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Fig. 1 in Effect of leaf decomposition stage and water temperature on fragmentation activity of a shredder invertebrate species in lotic ecosystems
Fig. 1. Schematic representation of the eXperimental design of the present study. EXperiment I: nine discs of senescent (S) and nine discs of conditioned senescent (SCD) wastes were used in each aquarium in the absence of shredder invertebrates. EXperiment II: nine discs of senescent (S), nine discs of conditioned senescent (SCD) and nine discs of green detritus (G) were used in each aquarium in the presence of shredded invertebrates (Phylloicus sp.).
Fig. 2 in Effect of leaf decomposition stage and water temperature on fragmentation activity of a shredder invertebrate species in lotic ecosystems
Fig. 2. Mean values and standard error of leaf mass loss (LML) of senescent (senescent plus conditioned senescent, due to the absence of visual distinction by coloration) and green detritus for larval case production by Phylloicus sp. in the different water temperature treatments at Capetinga Stream, Água Limpa Farm, Brasília, Brazil.
Fig. 1. IPS 31102, a left maxillary fragment with the upper incisor and P4–M2 in The Never-Ending Problem of Miocene Beaver Taxonomy
Fig. 1. IPS 31102, a left maxillary fragment with the upper incisor and P4–M2 of the castorid Chalicomys catalaunicus (Bataller, 1838) from Sant Quirze (MN7+8 from the Vallès−Penedès Basin, Catalonia, Spain). Note the abundant cement infilling all synclines.
Fig. 2 in Comparative analyses of the fragmented mitochondrial genomes of wild pig louse Haematopinus apri from China and Japan
Fig. 2. The complete mitochondrial genome of wild pig louse Haematopinus apri form China. Each minichromosome has a coding region and a non-coding region (NCR, in black). The names and transcript orientation of genes are indicated in the coding region and the minichromosomes are placed in alphabetical order of protein-coding genes and rRNA genes. Abbreviations: atp6 and atp8, ATP synthase F0 subunits 6 and 8; cytb, cytochrome b; cox1-3, cytochrome c oxidase subunits 1–3; nad1-6 and nad4L, NADH dehydrogenase subunits 1–6 and 4L; rrnS and rrnL, small and large subunits of ribosomal RNA. tRNA genes are indicated with their single-letter abbreviations of the corresponding amino acids.
FIGURE 6. Fossil eggshell fragments T92-88 in Identification of fossilized eggshells from the Taung hominin locality, Taung, Northwest Province, South Afric
FIGURE 6. Fossil eggshell fragments T92-88 (blue) and T93-17 (yellow) fit to eggs from five extant birds. Fits depicted visually in the figure (rigidly constrained size) correspond to root mean square (RMS) values reported in Table 2. Note that visual correspondence supports quantification of RMS values in that fossil eggshell fragment T92-88 fits best with the blunt pole of the extant guinea fowl egg. Extant black eagle (blunt pole) and giant eagle owl (apical pole) eggs provide the next closest, but still worse fits. Fossil eggshell fragment T93-17 fits best with the equatorial region of the black eagle egg. The extant guinea fowl egg provides the next closest fit for fossil eggshell fragment T93-17.
FIGURE 3 in Anthropogenic river fragmentation reduces long-term viability of the migratory fish Salminus brasiliensis (Characiformes: Bryconidae) populations
FIGURE 3 | A. Salminus brasiliensis population structure from the Bayesian cluster analysis for K = 2 (see also S1). Black lines separate the different sampled populations based on location (Pop1, Pop2, Pop3, Pop4 and Pop5; Fig. 1). B. DAPC scatterplots and membership probabilities show the first two principal components of the DAPC. Populations are represented in different colors: 1 - Lilac (Pop5); 2 - Green (Pop4), 3 - Orange (Pop3), 4 - Lilac (Pop2) and 5 - Brown (Pop1). C. Membership probabilities (in bar plots), represent individuals in different clusters.
FIGURE 2 in Anthropogenic river fragmentation reduces long-term viability of the migratory fish Salminus brasiliensis (Characiformes: Bryconidae) populations
FIGURE 2 | Predicted genetic diversity in Salminus brasiliensis populations with distinct fragmentation levels over the next 100 years. Using BOTTLESIM 2.6, we estimated the retained percentage of effective number of alleles (Ae) and expected heterozygosity (He) under 100%, 75% and 50% of retain bottleneck scenarios. In all populations, the current population size is unable to maintain 80% of current genetic diveristy, which it is indicated by a red line.
FIGURE 1 in Anthropogenic river fragmentation reduces long-term viability of the migratory fish Salminus brasiliensis (Characiformes: Bryconidae) populations
FIGURE 1 | Study area of Salminus brasiliensis populations in the Uruguay River basin, southern Brazil. A. Picture of Canyon Agusto César Gorge, Upper Uruguay River (acquired rights); B. Picture of Yucumã our Moconá Falls (google font: https://7mar.com.ar/mocona). Salminus brasiliensis (personal picture).
FIGURE 2. Agerinia roselli from Les Saleres. IPS-2543, left mandible fragment with P3 and P4 in New dental material and redescription of Agerinia roselli (Primates, Adapiformes) from Les Saleres (early Eocene, NE Iberian Peninsula)
FIGURE 2. Agerinia roselli from Les Saleres. IPS-2543, left mandible fragment with P3 and P4 in occlusal (1), buccal (3), lingual (5), and mesial (7) views; enlarged images of mesial roots of the same specimen in occlusal (2), buccal (4), lingual (6), and mesial (8) views; white arrows indicate the position of the most mesial root; black arrows indicate the position of the root immediately mesial with respect to the P3. Scale bar represents 3 mm in both cases.
Dataset belonging to Fragmented micro-growth habitats present opportunities for alternative competitive outcomes
<p>This Dataset contains the raw data, processed data and script/code underlying the results and figures presented in the manuscript "Fragmented micro-growth habitats present opportunities for alternative competitive outcomes", (deposited at BioRXiv 10.1101/2024.01.26.577336)</p> <p>by: Maxime Batsch<sup>1</sup>, Isaline Guex<sup>2</sup>, Helena Todorov<sup>1</sup>, Clara M. Heiman<sup>1</sup>, Jordan Vacheron<sup>1</sup>, Julia A. Vorholt<sup>3</sup>, Christoph Keel<sup>1</sup>, and Jan Roelof van der Meer<sup>1*</sup></p> <p>1) Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland</p> <p>2) Department of Mathematics, University of Fribourg, CH-1700 Fribourg, Switzerland</p> <p>3) Institute for Microbiology, Swiss Federal Institute of Technology (ETH Zürich), CH-8049 Zürich, Switzerland</p> <p>The raw data consists of microscopy droplet/cell image data, 96-well plate reader data, and flow cytometry cell counts.<br>Processed data are organised by Figure in the manuscript and/or the Supplementary figures belonging to the manuscript. Figure folders contain the main output, the input data, the code and scripts to produce the output from the input, and relevant statistical tests.</p>
FIGURE 3. Rodentia incisor fragments from the Clarno Formation, Oregon. JODA 16822, 3.1. anterior view, 3.2. lateral view, 3.3. distal view. UOMNH F-28304, 3.4. anterior view, 3.5. lateral view, 3.6. distal view. Scale bar equals 1 in The first Eocene rodents from the Pacific Northwest, USA
FIGURE 3. Rodentia incisor fragments from the Clarno Formation, Oregon. JODA 16822, 3.1. anterior view, 3.2. lateral view, 3.3. distal view. UOMNH F-28304, 3.4. anterior view, 3.5. lateral view, 3.6. distal view. Scale bar equals 1 mm.
Fig. 4. Proscapanussansaniensis. A. Left dentary fragment with canine root and p1–p4, Petersbuch 31, NHMA P31−163A1 in Moles (Talpidae) from the late Middle Miocene of South Germany
Fig. 4. Proscapanussansaniensis. A. Left dentary fragment with canine root and p1–p4, Petersbuch 31, NHMA P31−163A1, occlusal view; ca. × 10. B. Right m1–m3, Petersbuch 31, NHMA P31−163B2, occlusal view; ca. × 10. C. Right dentary fragment with p4–m2, Petersbuch 48, NHMA P48−89A1, buccal view; ca. × 10. D. Left P4, Petersbuch 31, NHMA P31−163C1, occlusal view; ca. × 10. E. Left M1, Petersbuch 48, NHMA P48−89B2, occlusal view; ca. × 10. F. Right M2, Petersbuch 31, NHMA P31−163E3, occlusal view; ca. × 10. G. Left humerus, Petersbuch 31, NHMA P31−164A1, anterior view; ca. × 5.
Fig. 4. Indeterminate olenid fragments. A in Phosphatised olenid trilobites and associated fauna from the Upper Cambrian of Västergötland, Sweden
Fig. 4. Indeterminate olenid fragments. A. Left pleura, SMNH Ar59745 (2.13), sample 2. B. Right pleura, SMNH Ar59746 (1.17), sample 1. C. Left pleura, SMNH Ar59747 (1.16), sample 1. D. Pleura in ventral view, SMNH Ar59748 (2.16), sample 2. E. Detached eye, SMNH Ar59749 (2.17), sample 2. F. Detached eye, SMNH Ar59750 (2.18), sample 2. G. Librigena with intact eye, SMNH Ar597451 (2.15), sample 2. H. Poorly preserved hypostome, SMNH Ar59752 (1.22), sample 1. Scale bars 0.1 mm.
UniSpec: Deep Learning for Predicting the Full Range of Peptide Fragment Ion Series to Enhance the Proteomics Data Analysis Workflow
<p>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. </p> <p>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".</p> <p>This includes UniSpec datasets, downstream evaluation and analysis, and application case studies.</p> <p>1. pre-processed training, evaluation and testing data for machine learning;</p> <p> UniSpec-Datasets.7z, Readme_UniSpecDatasets.txt</p> <p>2. Streamlined input datasets based on the fragmentation dictionary;</p> <p> Streamlined_inputdatasets.7z, Readme_Streamlined_inputdatasets.txt</p> <p>3. Predictions on the validation and test sets;</p> <p> UniSpecPred_Validation-Test.7z, Readme_Predictons_ValidationTest.txt</p> <p>4. Evaluation by comparison with Prosit;</p> <p> a. Predictions: prosit_and_unispec_predictions.7z, Readme_prosit_and_unispec_predictions.txt</p> <p> b. Cosine similarity scores: prosit_vs_unispec_CS.7z, Readme_prosit_vs_unispec_CS.txt</p> <p>5. CSS for Different HCD Fragment Ion Series;</p> <p> CS_for_ion_splits.tsv</p> <p>6. Application 1: PSM rescoring;</p> <p> PSM rescoring_zipfiles.7z, PSM rescoring_readme.txt</p> <p>7. Application 2: In-silico spectral library search </p> <p> in-silico_librarysearch.7z, in-silico_librarysearch_readme.txt</p> <p> </p>
Fig.1 in A spinose appendage fragment of a problematic arthropod from the Early Ordovician of Morocco
Fig.1. Several types of spinose arthropod appendages discussed in the text. A. Spiculate first appendage of the anomalocaridid Anomalocaris briggsi, Early Cambrian, Australia (redrawn from Nedin 1995). B. Pectinate first appendage of the anomalocaridid Laggania cambria, Middle Cambrian, Canada (redrawn from Dzik and Lendzion 1988). C. Third prosomal appendage of the megalograptid eurypterid Megalograptus ohioensis, Late Ordovician, USA (reproduced from Caster and Kjellesvig−Waering 1964). D. Third prosomal appendage of the mixopterid eurypterid Mixopterus kiaeri, Early Devonian, Norway (redrawn from Størmer 1934). E. Third prosomal appendage of the laurieipterid eurypterid Ctenopterus cestrotus, Late Silurian, USA (redrawn from Clarke and Ruedemann 1912). F. Chelicera of the pterygotid eurypterid Erettopterus osiliensis, Late Silurian, Estonia and USA (observations of O.E.T.). G. Angustidontus weihmannae, Late Devonian, Canada (drawing based on photograph in Copeland and Bolton 1960). H. Cheliped of the decapod malacostracan Thaumastocheles zaleucus, Recent, Caribbean region (redrawn from Tshudy and Sorhannus 2000). Scale bars 10 mm.
Fig. 2. A in A spinose appendage fragment of a problematic arthropod from the Early Ordovician of Morocco
Fig. 2. A. Geographical situation of Ordovician surface outcrops in Morocco, indicated in medium grey (adapted from Destombes et al. 1985). The rectangular marquee indicates the area shown in detail in B. Geographical situation of Ordovician surface outcrops to the north of Zagora according to the geological map (sheet 273, Zagora—Coude du Draa). Localities indicated with cross−hairs are numbered in stratigraphical order, with 1 and 2 being situated close to the boundary between the Lower and Upper Fezouata Formations.
Fig. 3 in Dry forest fragmentation in Brazilian Cerrado and its effects on communities of ground foraging ants
Fig. 3. Non-metric multidimensional scaling scores, obtained from data on the composition of ants recorded at sampling points in the dry forest area (P16 to P30) and in the surrounding matrix (P1 to P15), in the southeastern region of Goiás, Brazil. The dotted lines represent the confidence intervals for the fragment and surrounding cultivated fields compared by the similarity test, analysis of similarity (P = 0.001).
Fig. 2 in Dry forest fragmentation in Brazilian Cerrado and its effects on communities of ground foraging ants
Fig. 2. Observed and estimated species richness of ground foraging ants (Jackknife1 data); from (A) dry forest and surrounding cultivated land; (B) general ants collected in different periods over time - C1 (first crop), C2 (second crop), and C3 (inter-crop).
Fig. 1 in Dry forest fragmentation in Brazilian Cerrado and its effects on communities of ground foraging ants
Fig. 1. Geographical location of the experimental areas. The dry forest fragments with their respective areas ([1] = 16.4 ha; [2] = 20.9 ha; [3] = 38.8 ha; [4] = 8.5 ha; [5] = 4.22 ha; [6] = 55.4 ha; [7] = 13.3 ha; [8] = 33.4 ha; [9] = 10.3 ha; [10] = 47.4 ha). One of the dry forest fragments and part of the surrounding cropland is highlighted where pitfall traps were located (Ipameri, Goiás). Red dots represent sites where pitfall traps were installed along the transect.
Fig. 4 in Dry forest fragmentation in Brazilian Cerrado and its effects on communities of ground foraging ants
Fig. 4. (A) Dendrograms from standard hierarchical clustering based on the Jaccard Similarity Index of the ant assemblages associated with dry forest fragments and croplands of the whole community of ground foraging ants captured with baited traps at 3 different times: C1 = soybean (first crop), C2 = maize (second crop), and C3 = fields without crops. (B) F1 to F10 represent the different fragments of dry forest.
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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.