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7,742 results for “individuals”
Data of individual aerosol particle compositions using STEM-EDS
<p>Data set of aerosol particle compositions measured using scanning transmission electron microscopy with energy-dispersive X-ray spectroscopy (STEM-EDS) used in a paper by Adachi et al. TEM samples were collected during the Fire Influence on Regional to Global Environments and Air Quality (FIREX-AQ), the Biomass Burning Observation Project (BBOP), and the Megacity Initiative: Local and Global Research Observations (MILAGRO) campaigns. Here I show all EDS data and the sample average data measured using STEM-EDS.</p>
Data files for manuscript "Exome first approach to reduce diagnostic costs and time – retrospective analysis of 111 individuals with rare neurodevelopmental disorders"
<p>#2021-07-23<br> #Summary<br> This ZIP-file contains the Excel files used for the clinical and variant analyses for the manuscript "Exome first approach to reduce diagnostic costs and time – retrospective analysis of 111 individuals with rare neurodevelopmental disorders".</p> <p>#Folder structure<br> ./ (parent directory containing this README file and all subfolders)<br> ./Clinical/ (contains an Excel sheets with complete clinical data, costs and criteria)<br> ./Variants/ (contains an Excel sheet with all variant annotation)</p> <p>#Files and checksums<br> 6DB0EF10BE7A7AF5A18E523F33FB662A ./Clinical/FileS2_Clinical.xlsx<br> 0B0C1AFA0751B63A35DC99DB25546A38 ./Variants/FileS3_Variants.xlsx</p>
Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle
<p>Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. Whilst there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, there have been few GWAS for individual FT-MIR wavenumbers. Here we examine associations between genomic regions and individual FT-MIR wavenumber phenotypes within a population of 38,085 mixed-breed New Zealand dairy cattle with imputed whole-genome sequence. GWAS were conducted for each of 895 individual FT-MIR wavenumber phenotypes and three FT-MIR predicted milk composition traits, and gene annotation and mammary tissue gene expression datasets were employed to identify candidate causative genes and variants. This resulted in the identification of 38 co-locating, co-segregating expression QTL (eQTL), and 31 protein-sequence mutations for FT-MIR wavenumber phenotypes, the latter including a null mutation in <i>ABO</i> that has a potential role in changing milk oligosaccharide profiles. For the candidate causative genes implicated in these analyses, the strength of association between relevant loci and each wavenumber across the mid-infrared spectrum revealed shared association patterns for groups of genomically-distant loci, highlighting clusters of loci linked through their biological roles in lactation and their presumed impacts on the chemical composition of milk.</p>
A small vocal repertoire during the breeding season expresses complex behavioral motivations and individual signature in the Common Coot
<p><b>Backgroun</b><b>d:</b> Although acoustic communication plays an essential role in the social interactions of Rallidae, our knowledge of how Rallidae encode diverse types of information using simple vocalizations is limited. We recorded and examined the vocalizations of a Common Coot (<i>Fulica atra</i>) population during the breeding season to test the hypotheses that 1) different call types can be emitted under different behavioral contexts, and 2) variation in the vocal structure of a single call type may be influenced both by behavioral motivations and individual signature. We measured a total of 61 recordings of 30 adults while noting the behavioral activities in which individuals were engaged. We compared several acoustic parameters of the same call type emitted under different behavioral activities to determine how frequency and temporal parameters changed depending on behavioral motivations and individual differences.</p> <p><b>Results: </b>We found that adult Common Coots had a small vocal repertoire, including 4 types of call, composed of a single syllable that was used during 9 types of behaviors. The 4 calls significantly differed in both frequency and temporal parameters and can be clearly distinguished by discriminant function analysis. Minimum frequency of fundamental frequency (F<sub>0min</sub>) and duration of syllable (T) contributed the most to acoustic divergence between calls. Call <i>a</i> was the most commonly used (in 8 of the 9 behaviors detected), and maximum frequency of fundamental frequency (F<sub>0max</sub>) and interval of syllables (TI) contributed the most to variation in call <i>a</i>. Duration of syllable (T) in a single call <i>a</i> can vary with different behavioral motivations after individual vocal signature being controlled.</p> <p><b>Conclusions:</b> These results demonstrate that several call types of a small repertoire, and a single call with function-related changes in the temporal parameter in Common Coots could potentially indicate various behavioral motivations and individual signature. This study advances our knowledge of how Rallidae use "simple" vocal systems to express diverse motivations and provides new models for future studies on the role of vocalization in avian communication and behavior.</p>
Natural history of Lafora Disease: A Prognostic Systematic Review and Individual Participant Data Meta-Analysis (Dataset)
<p>Raw data used for statistical analysis of our paper "Natural history of Lafora Disease: A Prognostic Systematic Review and Individual Participant Data Meta-Analysis". </p>
Animal personality drives individual dietary specialisation across multiple dimensions in a mammalian herbivore
<p>1. Animal personality influences how individuals perceive and react to different stimuli, such as food quality and predation risk, thereby shaping foraging behaviour. As a consequence, animal personality is predicted to influence the diet and dietary specialisation of individuals within a population, but animal personality and dietary specialisation have yet to be linked.</p> <p>2. Here, we tested whether individual diet and dietary specialisation are a function of animal personality, using an arboreal herbivore, the common brushtail possum, as a model species. We hypothesised that pro-active individuals have more diverse foraging opportunities than reactive individuals. We therefore predicted that pro-active animals (more exploratory, bold and more active) would be less specialised, with a broader and higher-quality diet than their reactive counterparts. We quantified the personality traits and dietary niche using proportional similarity index and specialisation categories of possums (n = 30) in a population flanking native eucalypt woodland and residential gardens in suburban Sydney, Australia.</p> <p>3. We found that personality traits were related to the breadth and quality of the realised diets of individual possums. As predicted, proactive individuals had a broad, high-quality diet with less individual dietary specialisation than reactive individuals. Highly exploratory individuals had a more diverse diet than less exploratory individuals, and bold individuals were more likely than shy individuals to consume plants on the ground.</p> <p>4. Our study demonstrates an important link between animal personality and individual dietary specialisation. The finding that the personality of individuals is associated with different diet choices within the same landscape is fundamentally significant. First, personality as a driver of niche partitioning likely reduces within-species competition and hence could contribute to adaptive capacity. Second, the strength of ecological processes arising from interactions (e.g. predator-prey and plant-herbivore interactions) could differ among individuals according to their personality traits.</p> <p>5. Our findings are also relevant for effectively managing both threatened native, and invasive species. Management strategies will be improved by incorporating knowledge of individual traits and their ecological consequences, plus the ecological context of food- and fear-scapes.</p>
From individual to population level: Temperature and snow cover modulate fledging success through breeding phenology in Greylag geese (Anser anser)
<p>Local weather conditions may be used as environmental cues by animals to optimize their breeding behaviour, and could be affected by climate change. We measured associations between climate, breeding phenology, and reproductive output in greylag geese (<i>Anser anser</i>) across 29 years (1990-2018). The birds are individually marked, which allows accurate long-term monitoring of life-history parameters for all pairs within the flock. We had three aims: (1) identify climate patterns at a local scale in Upper Austria, (2) measure the association between climate and greylag goose breeding phenology, and (3) measure the relationship between climate and both clutch size and fledging success. Ambient temperature increased 2°C across the 29-years study period, and higher winter temperature was associated with earlier onset of egg-laying. Using the hatch-fledge ratio, average annual temperature was the strongest predictor for the proportion of fledged goslings per season. There is evidence for an optimum time window for egg-laying (the earliest and latest eggs laid had the lowest fledging success). These findings broaden our understanding of environmental effects and population-level shifts which could be associated with increased ambient temperature and can thus inform future research about the ecological consequences of climate changes and reproductive output in avian systems.</p>
Supplemental Material to Journal Article "Effect of individual blade pitch angle misalignment on the remaining useful life of wind turbines"
<p>This set supplements the figure data to the article "Effect of individual blade pitch angle misalignment on the remaining useful life of wind turbines", DOI: <a href="http://doi.org/10.5194/wes-6-1079-2021">10.5194/wes-6-1079-2021</a>.</p>
Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability
<p><span><strong>Background</strong>: </span>Variability is a hallmark of animal behavior. It contributes to survival by endowing individuals and populations with the capacity to adapt to ever-changing environmental conditions. Intra-individual variability is thought to reflect both endogenous and exogenous modulations of the neural dynamics of the central nervous system. However, how variability is internally regulated and modulated by external cues remains elusive. Here we address this question by analyzing the statistics of spontaneous exploration of freely swimming zebrafish larvae, and by probing how these locomotor patterns are impacted when changing the water temperatures within an ethologically relevant range.<br> <br> <span><strong>Results</strong>: </span>We show that, for this simple animal model, five short-term kinematic parameters - interbout interval, turn amplitude, travelled distance, turn probability and orientational flipping rate - together control the long-term exploratory dynamics. We establish that the bath temperature consistently impacts the means of these parameters, but leave their pairwise covariance unchanged. These results indicate that the temperature merely controls the sampling statistics within a well-defined kinematic space delineated by this robust statistical structure. At a given temperature, individual animals explore the behavioral space over a timescale of tens of minutes, suggestive of a slow internal state modulation that could be externally biased through the bath temperature. By combining these various observations into a minimal stochastic model of navigation, we show that this thermal modulation of locomotor kinematics results in a thermophobic behavior, complementing direct gradient-sensing mechanisms.<br> <br> <span><strong>Conclusions</strong>: </span>This study establishes the existence of a well-defined locomotor space accessible to zebrafish larvae during spontaneous exploration, and quantifies self-generated modulation of locomotor patterns. Intra-individual variability reflects a slow diffusive-like probing of this space by the animal. The bath temperature in turn restricts the sampling statistics to sub-regions, endowing the animal with basic thermophobicity. This study suggests that in Zebrafish, as well as in other ectothermic animals, ambient temperature could be used to efficiently manipulate internal states in a simple and ethological way.</p>
DMTA dataset. Detailed list of individual teeth from Cova de la Guineu
<p>Detailed list of individual teeth (N = 69) examined in this study. All teeth are lower left second molars (LLM2). DMTA analysis were performed on buccal (B), occlusal (O) or both (BO) enamel surfaces. Poor quality scans with obscured microwear features that were removed from study are indicated by dashes (-).</p>
Colorful traits in female birds relate to individual condition, reproductive performance, and male mate preferences: A meta-analytic approach dataset
<p>Colorful traits in females are suggested to have evolved and be maintained by sexual selection. Although several studies have evaluated this idea, support is still equivocal. <span><span>Evidence has been compiled in reviews, and a handful of quantitative synthesis have explored evidence of the link between condition and specific color traits in males and females. However, understanding the potential function of females' colorful traits in sexual communication has not been the primary focus of any of those previous studies</span></span><span>. </span>Here, using a meta-analytic approach, we find that evidence from empirical studies in birds supports the idea that colorful female ornaments are positively associated with residual mass and immune response, clutch size, and male-mate preferences. Hence, colorful traits in female birds likely evolved and are maintained by sexual selection.</p>
Individual-based networks reveal the highly skewed interactions of a frugivore mutualist with individual plants in a diverse community
<p>While plant-animal interactions occur fundamentally at the individual level, the bulk of research examining the mechanisms that drive interaction patterns has focused on the species or population level. In seed-dispersal mutualisms between frugivores and plants, little is known about the role of space and individual-level variation among plants in structuring patterns of frugivore foraging and, thus, seed dispersal in a plant community. Here we use an animal perspective to examine how space and variation between individual plants affect movement and visitation by frugivores foraging on individual fruiting plants. To do this, we used a spatially explicit network approach informed by observations of the movement and foraging of a frugivorous lemur species (Eulemur rubriventer) amongst individual plants in a diverse plant community in Madagascar. The resulting hierarchical networks, in which a few individual plants received the bulk of the interactions, demonstrated how a generalist frugivore species could act as an individual-plant specialist within a plant community. The few individual plants that dominated interactions with the lemurs shaped the modular spatial structure of frugivory interactions in the community and facilitated visitation to near neighbors. This interaction structure was primarily driven by extrinsic factors, as lemur movements among plants were significantly influenced by the individual plant's spatial position and the species richness of fruiting plants in its immediate neighborhood. Individual plants in central spatial locations, with a rich fruiting neighborhood and large fruit crops, received the most visits. The observed drastic inequality in the interactions of a generalist frugivore within a highly diverse plant community highlights the importance of considering individual-level variation for essential ecosystem processes, such as seed dispersal.</p>
FIGURE 2 in Scanning Electron Microscopy Vouchers And Genomic Data From An Individual Specimen: Maximizing The Utility Of Delicate And Rare Specimens
FIGURE 2: Image of agarose gel showing bright bands representing positive amplification of COI. A – Erythraeus sp; B – Trichosmaris sp; C – Raoiella indica; - negative control.
FIGURE 3 in Scanning Electron Microscopy Vouchers And Genomic Data From An Individual Specimen: Maximizing The Utility Of Delicate And Rare Specimens
FIGURE 3: Images (40X) of slide mounted Raoiella indica specimen (dorsal view on left, ventral view on right) after LTSEM imaging, DNA extraction, and KOH soak.
Tackling hepatocellular carcinoma with individual or combinatorial immunotherapy approaches
<p>Hepatocellular carcinoma (HCC) is the third leading cause of death from cancer globally. Indeed, there is a single drug approved as first-line systemic therapy in advanced unresectable HCC, providing a very limited survival benefit. In earlier stages, 5-year survival rates after surgical and loco-regional therapies are extremely variable depending on the stage of disease.</p> <p>Nevertheless, HCC is considered an immunogenic tumor arising in chronically inflamed livers. </p> <p>In such a scenario, immunotherapy strategies for HCC, in particular combinations including cancer vaccines, may represent a key therapeutic tool to improve clinical outcome in HCC patients. However, a lot of improvement is needed given the disappointing results obtained so far.</p>
Switch-like and persistent learning in individual Drosophila larvae
Associative learning allows animals to use past experience to predict future events. The circuits underlying memory formation support immediate and sustained changes in function, often in response to a single example. Larval Drosophila is a genetic model for memory formation that can be accessed at molecular, synaptic, cellular, and circuit levels, often simultaneously, but existing behavioral assays for larval learning and memory do not address individual animals, and it has been dicult to form long lasting memories, especially those requiring synaptic reorganization. We demonstrate a new assay for learning and memory capable of tracking the changing preferences of individual larvae. We use this assay to explore how activation of a pair of reward neurons changes the response to the innately aversive gas Carbon Dioxide (CO2). We conrm that when coupled to odor presentation in appropriate temporal sequence, optogenetic reward reduces avoidance of CO2. We nd that learning is switch-like: all-or-none and quantized in two states. Memories can be extinguished by repeated unrewarded exposure to CO2 but are stabilized against extinction by repeated training or overnight consolidation. Finally, we demonstrate long-lasting protein synthesis dependent and independent memory formation.
Diet DNA metabarcoding data from spiders (Heteropoda venatoria) from Palmyra Atoll (2015-2017) with both individual samples that have and have not been surface sterilized
<p>These are data and code from a study examining the potential for surface contamination to influence diet DNA metabarcoding datasets when DNA is sequenced from full body parts (in this case, the opisthosomas of spider individuals). These datasets include the raw sequencing data, all downstream datasets, and taxonomic assignments collected from database searches on BOLD and GenBank (accessed 2019). The code includes code to reproduce all bioinformatics (merge, filter, match to taxonomies, rarefy, sort) as well as all statistics and figures generated from analyses. Raw data are from DNA extractions of predator gut regions (opisthosomas) and amplification of the CO1 gene using PCR. The predator species is <em>Heteropoda venatoria </em>collected individually with sterilized implements and either the diet sequences from their natural diets were extracted or their diets following feeding spiders in a feeding trial. </p>
Extended data table 1: Taqman array card results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing.
<p>Data from study, protocol published at 10.5281/zenodo.5081880</p> <p><strong>Extended Data Table 1: TAC results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing. </strong>(BAL: bronchoalveolar lavage.) *Not included in validation numbers as duplicate at sub-species or genus level detection, **MecA was not included in validation numbers. TAC hits which did not pass the internal quality control standards required for reporting are indicated by (not reported). Samples which did not undergo sequencing indicated by <em>ND</em>. (✓) indicates low confidence hits from sequencing.</p>
Data for: Characterizing individual tree-level snags using airborne lidar-derived forest canopy gaps within closed-canopy conifer forests
<p><span>1. Airborne lidar is often used to calculate forest metrics about trees but it may also provide a wealth of information about the space between trees. Forest canopy gaps are defined by the absence of vegetative structure and serve important roles for wildlife, such as facilitating animal movement. Forest canopy gaps also occur around snags, keystone structures that provide important substrates to wildlife species for breeding, roosting, and foraging.</span></p> <p><span>2. We wanted to test a method for quantifying canopy gaps around individual snags and live trees, with the working hypothesis that snags would have more gaps surrounding them overall than live trees. We evaluated canopy gaps around individual snags (n=270) and live trees (n=2186) and evaluated correlations between canopy structure and snag occurrence in dense conifer stands of the Idaho Panhandle National Forest, USA. We paired airborne lidar with ground reference data collected at fixed-radius plots (n=53) to evaluate local gap structure. The R package ForestGapR was used to quantify canopy gaps throughout the canopy to determine where the differences were greatest. A canopy space profile was created for each tree by mapping gaps (a) vertically every 2 m in height (2–50 m above ground), and (b) horizontally across small (16 m<sup>2</sup>), medium (36 m<sup>2</sup>), and large (64 m<sup>2</sup>) footprint sizes.</span></p> <p><span>3. Our results suggest this method is robust for quantifying canopy gaps around individual trees. The canopy space profiles were distinctly different for snags and live trees, with more canopy gaps within the area surrounding snags relative to live trees. The greatest differences occurred at mid-canopy heights (~20 m above ground) and at the smallest footprint size (16 m<sup>2</sup>).</span></p> <p><span>4. These results show potential to improve understanding of gap dynamics in closed-canopy conifer forests, and we suggest snag modeling could be improved by incorporating lidar-derived canopy gap analyses alongside existing methodologies.</span></p>
melian009/Mispark: Preliminary analysis mutualistic networks in space, rarefaction, sierra size and sampling individuals, species, and traits
<p>Mutualistic networks in space, morphological traits and colors, or how to put all together to understand rare and common species in rapidly changing landscapes</p>
ScienceDex guides
Understand access before you commit
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.