12 from the brain hierarchy.</li> <li>clustering_output.csv: output of the GMM clustering.</li> <li>config_a_p.cfg: configuration file used to produce this analysis, with running the axonal projection code.</li> </ul> </li> <li>circuit: contains files describing the circuit synthesized with Blue Brain's circuit-build*. <ul> <li>bioname: parameters used to synthesize the circuit (regions to synthesize, cell densities per region, location of axons to graft...).</li> <li>sonata: files that contain nodes and edges of the circuit.</li> <li>auxiliary: various cell collections from the synthesized cells, filtered by region. Cell collections are to be read with <a href="https://github.com/BlueBrain/voxcell/tree/main">Voxcell.</a></li> <li>conn_mat.h5: the connectivity matrices obtained for the case where MOp5 long-range axons were synthesized, computed with <a href="https://github.com/BlueBrain/ConnectomeUtilities/tree/main">ConnectomeUtilities.</a>Contains connectivity matrices for the synthesized LRAs, biological LRAs, and grafted local axons.</li> </ul> </li> <li>local_axons: biological local axons that are grafted to the synthesized dendrites that do not have synthesized long-range axons.</li> <li>synthesized_MOp5_LRAs: 1695 synthesized cells with long-range axons of the MOp5 region, in the atlas reference frame. </li> <li>out_a_p_synth_MOp5: axonal projection analysis of the synthesized MOp5 axons.</li> <li>synthesized_isocortex_cells: all synthesized cells of the isocortex region, except MOp5 cells. They are in h5 format, which takes less space than asc and swc. The h5 format can be read and converted for instance with <a href="https://github.com/BlueBrain/MorphIO">MorphIO</a>.</li> <li>synthesized_isocortex_LRAs: 21680 synthesized cells with long-range axons of the isocortex regions for which a GMM cluster was created. </li> </ul> Additional files: <ul> <li>flatmap_both.nrrd: file used to generate a flat map visualization of the mouse isocortex, shown in the article.</li> <li>config_a_s.cfg: configuration file used to synthesize the long-range axons with the <a href="https://github.com/BlueBrain/axon-synthesis">axon-synthesis</a> code.</li> <li>target_pts: tufts common ancestors for the synthesized MOp5 axons.</li> <li>brain_atlas.zip: a lightweight version of the mouse brain atlas for the synthesis code example.</li> </ul> *These softwares might not be open-source at the time of publication of this data, but a public link will be provided as soon as they are.

opencc-zeroJan 2024View details →

Linked collectors and determiners for: Re-description and range extension of the Afrotropical mayfly Cloeon perkinsi (Ephemeroptera, Baetidae).

Natural history specimen data linked to collectors and determiners held within, "Re-description and range extension of the Afrotropical mayfly Cloeon perkinsi (Ephemeroptera, Baetidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/1f84a7e2-7d98-4857-ba28-f79bb43d7415">https://bionomia.net/dataset/1f84a7e2-7d98-4857-ba28-f79bb43d7415</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/1f84a7e2-7d98-4857-ba28-f79bb43d7415">https://gbif.org/dataset/1f84a7e2-7d98-4857-ba28-f79bb43d7415</a>. Formatted as a Frictionless Data package.