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Table of Individual MMT Hectochelle Observations of the Triangulum II Field
<p>Complete table of observations of the Triangulum II dwarf galaxy from MMT Hectochelle used in Buttry et. al 2022</p>
Niche overlap in rodents increases with competition but not ecological opportunity: A role of inter-individual difference
<div> <p><span>Niche variation at population level mediates niche packing (i.e., patterns of species' spread within the niche space) and species coexistence at community level. Competition and ecological opportunity (resource diversity) are two of the main mechanisms underlying niche variation. Dense niche packing could occur through increased niche partitioning or increased niche overlap.</span></p> <p><span>In this study we used stable carbon and nitrogen isotope data of 635 individual rodents from 4 species across 9 sites in the montane region of a subtropical island to test the effects of competition and ecological opportunity on population isotope niche size, inter-individual niche difference within population, and inter-specific niche overlap within community.</span></p> <p><span>We used the Bayesian Standard Ellipse Area (SEAB, the ellipse area enclosed by carbon and nitrogen isotope values of organisms on a bi-plot) to estimate population niche size and inter-specific niche overlap. Inter-individual niche difference within population was quantified as isotopic divergence and isotopic uniqueness. We used rodent abundance (the number of unique individuals captured) to measure competition and plant isotope niche size (plant SEAB) to measure ecological opportunity.</span></p> <p><span>The rodents experienced competition as evidenced by a negative relationship between population change rate and conspecific abundance. Rodent population niche size increased with ecological opportunity but not competition. The inter-individual niche difference (isotopic uniqueness) increased with competition (inter-specific competition only) but not ecological opportunity. At community level, inter-specific niche overlap (herbivore—omnivore pair only) increased with competition (the combined abundance of the pair) but not ecological opportunity.</span></p> <p><span>This study demonstrated that isotope niche variation of the rodents could be hierarchically influenced by ecological opportunity and competition, with the former setting the limit of population niche size across communities and the latter shaping inter-individual niche difference and inter-specific niche overlap within communities. Under strong intra-specific competition and limited ecological opportunity for niche expansion, individuals may choose to increase their isotopic uniqueness from conspecifics at the cost of overlapping with heterospecifics of different trophic roles within the community niche space as overall competition increases. Denser niche packing of these rodent communities might be achieved through increased niche overlap.</span></p> </div>
Raw videos of the experiments performed with small groups of sheep (N=2,3 and 4 individuals).
<p>Here we upload the videos used to study the spontaneous and intermittent collective motion observed in small groups of sheep. We used groups of size N=2, 3 and 4 individuals. Details on the analysis can be found in DOI: 10.1038/s41567-022-01769-8 (published in Nature Physics).</p>
Replication package for "Teams and Individuals in Standard Auction Formats: Decision and Emotions"
<p>This is the replication package for the paper "Teams and Individuals in Standard Auction Formats: Decision and Emotions" by Maria Karmeliuk, Martin Kocher and Georg Schmidt, forthcoming in <em>Experimental Economics</em>.</p> <p>The package contains instructions and zTree code for running the laboratory experiment, as well as raw data from the experiment including the data from face recognition software FaceReader. It also contains Stata and R code for data cleaning, cleaned datasets and Stata code for replicating data analysis and statistics reported in the paper.</p>
Individual TLS tree clouds collected from both Alto Tajo and Cuellar in Spain.
<p>36 30 x 30 m plots across two sites in Spain were scanned using a Leica HDS6200 scanner (3.2mm resolution at 10 m) following a grid pattern (see Owen et al., 2021 for more details). All 16 scans were co-registered and individual trees segmented using a combination of treeseg (Burt et al. 2019) and manual extraction/refinement. Trees in this database have been zero-centred and downsampled to 5 cm for the purpose of classifying species using deep learning. Individual tree species ID (Quercus faginea, Quercus ilex, Pinus nigra, Pinus sylvestris and Pinus pinaster) were appended to each tree using a combination of field derived hand drawn stem maps and TLS derived stem maps. Whether a tree is a multi-stem or single-stem has also been included in the metadata file.</p> <p>Owen et al 2021 - https://doi.org/10.1111/1365-2745.13670</p>
Vesicular release probability sets the strength of individual Schaffer collateral synapses
<p>This repository contains the data used to generate the figures of the manuscript entitled 'Vesicular release probability sets the strength of individual Schaffer collateral synapses' and all the data used for the quantal analysis.</p>
Epidendrum radicans – x, y coordinates and genetic data of individuals within 5 focal populations
<p>Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (<em>N</em> = 690) of the terrestrial orchid, <em>Epidendrum radicans</em>, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (<em>N</em> = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (<em>H<sub>e</sub></em> = 0.092–0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from <em>in</em> <em>situ</em> reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).</p>
Text-fig. 11. Permian ichthyofaunas from the French Massif Central. Preliminary comparisons based on total accounts of individuals (see text for explanations). Sharks in green, Acanthodes sp. in yellow, Actinopterygians in blue, Dipnoi in white (not visible but present at Autun; see Tab. 1 for details). Each circle is proportional to the total number of specimens recovered. Permian outcrops in black. Hercynian basement indicated by vertical lines. Map modified from Gand and Durand (2006). in New Actinopterygians From The Permian Of The Brive Basin, And The Ichthyofaunas Of The French Massif Central
Text-fig. 11. Permian ichthyofaunas from the French Massif Central. Preliminary comparisons based on total accounts of individuals (see text for explanations). Sharks in green, Acanthodes sp. in yellow, Actinopterygians in blue, Dipnoi in white (not visible but present at Autun; see Tab. 1 for details). Each circle is proportional to the total number of specimens recovered. Permian outcrops in black. Hercynian basement indicated by vertical lines. Map modified from Gand and Durand (2006).
Text-fig. 4. Briveichthys chantepieorum gen. et sp. nov. a, b: photograph and drawing of the parasphenoid in dorsal view, GMC 15, whitened, scale bars 5 mm; c: maxillary plate in medial view with horizontal lamina along the ventral edge of the bone, segment of the lower jaw with assembly of large slender teeth of the inner row and coronoids with small teeth, GMC 15, whitened, scale bar 5 mm; d: detail of the sculpture on the maxilla and dentalosplenial, GMC 126, whitened, scale bar 5 mm; e: detail of the teeth of the inner and outer row and coronoids on the lower jaw, the frame delineates the area illustrated in (f) at higher magnification, GMC 15, scale bar 2 mm; f: microsculpture formed by elliptical proximo-distally elongated protuberances on the large conical teeth, GMC 15, scale bar 100 µm; g: small fringing fulcra tightly attached to the anterior edge of a lepidotrichium, individual fulcral scales are indicated by arrows, GMC 18, scale bar 2 mm. Abbreviation: bhf – bucco-hypophysial foramen, Cor – coronoids, cp – corpus parasphenoidis, De – dentalosplenial, hl – horizontal lamina, mc – pores of the mandibular sensory canal, Mx – maxilla, paa – processus ascendens anterior, pap – processus ascendens posterior. in New Actinopterygians From The Permian Of The Brive Basin, And The Ichthyofaunas Of The French Massif Central
Text-fig. 4. Briveichthys chantepieorum gen. et sp. nov. a, b: photograph and drawing of the parasphenoid in dorsal view, GMC 15, whitened, scale bars 5 mm; c: maxillary plate in medial view with horizontal lamina along the ventral edge of the bone, segment of the lower jaw with assembly of large slender teeth of the inner row and coronoids with small teeth, GMC 15, whitened, scale bar 5 mm; d: detail of the sculpture on the maxilla and dentalosplenial, GMC 126, whitened, scale bar 5 mm; e: detail of the teeth of the inner and outer row and coronoids on the lower jaw, the frame delineates the area illustrated in (f) at higher magnification, GMC 15, scale bar 2 mm; f: microsculpture formed by elliptical proximo-distally elongated protuberances on the large conical teeth, GMC 15, scale bar 100 µm; g: small fringing fulcra tightly attached to the anterior edge of a lepidotrichium, individual fulcral scales are indicated by arrows, GMC 18, scale bar 2 mm. Abbreviation: bhf – bucco-hypophysial foramen, Cor – coronoids, cp – corpus parasphenoidis, De – dentalosplenial, hl – horizontal lamina, mc – pores of the mandibular sensory canal, Mx – maxilla, paa – processus ascendens anterior, pap – processus ascendens posterior.
Albertosaurus libratus adult and youngster? Or two species? Drawn to the same scale, note that the smaller individual's teeth, which are partly covered by the lips, are absolutely larger than the bigger one's. On the side of the lower jaw, the bulge of the surangular bone typical of tyrannosaurs can clearly be seen. in Predatory Dinosaurs of the World
Albertosaurus libratus adult and youngster? Or two species? Drawn to the same scale, note that the smaller individual's teeth, which are partly covered by the lips, are absolutely larger than the bigger one's. On the side of the lower jaw, the bulge of the surangular bone typical of tyrannosaurs can clearly be seen.
Group-level trait and individual performance: the impact of in-nest activity on food recruitment in ants
<p>Dataset, R and Python scripts corresponding to the results displayed in the article "Group-level trait and individual performance: the impact of in-nest activity on food recruitment in ants".</p> <p>R script works in pair with all three .csv files.</p> <p>.txt files are example of output generated by the Python script that analyses a worker's path inside the nest.</p> <p>3 videos from the experiment are also available. They allow visualization of the setup as well as testing of Python scripts.</p>
UAV-derived cluster greenness and pathlength of individual trees collected at Marden Park, UK
<p>Inidivual tree cluster greenness (gcc) and pathlength used in the study "UAV-derived greenness and within-crown spatial patterning can detect ash dieback in individual trees".</p>
Data from: Digital twin mathematical models suggest individualized hemorrhagic shock resuscitation strategies
<p><strong>Background:</strong> Optimizing resuscitation to reduce inflammation and organ dysfunction following human trauma-associated hemorrhagic shock is a major clinical hurdle. This is limited by the short duration of pre-clinical studies and the sparsity of early data in the clinical setting.</p> <p><strong>Methods:</strong> We sought to bridge this gap by linking preclinical data in the porcine model with clinical data from patients from the Prospective, Observational, Multicenter, Major Trauma Transfusion (PROMMTT) study via a three-compartment ordinary differential equation model of inflammation and coagulation.</p> <p><strong>Results:</strong> The model accurately predicts physiologic, inflammatory, and laboratory measures in both the porcine model and patients, as well as the outcome and time of death in the PROMMTT cohort. Model simulation suggests that resuscitation with plasma and red blood cells outperformed resuscitation with crystalloid or plasma alone, and that earlier plasma resuscitation reduced injury severity and increased survival time.</p> <p><strong>Conclusions:</strong> This workflow may serve as a translational bridge from pre-clinical to clinical studies in trauma-associated hemorrhagic shock and other complex disease settings.</p>
Data from: Individual energetics scale up to community coexistence: Movement, metabolism and biodiversity dynamics in fragmented landscapes
<p>Unraveling the intricate mechanisms that govern community coexistence remains a daunting challenge, particularly amidst ongoing environmental change. To understand the response of individual animals to environmental change, physiology and individual metabolism are often studied. However, this perspective is currently largely lacking in community ecology. We argue that the integration of individual metabolism into community theory can offer new insights into coexistence. We present the first individual-based metabolic community model for a terrestrial mammal community to simulate energy dynamics and home range behavior in different environments. Using this model, we investigate how ecologically similar species coexist and maintain their energy balance under food competition. Only if individuals of different species are able to balance their incoming and outgoing energy over the long-term will they be able to coexist. After thoroughly testing and validating the model against real-world patterns such as of home range dynamics and field metabolic rates, we applied it as a case study to scenarios of habitat fragmentation - a widely discussed topic in biodiversity research. First, comparing single-species simulations with community simulations, we find that the effect of habitat fragmentation on populations is strongly context-dependent. While populations of species living alone in the landscape were mostly positively affected by fragmentation, the diversity of a community of species was highest under medium fragmentation scenarios. Under medium fragmentation, energy balance and reproductive investment were also most similar among species. We therefore suggest that similarity in energy balance among species promotes coexistence. We argue that energetics should be part of community ecology theory, as the relative energetic status and reproductive investment can reveal why and under what environmental conditions coexistence is likely to occur. As a result, landscapes can potentially be protected and designed to maximize coexistence. The metabolic community model presented here can be a promising tool to investigate other scenarios of environmental change or other species communities to further disentangle global change effects and preserve biodiversity.</p>
Figure 2 in Adaptations in wild radish (Raphanus raphanistrum) flowering time, Part 1: Individual-based modeling of a polygenic trait
Figure 2. The relationship between the number of semidominant larger M1 alleles and days to first flower (DFF), needed to model the long-day selections. Note that six smallereffect M2 genes will add another 0 to 18 days to DFF. If each M1 allele added the same amount in the long-day selections, the relationship would be linear.
Figure 1 in Adaptations in wild radish (Raphanus raphanistrum) flowering time, Part 1: Individual-based modeling of a polygenic trait
Figure 1. Goodness of fit of the modeled data (A) when compared with the recorded glasshouse data (B). Graphs show cumulative days to first flowering (DFF) adaptations in Raphanus raphanistrum populations as a result of repeated early and late days to flowering selection. In both graphs, the basal population is the black solid line in the center,the darker lines are the matched generations of early flowering (EF1, EF3, FE4,and EF5; colored orange), and late flowering (LF2 and LF3; colored purple), with and late flowering (LF2 and LF3),with the two unmatched generations (EF2 and LF2) shown in lighter tones.The far-left population (early flowering EF5) displays very little phenotypic variability, whereas the far-right population (late flowering 3) is very diverse.
AI Tool Use and Adoption in Software Development by Individuals and Organizations: A Grounded Theory Study
<div> <p>This data represents four artifacts from our research in studying what impacts AI adoption and use in SE. It includes our interview questions, the codebook with example quotes, survey questions, and table with the code to category generation.</p> <p>This page includes supplementary materials associated with our paper entitled "<span>AI Tool Use and Adoption in Software Development by </span><span>Individuals and Organizations: A Grounded Theory Study</span>".</p> </div>
Fig. 2 in Anticarsia gemmatalis nucleopolyhedrovirus from soybean crops in Tamaulipas, Mexico: diversity and insecticidal characteristics of individual variants and their co-occluded mixtures
Fig. 2. Mortality of second instar Anticarsia gemmatalis following inoculation with 2 × 105 occlusion bodies per mL of (A) genotypic variants compared with a mixture of 30 field isolates (30wt) and reference Brazilian variant AgMNPV-2D (Ag-2D), and (B) co-occluded mixtures of variants (M1–M4).
Fig. 4 in Anticarsia gemmatalis nucleopolyhedrovirus from soybean crops in Tamaulipas, Mexico: diversity and insecticidal characteristics of individual variants and their co-occluded mixtures
Fig. 4. Weibull estimates of mean time to death of fourth instar Anticarsia gemmatalis infected by (A) the individual genotypic variants compared with a mixture of 30 field isolates (30wt) and reference Brazilian variant AgMNPV-2D (Ag-2D) (shape parameter a = 6.776), and (B) co-occluded mixtures of variants (M1–M4) (shape parameter a = 7.509).
Fig. 1 in Anticarsia gemmatalis nucleopolyhedrovirus from soybean crops in Tamaulipas, Mexico: diversity and insecticidal characteristics of individual variants and their co-occluded mixtures
Fig. 1. (A) HindIII restriction endonuclease profiles of 5 individual genotypic variants (G1–G5) compared with a mixture of 30 field isolates (30wt) obtained from pooled field-collected larvae and the reference Brazilian variant AgMNPV-2D (Ag-2D). Arrows indicate the position of marker fragments for each of the variants. (B) Prevalence of plaque purified variants in pooled sample of 30 Anticarsia gemmatalis larvae that died from polyhedrosis during laboratory rearing (n indicates total number of plaques of each genotypic variant out of a total of 52 plaques).
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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.