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1,663 results for “BIAS”
Data from: A circuit mechanism for decision making biases and NMDA receptor hypofunction
<table> <tbody> <tr> <td>Decision-making biases can be features of normal behaviour, or deficits underlying neuropsychiatric symptoms. We used behavioural psychophysics, spiking-circuit modelling and pharmacological manipulations to explore decision-making biases during evidence integration. Monkeys showed a pro-variance bias (PVB): a preference to choose options with more variable evidence. The PVB was also present in a spiking circuit model, revealing a potential neural mechanism for this behaviour. To model possible effects of NMDA receptor (NMDA-R) antagonism on this behaviour, we simulated the effects of NMDA-R hypofunction onto either excitatory or inhibitory neurons in the model. These were then tested experimentally using the NMDA-R antagonist ketamine, a pharmacological model of schizophrenia. Ketamine yielded an increase in subjects' PVB consistent with lowered cortical excitation/inhibition balance from NMDA-R hypofunction predominantly onto excitatory neurons. These results provide a circuit-level mechanism that bridges across explanatory scales, from the synaptic to the behavioural, in neuropsychiatric disorders where decision-making biases are prominent.</td> </tr> <tr> </tr> </tbody> </table>
Psocodea Phylogenomic dataset from: Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): combining sequence data and Exploring compositional bias solutions in Next Generation Datasets
<p>This dataset includes all alignments used for the phylogenomic analysis of Psocodea. In this dataset, includes all result files of phylogenomic analyses completed. This includes maximum likelihood, astral, MCMCtree, quartet sampling, and all gene trees. Any relevant input files are included, and any materials are available upon request.</p> <p>The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.</p>
Raw fitness data (offspring number and weight), main dataset for manuscript: Female-specific resource limitation does not make the opportunity for selection more female biased
<p>The present dataset contains the entirety of the raw empirical data used in the manuscript entitled: "Female-specific resource limitation does not make the opportunity for selection more female biased". This data is composed of offspring count and weight, which represent proxys of fitness. Fitness was assessed for males and females independently, and across three different experimental treatments. These fitness measures are used to calculate the opportunity for selection, as the variance in realtive fitness. Detailed methods regarding data collection can be found in the main manuscript.</p>
WinoST: Evaluating Gender Bias in Speech Translation
<p>WinoST is a challenge set for evaluating gender bias in speech translation. WinoST is the speech version of WinoMT (Stanovsky et al., 2019) which is an MT challenge set and both follow an evaluation protocol to measure gender accuracy. WinoST consists of 3888 speech audios in English plus a text file with the the text of these audios. For further details, please refer to the publication entitled "Evaluating Gender Bias in Speech Translation" (Costa-jussà et al., 2020). Also cite this publication if using this corpus.</p>
Data from: Sampling beetle communities: trap design interacts with weather and species traits to bias capture rates
<p>Globally, many insect populations are declining, prompting calls for action. Yet these findings have also prompted discussion about sampling methods and interpretation of long-term datasets. As insect monitoring and research efforts increase, it is critical to quantify the effectiveness of sampling methods. This is especially true if sampling biases of different methods covary with climate, which is also changing over time. We assess the effectiveness of two types of flight intercept traps commonly used for beetles, a diverse insect group responsible for numerous ecosystem services, under different climatic conditions in Norwegian boreal forest. One of these trap designs includes a device to prevent rainwater from entering the collection vial, diluting preservatives and flushing out beetles. This design is compared to a standard trap. We ask how beetle capture rates vary between these traps, and how these differences vary based on precipitation levels and beetle body size, an important species trait. Bayesian mixed models reveal that the standard and modified traps differ in their beetle capture rates, but that the magnitude and direction of these differences change with precipitation levels and beetle body size. At low rainfall levels standard traps catch more beetles, but as precipitation increases the catch rates of modified traps overtake those of standard traps. This effect is most pronounced for large-bodied beetles. Sampling methods are known to differ in their effectiveness. Here, we present evidence for a less well-known but likely common phenomenon - an interaction between climate and sampling, such that relative effectiveness of trap types for beetle sampling differs depending on precipitation levels and species traits. This highlights a challenge for long-term monitoring programs, where both climate and insect populations are changing. Sampling methods should be sought that eliminate climate interactions, any biases should be quantified, and all insect datasets should include detailed methodological metadata.</p>
Figure S1. Tear break-up time value in hyaluronic acid (HA) group and non-HA group after excluding the source of publication bias
<p>Figure S1. Tear break-up time value in hyaluronic acid (HA) group and non-HA group after excluding the source of publication bias <br> </p>
The mycorrhizal community of the epiphytic orchid Thrixspermum japonicum is strongly biased toward a single Ceratobasidiaceae fungus, despite a wide range of fungal partners
<p>PREMISE: Orchids depend primarily on mycorrhizal fungi to obtain nutrients throughout their life cycle. Epiphytic orchids account for 69% of orchid diversity. The unstable availability of water and nutrients in their arboreal habitats often results in severe water and nutrient stresses. Consequently, mycorrhizal associations may be important for the survival of epiphytic orchids, but our understanding thereof remains limited. Here, we investigated the mycorrhizal community in a single epiphytic orchid species, using more samples than in any previous study.</p> <p>METHODS: We assessed the mycorrhizal communities of Thrixspermum japonicum, one of the most common epiphytic orchids in the temperate region of Japan. In total, 144 individuals were collected from 28 host tree species at 20 sites across 1300 km. The mycorrhizal fungi were identified based on nuclear ribosomal DNA internal transcribed spacer sequences and assigned operational taxonomic units (OTUs) based on 97% sequence similarity.</p> <p>RESULTS: We obtained 24 OTUs, of which 9 and 15 belonged to the Ceratobasidiaceae and Tulasnellaceae, respectively. These OTUs are widely distributed throughout the phylogenetic trees of the two fungal families. However, a single Ceratobasidiaceae OTU accounted for 49.7% of all fungal sequences and was predominant in samples from 15 host tree species and 12 sites.</p> <p>CONCLUSIONS: Our results imply that despite having a broad range of mycorrhizal partners, T. japonicum was predominantly associated with a single fungal taxon at most of the sites among the host-tree species investigated. These findings contribute to elucidating mycorrhizal symbiosis in epiphytic ha</p>
Male-biased sexual selection, but not sexual dichromatism, predicts speciation in birds
<p>Sexual selection is thought to shape phylogenetic diversity by affecting speciation or extinction rates. However, the net effect of sexual selection on diversification is hard to predict, because many of the hypothesised effects on speciation or extinction have opposing signs and uncertain magnitudes. Theoretical work also suggests that the net effect of sexual selection on diversification should depend strongly on ecological factors, though this prediction has seldom been tested. Here, we test whether variation in sexual selection can predict speciation and extinction rates across passerine birds (up to 5,812 species, covering most genera) and whether this relationship is mediated by environmental factors. Male-biased sexual selection, and specifically sexual size dimorphism, predicted two of the three measures of speciation rates that we examined. The link we observed between sexual selection and speciation was independent of environmental variability, though species with smaller ranges had higher speciation rates. There was no association between any proxies of sexual selection and extinction rate. Our findings support the view that male-biased sexual selection, as measured by frequent predictors of male-male competition, has shaped diversification in the largest radiation of birds.</p>
Large zero-bias peaks in InSb-Al hybrid semiconductor-superconductor nanowire devices
<p>Measurement data, data processing scripts and figure generating notebooks for Zhang et al., "Large zero-bias peaks in InSb-Al hybrid semiconductor-superconductor nanowire devices".</p>
Data from: A hidden Markov model to identify and adjust for selection bias: an example involving mixed migration strategies
An important assumption in observational studies is that sampled individuals are representative of some larger study population. Yet, this assumption is often unrealistic. Notable examples include online public-opinion polls, publication biases associated with statistically significant results, and in ecology, telemetry studies with significant habitat-induced probabilities of missed locations. This problem can be overcome by modeling selection probabilities simultaneously with other predictor–response relationships or by weighting observations by inverse selection probabilities. We illustrate the problem and a solution when modeling mixed migration strategies of northern white-tailed deer (Odocoileus virginianus). Captures occur on winter yards where deer migrate in response to changing environmental conditions. Yet, not all deer migrate in all years, and captures during mild years are more likely to target deer that migrate every year (i.e., obligate migrators). Characterizing deer as conditional or obligate migrators is also challenging unless deer are observed for many years and under a variety of winter conditions. We developed a hidden Markov model where the probability of capture depends on each individual's migration strategy (conditional versus obligate migrator), a partially latent variable that depends on winter severity in the year of capture. In a 15-year study, involving 168 white-tailed deer, the estimated probability of migrating for conditional migrators increased nonlinearly with an index of winter severity. We estimated a higher proportion of obligates in the study cohort than in the population, except during a span of 3 years surrounding back-to-back severe winters. These results support the hypothesis that selection biases occur as a result of capturing deer on winter yards, with the magnitude of bias depending on the severity of winter weather. Hidden Markov models offer an attractive framework for addressing selection biases due to their ability to incorporate latent variables and model direct and indirect links between state variables and capture probabilities.
Data from: Sex-biased transcriptomic response of the reproductive axis to stress
Stress is a well-known cause of reproductive dysfunction in many species, including birds, rodents, and humans, though males and females may respond differently. A powerful way to investigate how stress affects re- production is by examining its effects on a biological system essential for regulating reproduction, the hy- pothalamic-pituitary-gonadal (HPG) axis. Often this is done by observing how a stressor affects the amount of glucocorticoids, such as cortisol or corticosterone, circulating in the blood and their relationship with a handful of known HPG-producing reproductive hormones, like testosterone and estradiol. Until now, we have lacked a full understanding of how stress affects all genomic activity of the HPG axis and how this might differ between the sexes. We leveraged a highly replicated and sex-balanced experimental approach to test how male and female rock doves (Columba livia) respond to stress at the level of their transcriptome. Females exhibit increased genomic responsiveness to stress at all levels of their HPG axis as compared to males, and these responsive genes are mostly unique to females. Reasons for this may be due to fluctuations in the female endocrine environment over the reproductive cycle and/or their evolutionary history, including parental investment and the potential for maternal effects. Direct links between genome to phenome cause and effect cannot be ascertained at this stage; however, the data we report provide a vital genomic foundation on which sex-specific reproductive dysfunction and adaptation in the face of stress can be further experimentally studied, as well as novel gene targets for genetic intervention and therapy investigations.
Data from: Architectural constraints, male fertility variation and biased floral morph ratios in tristylous populations
Tristyly is a genetic polymorphism in which populations are comprised of three floral morphs (mating types) differing reciprocally in sex-organ height. Intermorph (disassortative) mating governed by a trimorphic incompatibility system should result in 1:1:1 morph ratio at equilibrium, but both deterministic and stochastic processes can cause skewed morph ratios in tristylous populations. Here, we investigate mechanisms causing morph-ratio bias in Pontederia parviflora, an emergent aquatic native to tropical America. We compared reproductive traits among morphs and surveyed 71 populations to determine patterns of morph-ratio bias. We then used simulation models of morph-frequency dynamics to test the hypothesis that morph-specific differences in pollen production and their influence on male fertility can explain patterns of morph-ratio bias. Ninety-seven percent of populations that we sampled were tristylous, but with a significant excess of the short-styled morph and a deficiency of the long-styled morph. Atypically for a tristylous species, mid-level anthers of the short-styled morph produced over twice as much pollen compared with the corresponding anthers of the long-styled morph. Our computer models incorporating this difference in male fertility resulted in morph ratios not significantly different from the average frequencies from our survey suggesting that the short-styled morph is more successful than the long-styled morphs in siring ovules of the mid-styled morph. We propose that the difference in male fertility between morphs may be a non-adaptive consequence of a developmental constraint caused by the architecture of tristyly in Pontederiaceae.
Data from: Female-biased gape and body-size dimorphism in the New World watersnakes (tribe: Thamnophiini) oppose predictions from Rensch's Rule
Sexual size dimorphism (SSD) is ubiquitous across animals with female bias most prominent in snakes and other ectothermic organisms. To understand how SSD evolves across species, Rensch's Rule predicts that in taxa where males are larger, SSD increases with body size. In contrast, where females are larger, SSD decreases with body size. While this rule holds for many taxa, it may be ambiguous for others, particularly ectothermic vertebrates. Importantly, this rule suggests that the outcomes of SSD over phylogenetic time scales depends on the direction of dimorphism predicated on the difference in reproductive efforts between males and females. Here we examine SSD in the context of Rensch's Rule in Thamnophiini, the garter and waternsakes, a prominent group composing the North American snake biota. Using a dated phylogeny, measurements of gape, body and tail size, we show that these snakes do not follow Rensch's Rule, but rather female-biased SSD increases with body size. We in turn find that this allometry is most pronounced with gape and is correlated with both neonate and litter size, suggesting that acquiring prey of increased size may be directly related to fecundity selection. These changes in SSD are not constrained to any particular clade; we find no evidence of phylogenetic shifts in those traits showing SSD. We suggest several ways forward to better understand the anatomical units of selection for SSD and modularity
Data from: Slower senescence in a wild insect population in years with a more female-biased sex ratio
Life-history theories of senescence are based on the existence of a trade-off in resource allocation between body maintenance and reproduction. This putative trade-off means that environmental and demographic factors affecting the costs of reproduction should be associated with changes in patterns of senescence. In many species, competition among males is a major component of male reproductive investment, and hence variation in the sex ratio is expected to affect rates of senescence. We test this prediction using nine years of demographic and behavioural data from a wild population of the annual field cricket Gryllus campestris. Over these generations the sex ratio at adulthood varied substantially, from years with an equal number of each sex to years with twice as many females as males. Consistent with the predictions of theory, we found that in years with a greater proportion of females, both sexes experienced a slower increase in mortality rate with age. Additionally, phenotypic senescence in males was slower in years when there were more females. Sex ratio did not affect the baseline mortality rate in males, but females suffered higher age-independent mortality rates when males were in short supply.
Data from: Male-biased dispersal causes intersexual differences in the subpopulation structure of the gray-sided vole
The genetic structure of gray-sided voles was investigated at a spatial scale of 2 km using mtDNA sequences. The control region (674bp) of 162 voles was sequenced and 18 haplotypes were identified. Within 0.5-ha trapping plots (n = 8), the number of haplotypes and gene diversity was significantly greater in males than in females. The fixation index among plots for females (F GP = 0.241) was 3 times as large as that for males (0.075), implying male-biased dispersal. A simulation analysis showed that the observed genetic structure in males could be generated by modifying the observed haplotype distribution of females by adding the effects of local male dispersal. Half of the pairwise F GP (15/28) showed significant differentiation in females, whereas almost none (1/28) were significant in males. Isolation by distance was observed in females, whereas no clear spatial pattern was observed in males. Most pairwise F GP for females were not significant in the short- and intermediate-distance classes (≤1.0 km) as with those for males, whereas all showed significant differentiation in the long-distance class (>1.0 km) for females, but not for males. These findings indicate that the extent of subpopulations within which individuals interact differs between sexes.
Data from: Field measurements give biased estimates of functional response parameters, but help explain foraging distributions
1. Mechanistic insights and predictive understanding of the spatial distributions of foragers are typically derived by fitting either field measurements on intake rates and food abundance, or observations from controlled experiments, to functional response models. It has remained unclear, however, whether and why one approach should be favoured above the other, as direct comparative studies are rare. 2. The field measurements required to parameterize either single or multi-species functional response models are relatively easy to obtain, except at sites with low food densities and at places with high food densities, as the former will be avoided and the second will be rare. Also, in foragers facing a digestive bottleneck, intake rates (calculated over total time) will be constant over a wide range of food densities. In addition, interference effects may further depress intake rates. All of this hinders the appropriate estimation of parameters such as the 'instantaneous area of discovery' and the handling time, using a type II functional response model also known as 'Holling's disc equation'. 3. Here we compare field- and controlled experimental measurements of intake rate as a function of food abundance in female bar-tailed godwits Limosa lapponica feeding on lugworms Arenicola marina. 4. We show that a fit of the type II functional response model to field measurements predicts lower intake rates (about 2.5 times), longer handling times (about 4 times) and lower 'instantaneous areas of discovery' (about 30 to 70 times), compared with measurements from controlled experimental conditions. 5. In agreement with the assumptions of Holling's disc equation, under controlled experimental settings both the instantaneous area of discovery and handling time remained constant with an increase in food density. The field data, however, would lead us to conclude that although handling time remains constant, the instantaneous area of discovery decreased with increasing prey densities. This will result into highly underestimated sensory capacities when using field data. 6. Our results demonstrate that the elucidation of the fundamental mechanisms behind prey detection and prey processing capacities of a species necessitates measurements of functional response functions under the whole range of prey densities on solitary feeding individuals, which is only possible under controlled conditions. Field measurements yield 'consistency tests' of the distributional patterns in a specific ecological context.
Data from: Stimulus discriminability may bias value-based probabilistic learning
Reinforcement learning tasks are often used to assess participants' tendency to learn more from the positive or more from the negative consequences of one's action. However, this assessment often requires comparison in learning performance across different task conditions, which may differ in the relative salience or discriminability of the stimuli associated with more and less rewarding outcomes, respectively. To address this issue, in a first set of studies, participants were subjected to two versions of a common probabilistic learning task. The two versions differed with respect to the stimulus (Hiragana) characters associated with reward probability. The assignment of character to reward probability was fixed within version but reversed between versions. We found that performance was highly influenced by task version, which could be explained by the relative perceptual discriminability of characters assigned to high or low reward probabilities, as assessed by a separate discrimination experiment. Participants were more reliable in selecting rewarding characters that were more discriminable, leading to differences in learning curves and their sensitivity to reward probability. This difference in experienced reinforcement history was accompanied by performance biases in a test phase assessing ability to learn from positive vs. negative outcomes. In a subsequent large-scale web-based experiment, this impact of task version on learning and test measures was replicated and extended. Collectively, these findings imply a key role for perceptual factors in guiding reward learning and underscore the need to control stimulus discriminability when making inferences about individual differences in reinforcement learning.
Data from: Heterospecific aggression bias towards a rarer colour morph
Colour polymorphisms are a striking example of phenotypic diversity, yet the sources of selection that allow different morphs to persist within populations remain poorly understood. In particular, despite the importance of aggression in mediating social dominance, few studies have considered how heterospecific aggression might contribute to the maintenance or divergence of different colour morphs. To redress this gap, we carried out a field-based study in a Nicaraguan crater lake to investigate patterns of heterospecific aggression directed by the cichlid fish, Hypsophrys nicaraguensis, towards colour polymorphic cichlids in the genus Amphilophus. We found that H. nicaraguensis was the most frequent territorial neighbour of the colour polymorphic A. sagittae. Furthermore, when manipulating territorial intrusions using models, H. nicaraguensis were more aggressive towards the gold than dark colour morph of the sympatric Amphilophus species, including A. sagittae. Such a pattern of heterospecific aggression should be costly to the gold colour morph, potentially accounting for its lower than expected frequency and, more generally, highlighting the importance of considering heterospecific aggression in the context of morph frequencies and coexistence in the wild.
Data from: Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages
Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained under-explored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome, and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390 kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found (i) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, (ii) male-biased gene flow across continents and on phylogeographic time scales, and (iii) male dispersal that links the Alaskan ABC-islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be re-evaluated. Recent advances in sequencing technology render the analysis of Y chromosomal variation feasible, even in non-model organisms.
Data from: Pedigree error due to extra-pair reproduction substantially biases estimates of inbreeding depression
Understanding the evolutionary dynamics of inbreeding and inbreeding depression requires unbiased estimation of inbreeding depression across diverse mating systems. However, studies estimating inbreeding depression often measure inbreeding with error, for example, based on pedigree data derived from observed parental behavior that ignore paternity error stemming from multiple mating. Such paternity error causes error in estimated coefficients of inbreeding (f) and reproductive success and could bias estimates of inbreeding depression. We used complete "apparent" pedigree data compiled from observed parental behavior and analogous "actual" pedigree data comprising genetic parentage to quantify effects of paternity error stemming from extra-pair reproduction on estimates of f, reproductive success, and inbreeding depression in free-living song sparrows (Melospiza melodia). Paternity error caused widespread error in estimates of f and male reproductive success, causing inbreeding depression in male and female annual and lifetime reproductive success and juvenile male survival to be substantially underestimated. Conversely, inbreeding depression in adult male survival tended to be overestimated when paternity error was ignored. Pedigree error stemming from extra-pair reproduction therefore caused substantial and divergent bias in estimates of inbreeding depression that could bias tests of evolutionary theories regarding inbreeding and inbreeding depression and their links to variation in mating system.
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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.