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1,663 results for “BIAS”
Data from: When policy and psychology meet: mitigating the consequences of bias in schools
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Datasets for Age, Gender, and International Author Networks in the Earth and Space Sciences: Implications for Addressing Implicit Bias
<p>These files provide supplemental information and tabular data for figures in Hanson, Wooden, Lerback: Age, Gender, and International Author Networks in the Earth and Space Sciences: Implications for Addressing Implicit Bias, Submitted to Earth and Space Science.</p>
Abstractive Snippet Generation (query-biased anchor context)
<p>Abstractive Snippet Generation (query-biased anchor context)</p>
Data for "Molecular mechanism of biased signaling in a prototypical G protein–coupled receptor"
<p>Data and analysis code for "Molecular mechanism of biased signaling in a prototypical G protein–coupled receptor" (Suomivuori <em>et al.</em>, Science 367, 881–887 (2020)). See the included READMEs for more details. Please cite the paper if you use these data.</p>
Bias corrected climate projections from CMIP6 models for Indian sub-continental river basins
<p>Bias-corrected daily projections of precipitation, maximum temperature, and minimum temperature are developed using output from 13 CMIP6-GCMs for the 18 Indian sub-continental river basins. Spatial resolution of bias corrected projections is 0.25 deg. Each zipped basin file contains projections for 13 CMIP6-GCMs for five scenarios (historical, ssp126, ssp245, ssp370, and ssp585). Please see the readme file for further details.</p>
How biased is our perception of plant-pollinator networks? A comparison of visit- and pollen-based representations of the same networks
<p>These are the files (.txt) used to run the analyses in the paper "<em>How biased is our perception of plant-pollinator networks? A comparison of visit- and pollen-based representations of the same networks</em>" by de Manincor et al., 2020, Acta Oecologica, volume 105 (<a href="https://doi.org/10.1016/j.actao.2020.103551">https://doi.org/10.1016/j.actao.2020.103551</a>).</p> <p>The "netwoks_txt.zip" were used to run the motifs and positions analysis and the LBMs (+ alluvial).</p> <p>The "quilt.plot_txt.zip" were used to create the quiltplots (in the Supplementary materials of the paper).</p> <p>The "plant species list" provides information about the presence of plant species in the three sites/regions, and which species have been grouped at the genus level for the comparison between visits (obs) and pollen matrix.</p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>Most plant-pollinator networks are based on observations of contact between an insect and a flower in the field. Despite significant sampling efforts, some links are easier to report, while others remain unobserved. Therefore, visit-based networks represent a subsample of possible interactions in which the ignored part is variable. Pollen is a natural marker of insect visits to flowers. The identification of pollen found on insect bodies can be used as an alternative method to study plant-pollinator interactions, with a potentially lower risk of bias than the observation of visits, since it increases the number of interactions in the network. Here we compare plant-pollinator networks constructed (i) from direct observation of pollinator visits and (ii) from identification of pollen found<br> on the same insects. We focused on three calcareous grasslands in France, with different plant and pollinator species diversities. Since pollen identification always yields richer, more connected networks, we focused our comparisons on sampling bias at equal network connectance. To do so, we first compared network structures with an analysis of latent blocks and motifs. We then compared species roles between both types of networks with an analysis of specialization and species positions within motifs. Our results suggest that the sampling from observations of insect visits does not lead to the construction of a network intrinsically different from the one obtained using pollen found on insect bodies, at least when field sampling strives to be exhaustive. Most of the<br> significant differences are found at the species level, not at the network structure level, with singleton species accounting for a respectable fraction of these differences. Overall, this suggests that recording plant-pollinator interactions from pollinator visit observation does not provide a biased picture of the network structure, regardless of species richness; however, it provided less information on species roles than the pollen-based network.</p>
Simulated read data analysed in "Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph"
<p>Simulated read data analyzed in "Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph".</p> <p><strong>1) Human sequence data</strong></p> <p><strong>HO_chr11_50bp_sliding_window*fq.gz:</strong><br> All possible 50 bp reads overlapping chromosome 11 SNPs in the Human Origins dataset. Files with the word "alternate" in their filename carry the alternate allele, otherwise, they carry the reference allele. Deamination has been added into these simulated reads using gargammel (Renaud 2016) based on empirically estimated post-mortem damage in a dataset of 102 ancient genomes (Allentoft et al., 2015).</p> <p><strong>2) microbial data</strong></p> <p><strong>simulation_*_s.fq.gz:</strong><br> Simulated microbial read data from a set of microbial reference genomes identified in the ancient Clovis genome (Rasmussen 2014), using gargammel.</p>
High-resolution gridded climate data for Europe based on bias-corrected EURO-CORDEX: the ECLIPS-2.0 dataset
<p>We developed a new climate dataset for Europe referred to as ECLIPS (European CLimate Index ProjectionS), which contains gridded data for 80 annual, seasonal, and monthly climate variables for two past (1961-1990, 1991-2010) and five future periods (2011-2020, 2021-2140, 2041-2060, 2061-2080, 2081-2100). The future data are based on five Regional Climate Models (RCMs)driven by two greenhouse gas concentration scenarios, RCP 4.5 and 8.5.</p> <p>The ECLIPS dataset has two versions; ECLIPS 1.1 contains data with spatial resolution of 0.11° × 0.11°, which is the resolution of underlying RCMs. ECLIPS1.1 is available at <a href="https://doi.org/10.5281/zenodo.1181780">https://doi.org/10.5281/zenodo.1181780</a>.</p> <p>The ECLIPS 2.0 presented here contains a subset of climate indices of ECLIPS 1.1, downscaled to the resolution of 30 arcsec by means of the delta correction approach. Both ECLIPS versions were evaluated by testing their relationship with independent station data from the European Climate Assessment (ECA) dataset. Correlations of the empirical testing data to ECLIPS 1.1 ranged from 0.63 to 0.78,and to ECLIPS 2.0 from 0.78 to 0.93. suggesting substantial improvement due to downscaling. A large number of climate projections, time periods and indices as well as the availability of these data at two different spatial resolutions can support diverse studies across a range of disciplines and thus extend our understanding of climate-sensitive dynamics of many social-ecological systems</p> <p>The zipfile ECLIPS2.0 contains 5 folders with subfolders</p> <p>File naming system for the subfolders / folder are as follows</p> <p>ECLIPS2.0_196191: past climate 1961-1990: < climate index><period></p> <p>ECLIPS2.0_199110: past climate 1991-2010 < climate index><period></p> <p>ECLIPS2.0_45 : future climate RCP4.5 <subfolder-Model name> < climate index><period></p> <p>ECLIPS2.0_85 : future climate RCP8.5 <subfolder-Model name> < climate index><period></p> <p>Incase zpfile reader 7zip is not available, please install from here: <a href="https://www.7-zip.org/">https://www.7-zip.org/</a></p>
Data from: Sampling schemes and drift can bias admixture proportions inferred by STRUCTURE
<p><span>The interbreeding of individuals coming from genetically differentiated but incompletely isolated populations can lead to the formation of admixed populations, having important implications in ecology and evolution. In this simulation study, we evaluate how individual admixture proportions estimated by the software <span>structure</span> are quantitatively affected by different factors. Using various scenarios of admixture between two diverging populations, we found that unbalanced sampling from parental populations may seriously bias the inferred admixture proportions; moreover, proportionally large samples from the admixed population can also decrease the accuracy and precision of the inferences. As expected, weak differentiation between parental populations and drift after the admixture event strongly increase the biases caused by uneven sampling. We also show that admixture proportions are generally more biased when parental populations unequally contributed to the admixed population. Finally, with few exceptions, using a large number of markers reduces those biases, but using alternative priors for individual ancestry or the uncorrelated allele model only marginally affect the inference of admixture in most situations. We conclude that unbalanced sampling may cause important biases in the admixture proportions estimated by <span>structure</span>, especially when a small number of markers are used, and those biases can be worsened by the effect of drift and unequal genetic contribution of parental populations. Empirical studies should thus be careful with their sampling design and consider historical characteristics when using this software to estimate the ancestry of individuals from admixed populations.</span></p>
Conductance asymmetries in mesoscopic superconducting devices due to finite bias
<p>Dataset and code for publication "Conductance asymmetries in mesoscopic superconducting devices due to finite bias".</p>
Bias Corrected Climate Projections from CMIP6 Models for South Asia
<p>Bias-corrected data of precipitation, maximum temperature, and minimum temperature are developed for six countries in South Asia. Each zipped country file contains 13 models, and each model includes five scenarios (historical, ssp126, ssp245, ssp370, and ssp585). Inside a scenario folder, a file named PrecipData can be read as the first three columns from the 3rd row contain year month and day numbers. 1st two rows from the 3rd column represent the longitude and latitude.</p> <p>Separate ObservedData.zip file contains daily observed precipitation (mm), maximum temperature (deg C), and minimum temperature (deg C) data in each grid file.</p>
Data from: Context-dependent consequences of colour biases in a social fish
<p>Colourful visual signals can provide receivers with valuable information about food, danger, and the quality of social partners. However, the value of the information that colour provides varies depending on the situation, and colour may even act as a sensory trap where signals that evolved under one context are exploited in another. Despite some elegant early work on colour as a sensory trap, few empirical studies have examined how colour biases may vary depending on context and under which situations biases can be overridden. Here, using <i>Neolamprologus pulcher</i>, a highly social cichlid fish from Lake Tanganyika, we conducted a series of experiments to determine colour biases and investigate the effects of these biases under different contexts. We found that <i>N. pulcher</i> interacted the most with yellow items and the least with blue items. These biases were maintained during a foraging-based associative learning assay, with fish trained using yellow stimuli performing better than those trained using blue stimuli. However, these differences in learning performance did not extend to reversal learning; fish were equally capable of forming new associations regardless of the colour they were initially trained on. Finally, in a social choice assay, <i>N. pulcher</i> did not display a stronger preference for conspecifics whose yellow facial markings had been artificially enhanced. Together, these findings suggest that the influence of colour biases varies under different contexts and support the situational dependency of colour functions.</p>
Code and processed data accompanying "Widespread haploid-biased gene expression enables sperm-level natural selection"
<p>Code and processed data required to reproduce the analysis in "Widespread haploid-biased gene expression enables sperm-level natural selection".</p>
Exploring protocol bias in airway microbiome studies: One versus two PCR steps and 16S rRNA gene region V3 V4 versus V4
<p>Background: Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the impact of number of polymerase chain reaction (PCR) steps (1- or 2-steps) and choice of target marker gene region (V3 V4 and V4) on the presentation of the upper and lower airway microbiome. Our analyses included lllumina MiSeq sequencing following three setups: Setup 1 (2-step PCR; V3 V4 region), Setup 2 (2-step PCR; V4 region), Setup 3 (1-step PCR; V4 region). Samples included oral wash, protected specimen brushes and protected bronchoalveolar lavage (healthy and obstructive lung disease), and negative controls. Results: The number of sequences and amplicon sequence variants (ASV) decreased in order setup1>setup2>setup3. This trend appeared to be associated with an increased taxonomic resolution when sequencing the V3 V4 region (setup 1) and an increased number of small ASVs in setups 1 and 2. The latter was considered a result of contamination in the two-step PCR protocols as well as sequencing across multiple runs (setup 1). Although genera <i>Streptococcus</i>, <i>Prevotella</i>, <i>Veillonella</i> and <i>Rothia</i> dominated, differences in relative abundance were observed across all setups. Analyses of beta-diversity revealed that while oral wash samples (high biomass) clustered together regardless of number of PCR steps, samples from the lungs (low biomass) separated. The removal of contaminants identified using the Decontam package in R, did not resolve differences in results between sequencing setups. Conclusions: Differences in number of PCR steps will have an impact of final bacterial community descriptions, and more so for samples of low bacterial load. Our findings could not be explained by differences in contamination levels alone, and more research is needed to understand how variations in PCR-setups and reagents may be contributing to the observed protocol bias.</p>
The plot thickens: Haploid and triploid-like thalli, hybridization, and biased mating type ratios in Letharia
<p>The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex and symbiotic lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in <em>Letharia</em>. Here, we used genomic data from a pure culture and from thalli, together with a PCR survey of the MAT locus, to infer the genome organization and reproduction in <em>Letharia</em>. We found that the read count variation in the four <em>Letharia</em> specimens, including the pure culture derived from a single sexual spore of <em>L. lupina</em>, is consistent with haploidy. By contrast, the <em>L. lupina </em>read counts from a thallus' metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for <em>L. vulpina</em> and <em>L. lupina</em>, suggesting widespread sexual reproduction, but highly skewed in Europe for <em>L. vulpina</em>, consistent with predominant asexuality. Taken together, we propose that <em>Letharia</em> fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are rare hybrids between <em>L. lupina</em> and an unknown <em>Letharia</em> lineage, reconciling classic systematic and genetic studies with recent genomic observations.</p>
Supplementary material for: Long branch attraction biases in phylogenetics
<p>Long branch attraction is a prevalent form of bias in phylogenetic estimation but the reasons for it are only partially understood. We argue here that it is largely due to differences in the sizes of the model spaces corresponding to different trees. Trees with long branches together allow much more flexible internal branch-length parameter estimation. Consequently, although each tree has the same number of parameters, trees with long branches together have larger effective model spaces. The problem of long branch attraction becomes particularly pronounced with partitioned data. Formulation of tree estimation as model selection leads us to propose bootstrap bias corrections as cross-checks on estimation when long branches end up being estimated together. </p>
Macroevolution of flower color patterning: biased transition rates and correlated evolution with flower size
<p>Floral pigmentation patterns can both mediate plant-pollinator interactions and modify the abiotic environment of reproductive structures. To date there have been no inquiries into the rate and directionality of macroevolutionary transitions between patterned and non-patterned petals despite their ecological importance and ubiquity across angiosperms. Petals in the Potentilleae tribe (Rosaceae) display color patterns in the ultraviolet (UV) and human-visible spectrum, or can be uniform in color (i.e., patternless). Using a phylogeny of Potentilleae, I test whether evolutionary transition rates between patterned and non-patterned petals are biased in either direction. I then examine whether UV and human-visible patterns are phylogenetically correlated and test the prediction that color patterns will evolve in concert with larger flowers if they function as guides to orient pollinators to floral rewards. I found that transition rates were biased toward petals that were uniform in color. Transition rates from patterned to uniformly-colored petals were two and six times higher than the reverse for UV and human-visible pattern, respectively. The presence of UV and human-visible pattern evolved independently from one another. However, the evolution of human-visible pattern was associated with the evolution of larger flowers but the evolution of UV pattern was correlated with the evolution of smaller flowers. I posit that the transition bias towards non-patterned flowers may reflect developmental constraints on spatial regulation of pigments required to produce floral color patterning. The correlated evolution of larger flowers and human-visible pigmentation patterns support the hypothesis that nectar or pollen guides are more likely to evolve in larger-flowered species. This work provides insight into how transition rate bias and trait correlations can shape phylogenetic patterns of floral color pattern diversity.</p>
Data for: Female-biased sex ratios in urban centres create a fertility trap in post war Finland
<p>Because sex ratios are a key factor regulating mating success and subsequent fitness both across and within species, there is widespread interest in how population-wide sex ratio imbalances affect marriage markets and the formation of families in human societies. Although most modern cities have more women than men and suffer from low fertility rates, the effects of female-biased sex ratios have garnered less attention than male-biased ratios. Here, we analyze how sex ratios are linked to marriages, reproductive histories, dispersal and urbanization by taking advantage of a natural experiment in which an entire population was forcibly displaced during World War II to other local Finnish populations of varying sizes and sex ratios. Using a discrete time-event generalised linear mixed-effects model, and including factors that change across time, such as annual sex ratio, we show how sex ratios, reproduction, and migration are connected in a female-dominated environment. Young childless women migrated toward urban centers where work was available to women, and away from male-biased rural areas. In such areas where there were more females, women were less likely to start reproduction. Despite this constraint, women showed little flexibility in mate choice, with no evidence for an increase in partner age difference in female-biased areas. We propose that together these behaviours and conditions combine to generate an 'urban fertility trap' which may have important consequences for our understanding of the fertility dynamics of today including the current fertility decline across the developed world.</p>
Data from: Sexual selection on male size drives the evolution of male-biased sexual size dimorphism via the prolongation of male development
Sexual size dimorphism (SSD) arises when the net effects of natural and sexual selection on body size differ between the sexes. Quantitative SSD variation between taxa is common, but directional intraspecific SSD reversals are rare. We combined micro- and macroevolutionary approaches to study geographic SSD variation in closely related black scavenger flies. Common garden experiments revealed stark intra and interspecific variation: Sepsis biflexuosa is monomorphic across the Holarctic, while S. cynipsea (only in Europe) consistently exhibits female-biased SSD. Interestingly, S. neocynipsea displays contrasting SSD in Europe (females larger) and North America (males larger), a pattern opposite to the geographic reversal in SSD of S. punctum documented in a previous study. In accordance with the differential equilibrium model for the evolution of SSD, the intensity of sexual selection on male size varied between continents (weaker in Europe) whereas fecundity selection on female body size did not. Subsequent comparative analyses of 49 taxa documented at least six independent origins of male-biased SSD in Sepsidae, which is likely caused by sexual selection on male size and mediated by bimaturism. Therefore, reversals in SSD and the associated changes in larval development might be much more common and rapid and less constrained than currently assumed.
Data from: Palaeodiversity and formation counts: redundancy or bias?
A key question in palaeontology is whether the fossil record taken at face value is adequate to represent true patterns of diversity through time. Some methods of assessing data quality have depended on the commonly observed covariation of palaeodiversity and fossiliferous formation counts through time, based on the assumption that the count of formations containing fossils, to a greater or lesser extent, drives diversity; but what if diversity drives formations? Close study of two fossil records, early tetrapods (Devonian–Jurassic) and dinosaurs, shows how the relationship between new taxa and new fossiliferous formations varies through research time. Initially, each new find represents a new fossiliferous formation and discovery follows the 'bonanza' model (fossils drive formations). In unexplored parts of the world, new taxa are identified frequently in new regions/formations. Only after time, in well-explored continents such as Europe and North America, does collecting style switch to a mix of exploration for new formations and re-sampling of known fossiliferous formations. Data are most striking for dinosaurs, where the Triassic–Jurassic record largely comprises finds from Europe and North America, where new formation discoveries reached their half-life in 1914. This contrasts with the Cretaceous, which is dominated by rapidly rising discoveries from regions outside Europe and North America and the formation half-life for these 'new' lands is 1986, showing that 50% of new Cretaceous dinosaur-bearing formations were identified only in the past 30 years. The relationship between dinosaur-bearing formations and palaeodiversity then combines three signals in variable amounts, reflecting the original diversity (relative abundances of particular taxa in different formations), redundancy (new fossiliferous formations accruing because of new fossil finds) and sampling (intensity of exploration for new fossiliferous formations, and of search within already-sampled formations). For fossil vertebrates at least, formation counts of various kinds are poor predictors of sampling, missing, for example, the bonanza samples of Lagerstätten such as the Yixian Formation in China: thousands of specimens, dozens of species, but counted as one formation. These observations suggest that formation count cannot be regarded as an unbiased metric of sampling.
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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.