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Dataset: Location- and feature-based selection histories make independent, qualitatively distinct contributions to urgent visuomotor performance
<p>This dataset (packaged as the zip file history_share.zip) accompanies the article titled "Location- and feature-based selection histories make independent, qualitatively distinct contributions to urgent visuomotor performance" by EE Oor, E Salinas, and TR Stanford which is available as a preprint in bioRxiv. The experimental results in the article are based on behavioral data collected from 2 monkey subjects during performance of a visuomotor task (the compelled oddball task), as described in the text. This dataset contains the trial-by-trial behavioral results collected for each subject and upon which all subsequent analyses were based.</p> <p>In addition to the trial-wise data arrays (stored in the files dataC.csv, dataN.csv, and dataCN.csv), the package includes Matlab functions and scripts (*.m files) used to analyze the data and recreate the results and figures in the article. Instructions and specifics are detailed in the README file. </p>
Data from: How many specimens make a sufficient training set for automated three dimensional feature extraction?
<p>Deep learning has emerged as a robust tool for automating feature extraction from 3D images, offering an efficient alternative to labour-intensive and potentially biased manual image segmentation methods. However, there has been limited exploration into the optimal training set sizes, including assessing whether artificial expansion by data augmentation can achieve consistent results in less time and how consistent these benefits are across different types of traits. In this study, we manually segmented 50 planktonic foraminifera specimens from the genus Menardella to determine the minimum number of training images required to produce accurate volumetric and shape data from internal and external structures. The results reveal unsurprisingly that deep learning models improve with a larger number of training images with eight specimens being required to achieve 95% accuracy. Furthermore, data augmentation can enhance network accuracy by up to 8.0%. Notably, predicting both volumetric and shape measurements for the internal structure poses a greater challenge compared to the external structure, due to low contrast differences between different materials and increased geometric complexity. These results provide novel insight into optimal training set sizes for precise image segmentation of diverse traits and highlight the potential of data augmentation for enhancing multivariate feature extraction from 3D images. </p>
Figure 3 in Getting to a decision: using structured decision-making to gain consensus on approaches to invasive species control
Figure 3. Total multi-attribute utility including all weighted objectives for responding to smallmouth bass in Cultus Lake, BC, across all management activities. Each utility was on a scale from 0-1, so the multi-attribute scale also ranges from 0–1.
Figure 1 in Getting to a decision: using structured decision-making to gain consensus on approaches to invasive species control
Figure 1. Steps involved in structured decision-making. Steps can be re-evaluated at any point; responses should be re-evaluated once new data is gathered following implementation. Adapted from Liu and Cook (2016).
Figure 2 in Getting to a decision: using structured decision-making to gain consensus on approaches to invasive species control
Figure 2. Calculated utility of avoiding fish species at-risk and not at-risk of extirpation in Cultus Lake, BC, across all combinations of smallmouth bass control. Utility is presented on a scale from 0–1.
FIGURE 7 in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India
FIGURE 7. Feeding strategies and progressive growth of the Dotilla pellet structures. Note four types of feeding modes: sector (of a circle) feeding mode covering growth (top to bottom) of the pellet structures arranged in four columns (1-4) corresponding to four different types of pellet designs (homogeneous pellet spread, radial, concentric and concentric-radial); radially diverging feeding mode covering growth (top to bottom) of the radial and asteroid pellet designs (column 5); concentric feeding mode covering growth (top to bottom) of the concentric pellet designs (column 6) and combined concentric-radial feeding mode covering growth (top to bottom) of the concentric-radial pellet design (column 7). Note development of different designs under sector (of a circle) feeding mode within feeding sectors having similar shape and size (column 1- 4 top structures). Also note a pellet design may originate in different feeding modes, but with subtle differences. The lower half of the figure incorporates schematic representation of the growth stages (I - Initial, M - Middle, F - Final from top to bottom) of all the above pellet designs with time and progressive feeding activity under different feeding modes (columns 1-7 are extended from upper to lower half of the figure to maintain analogy). Also note for each schematic structure (not to scale) presented, there is a physical (natural) analogue recorded from the field. Also visualize the growth of structural complexities, acquisition of described barrier elements and SI index along each column from top to bottom in both the natural and schematic presentations.
FIGURE 8. A in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India
FIGURE 8. A: Ex situ preservation (aided by wind action) of Dotilla pellets as pellet-filled burrow tubes in the supratidal flat during low tide situation. B: Ex situ preservation of Dotilla pellets (aided by wind action) in ripple troughs during low tide situation. C: Schematic profile section of the studied beach showing positions of the Dotilla pellet spread and burrow zone, spread of Ocypode burrows, mutual dispositions of different geomorphic units (dune, supratidal, upper - middle intertidal flats) relative to land - sea positions and High and Low Tide Levels (HTL and LTL). Note gradual spreading of the Dotilla pellet and burrow zone towards sea with gradual lowering of substrate water levels (WLs) during tidal recession of sea. D-E: Possible stratigraphic development of the coastal sedimentary units (1-3) and contained burrow zones and other associated features in transgressive (E) and regressive (D) situations. Note the possible position of preserved Dotilla pellets and burrows between Unit 1 and 2 under transgressiveregressive sea conditions. Features are schematic and not to scale.
FIGURE 4 in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India
FIGURE 4. Concentric - radial pellet design (Figures 3 A, C, E, G, I, K, M, O, Q, S, U and W) produced by the crab Dotilla in the upper intertidal flat of the Bakkhali beach, Bay of Bengal coast, Eastern India. Figures 3 B, D, F, H, J, L, N, P, R, T, V and Xl represent the corresponding line tracings made for measurement of Attack Index (AI) and Safety Index (SI). Figures Q and W represent conjugate concentric - radial structures made by several individuals and possesses shared concentric rows of pellets (Scrp) and very high Combined Safety index (CSI) of 97.23% and 98.33% respectively. Note the majority of the structures are made by young and adults and rarely by juveniles (example Figure 4 E, G). Also note that pellet design at the earlier stage of development has lower safety index (SI) than those in the advanced or final stage of development (SI 70.57% for Figure C vs. 100% for Figure 4 O and S). Note that structures with closed burrow opening have SI value 100% (Figure 4 G and M). Compare size of the feeding territories between A, M, O (larger for the adults) vs E (smaller for the juvenile). Scale bar equals 1 cm.
FIGURE 6 in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India
FIGURE 6. Other pellet structures produced by the crab Dotilla on the upper intertidal flat of the Bakkhali beach, Bay of Bengal coast of Eastern India. (A) Petaloid pellet design produced by petal shaped radial rows of pellets and conjugate petals formed around burrow opening. (B) The line tracing corresponding to A shows SI value 100% as the burrow mouth is closed. (C) Leaf-shaped pellet design and (D) its corresponding line tracing shows very poor SI value (13.89%). (E) Asteroid pellet design contains several radiating runways that are well enclosed within the pellet spread areas and (F) its corresponding line tracing shows 100% SI value. (G, J and K) Different stages of formation of pellet mat design in pellet – microzone 1 wherein entire surface is covered by dense population of pellets leaving no space for the predators to sneak into burrow opening (SI = 100%). Note high population density and small size of the pellet designs. (H) Mossy pellet design formed by the crab community. Several burrow openings and corresponding runways are partially to fully covered by pellet spread zones. (I) Line tracing shows variable SI values of the individual structures (marked here by red, yellow and green circles having SI values <70%, 70% - 90% and> 90% respectively) averaged at 85% for the community structure. Arrows indicate possible entry routes of predators into the burrows. (L and M) Concentric radial and concentric pellet structures formed on rippled surface. (N) At times, pellets are formed selectively along the ripple troughs. (O) Beach profile showing extends of lower, middle and upper intertidal flats, besides mudground, supratidal flat and coastal dunes. Note smaller size of the structures (G, H, J, K) due to increased population density and predation pressure.
FIGURE 2 in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India
FIGURE 2. Radial pellet structures (A, C, E, G, I and K) produced by the crab Dotilla in the upper intertidal beach of Bakkhali, Eastern India. Corresponding line tracings (B, D, F, H, J and L) are made to calculate Safety Index (SI) and Attack Index (AI). Structures represented by figures I and K suggest early stage of development of radial pellet design and possess lower Safety Index (SI = 61.53% and 46.41%, respectively) compared to other structures (A, C, E and G) that represent later stage of development of radial design and possess very high Safety Index (SI ranging from 100% to 94.74%). Figure GLeft represents a juvenile structure and the rest are produced by young and adult Dotilla. Note larger size of feeding areas made by adults (A, E, K) compared to that of juvenile (GLeft). A represents a more advanced feeding stage (over larger area) than I (over smaller area). Scale bar equals 1 cm.
FIGURE 1 in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India
FIGURE 1. Different ichnozones and geomorphic features developed in the Bakkhali (21° 33' 50" N and 88° 15' 49" E) beach of the Bay of Bengal coast, Eastern India (re-mapped in 2015 by the author and modified after De, 2019, 2000). Note field photographs of the pellet making bubbler crabs Dotilla spp. and their burrow casts.
FIGURE 5 in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India
FIGURE 5. Plan outlays for the radial, concentric and concentric-radial pellet designs produced by the bubbler crab Dotilla have been drawn from the corresponding line tracings (as referenced in each case) to highlight how structural elements are constructed to enhance burrow protection. For radial designs dense radial rows of pellets (Rrp), curved rings of pellets (Crp), pellet walls (Pw) and turned around pellet rows (Rta) are increasingly added to the structure to increase the Safety Index (SI) by closing or cutting off the probable routes of entry of the predators into the burrow openings. Note plan outlays A to D depicting gradual increase in SI values from 46.41% to 100%. Plan outlays (F. H, J, L, N and P) corresponding to the concentric pellet designs show that addition of concentrically oriented curved rings of pellets (Crp) and formation of clockwise and anticlockwise closures of the pellet rings (Cpr marked by red lines) are two basic measures taken by the crabs to enhance SI (compare the plan outlays from E to J where SI values have improved from 68.39% to 98.06%). Note that for concentric-radial designs, as displayed by the plan outlays (R, T, V and X), all the above measures, besides formation of outgoing radial pellet rows from curved rings of pellets (Crp) that act as innumerable barriers for the predators to sneak through spaces between curved rings of pellets, are taken to improve SI values (compare 70.57% for Q to 100% for W).
FIGURE 3 in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India
FIGURE 3. Concentric pellet design (A, C, E, G, I, K, M, O, Q, S, U and W) produced by the crab Dotilla in the upper intertidal flat of the Bakkhali beach, Bay of Bengal, Eastern India. Figures B, D, F, H. J. L, N P, R, T, V and X represent the corresponding line tracings drawn for measurement of Attack Index (AI) and Safety Index (SI). Note formation of both clockwise and anticlockwise closures of pellet rings (Cpr), pellet walls (Pw), surface foraged (Sf), open and closed burrow openings (Obo and Cbo respectively) and curved rings of pellets (Crp). Figures L, R Left and Middle, VTop and Q correspond to concentric designs at early to middle stages of formation and possess relatively lower SI values (67.39%, 88.34%, 87.23%, 72.51% and 84.73% respectively) than the other nearly fully developed structures (SI varying between 98.06% for d to 91.04% for j). Compare size of the feeding territory between Figure I (larger for the adult) and U (smaller for the juvenile). Note SI attains 100% value for pellet designs having closed burrow opening (Cbo). Arrow heads in line tracing Figures point to possible entry routes of predators or enemies of Dotilla. Scale bar equals 1 cm.
Fig. 8 in Haemoprotozoa: Making biological sense of molecular phylogenies
Fig. 8. Phenotypic characters mapped against broad molecular phylogenies of haemosporidian parasites. Molecular phylogenetic relationships are indicated on the left as a consensus (macro-evolutionary) tree derived from multiple studies cited within the text.
Fig. 7 in Haemoprotozoa: Making biological sense of molecular phylogenies
Fig. 7. Phenotypic characters mapped against broad molecular phylogenies of haemogregarine parasites. Molecular phylogenetic relationships are indicated on the left as a consensus (macro-evolutionary) tree derived from multiple studies cited within the text.
Fig. 6 in Haemoprotozoa: Making biological sense of molecular phylogenies
Fig. 6. Phenotypic characters mapped against broad molecular phylogenies of haemococcidian parasites (blood-borne genera shown in red). Molecular phylogenetic relationships are indicated on the left as a consensus (macro-evolutionary) tree derived from multiple studies cited within the text. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig. 5 in Haemoprotozoa: Making biological sense of molecular phylogenies
Fig. 5. Developmental cycles and hosts for apicomplexan blood parasites (DH = definitive host; IH = intermediate host; PH = paratenic host; bm = blood meal; bmi = injected during blood meal; ve = vector eaten).
Fig. 3 in Haemoprotozoa: Making biological sense of molecular phylogenies
Fig. 3. Developmental stages formed by kinetoplastid flagellates (blood-borne genera shown in red). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig. 2 in Haemoprotozoa: Making biological sense of molecular phylogenies
Fig. 2. Geological time periods with milestones in the development of life on Earth, together with historical extent of fossil records for particular assemblages.
Fig. 10 in Haemoprotozoa: Making biological sense of molecular phylogenies
Fig. 10. Probable evolutionary origins of haemoprotozoan parasites (solid lines = strong inferential support; dotted lines = presumptive).
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.