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1,663 results for “BIAS”
How biases in sperm storage relate to sperm use during oviposition in female yellow dung flies
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Age and atitude: How longevity influences cognitive biases in honeybee workers
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Moss functional trait ecology: Trends, gaps, and biases in the current literature
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Common field data limitations can substantially bias sexual selection metrics
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Data from: Sea-surface temperature pattern effects have slowed global warming and biased warming-based constraints on climate sensitivity
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Simulated data for: The evolution of mating preferences for genetic attractiveness and quality in the presence of sensory bias
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Biogeography of the world’s worst invasive species has spatially-biased knowledge gaps but is predictable
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Data for: Mechanisms that can cause population decline under heavily skewed male-biased adult sex ratios
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A simple method to estimate capture height biases at landbird banding stations: opportunities and limitations
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Phylogenetic comparative methods are problematic when applied to gene trees with speciation and duplication nodes: correcting for biases in testing the ortholog conjecture
<p>This repository contains “manuscript_dunn.RData” file, which is reproduced by using the files and scripts of Dunn et al. (Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A (2018) Pairwise comparisons across species are problematic when analyzing functional genomic data. Proc Natl Acad Sci U S A 115: E409–E417. <a href="http://dx.doi.org/10.1073/pnas.1707515115">doi:10.1073/pnas.1707515115</a>).</p> <p>In this repository, we also supplied “Data_TMRR_latest.rda” file, containing the results generated by using our own scripts. Our scripts are available on GitHub: <a href="https://github.com/tbegum/Testing_the_ortholog_conjecture">https://github.com/tbegum/Testing_the_ortholog_conjecture</a>.</p> <p> </p>
MiRoR10 - P1 - Dataset A systematic review finds that spin or interpretation bias is abundant in evaluations of ovarian cancer biomarkers
<p>This dataset is related to "A systematic review finds that spin or interpretation bias is abundant in evaluations of ovarian cancer biomarkers" (Mona Ghannad, Maria Olsen, Isabelle Boutron, Patrick M. Bossuyt)</p>
A Skeptic's Guide to Open Science: Steven Novella on tackling biases, publication noise, and pseudoscience
<p><strong>Episode Summary: </strong></p> <p>Our guest this week is the influential skeptic Professor Steven Novella who is the producer and co-host of the very successful podcast A Skeptic's Guide to the Universe and author of a book by the same name. Novella is also an American clinical neurologist and assistant professor at Yale University School of Medicine. In this episode he talks to us about his views on how best to promote Open Science in medicine, the challenges of creating a new publication method, and the importance of communicating science to the public. </p> <p><strong>Links:</strong></p> <p><a href="https://www.theskepticsguide.org/podcasts">A Skeptic's Guide to the Universe Podcast</a></p> <p><a href="https://www.theskepticsguide.org/our-book">A Skeptic's Guide to the Universe: How to Know What’s Really Real in a World Increasingly Full of Fake Book</a></p> <p><em>Steven Novella:</em></p> <ul> <li><a href="https://twitter.com/stevennovella?lang=en">Twitter</a></li> <li><a href="https://medicine.yale.edu/neurology/people/steven_novella.profile">Yale Profile</a></li> </ul> <p><strong>Episode Quotes:</strong></p> <p>"They are uncomfortable with anything that is in and of itself pseudoscience because they think it taints them"</p> <p>"It doesn't really matter what you say your priorities are, your priorities are whatever it is that you promote people for"</p> <p>"We have an opportunity to completely rethink how we publish science"</p>
z-sh/fse20: Replication package for paper#133 - Gender Bias in Code Review
<p>The replication package for paper#133 - Gender Bias in Code Review written by Huang et. al.</p>
Bias Away - Background sequence repositories
<p>This repository contains all Background Sequences available for the following modules of our <a href="https://biasaway.uio.no/">BiasAway</a> web interface:</p> <ul> <li>Mononucleotide distribution matched (subcommand g in the command-line tool).</li> <li>Mononucleotide distribution within a sliding window (subcommand c in the command-line tool).</li> </ul> <p>For every organism, we provide background sequences with the following lengths: 100bp, 250bp, 500bp, 750bp and 1000bp. The genome assemblies used were:</p> <ul> <li>Homo sapiens: hg38.</li> <li>Mus musculus: mm10.</li> <li>Rattus norvegicus: Rnor_6.0.</li> <li>Arabidopsis thaliana: TAIR10.</li> <li>Danio rerio: GRCz11.</li> <li>Drosophila melanogaster: dm6.</li> <li>Caenorhabditis elegans: WBcel235.</li> <li>Saccharomyces cerevisiae: R64-1-1.</li> <li>Schizosaccharomyces pombe: ASM294v2.</li> </ul> <p>The code and necessary documentation to generate them can be found at our <a href="https://bitbucket.org/CBGR/biasaway_background_construction/src/master/">BitBucket repository</a>.</p> <p>The documentation for the BiasAway tool can be found at <a href="https://biasaway.readthedocs.io/en/latest/">readthedocs</a>.</p>
Data from: A quantitative review of density-dependent growth and survival in salmonids: biological mechanisms, methodological biases, and management implications
<p>Understanding the complex variation in patterns of density-dependent individual growth and survival across populations is critical to adaptive fisheries management, but the extent to which this variation is caused by biological or methodological differences is unclear. Consequently, we conducted a correlational meta-analysis of published literature to investigate the relative importance of methodological and biological predictors on the shape and strength of density-dependent individual growth and survival in salmonids. We obtained 160 effect sizes from 75 studies of 12 species conducted between 1977-2019 that differed in experimental approach (sensu Hurlbert, 1984; 65 laboratory experiments, 60 observational field studies, and 35 field experiments). The experimental approach was the strongest factor influencing the strength of density-dependence across studies: density-dependent survival was stronger than growth in field observational studies, whereas laboratory experiments detected stronger density-dependent growth than survival. The difference between density-dependent growth and survival was minimal in field experiments, and between lotic and lentic habitats. The shape of density-dependence (logarithmic, linear, exponential, or density-independent) could be predicted with 66.7% accuracy based solely on the experimental approach and the density gradient (highest/lowest*100) of the study. Overall, the strength and shape of density-dependence were primarily influenced by methodological predictors, while biological factors (predator presence, food abundance, and species) had predictable but modest effects. For both empirical studies and adaptive fisheries management, we recommend using field experiments with a density gradient of at least 460% to detect the proper shape of the density-dependent response, or accounting for potential biases if observational or laboratory studies are conducted.</p>
Data from: Aphid cards – useful model for assessing predation rates or bias prone nonsense?
Predation on pest organisms is an essential ecosystem function supporting yields in modern agriculture. However, assessing predation rates is intricate and they can rarely be linked directly to predator densities or functions. We tested whether sentinel prey aphid cards are useful tools to assess predation rates in the field. Therefore, we looked at aphid cards of different sizes on the ground level as well as within the vegetation. Additionally, by trapping ground dwelling predators, we examined whether obtained predation rates could be linked to predator densities and traits. Predation rates recorded with aphid cards were independent of aphid card size. However, predation rates on the ground level were three times higher than within the vegetation. We found both predatory carabid activity densities as well as community weighted mean body size to be good predictors for predation rates. Predation rates obtained from aphid cards are stable over card type and related to predator assemblages. Aphid cards therefore are a useful, efficient method for rapidly assessing the ecosystem function predation. Their use might especially be recommended for assessments on the ground level and when time and resource limitations rule out more elaborate sentinel prey methods using exclosures with living prey animals.
Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli
Abstract All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good, et al. 2017), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels, and mobile element insertions, due to the fixation of various hypermutator and antimutator alleles. One LTEE population, called Ara+3, shows a strong, symmetric wave pattern in its density of point mutations, radiating from the origin of replication. This pattern is largely missing from the other LTEE populations, most of which evolved missense, indel, or structural mutations in topA, fis, and dusB— loci that all affect DNA topology. The distribution of mutations in those genes over time suggests epistasis and historical contingency in the evolution of DNA topology, which may have in turn affected local mutation rates. Overall, the replicate populations of the LTEE have largely diverged in their mutation rates and biases, even though they have adapted to identical abiotic conditions.
Causes and consequences of an unusually male-biased adult sex ratio in an unmanaged feral horse population
<p>1. The adult sex ratio (ASR) is important within ecology due to its predicted effects on behaviour, demography, and evolution, but research examining the causes and consequences of ASR bias have lagged behind studies of sex ratios at earlier life stages. Although ungulate ASR is relatively well-studied, exceptions to the usual female-biased ASR challenge our understanding of the underlying drivers of biased ASR, and provide an opportunity to better understand its consequences.</p> <p>2. Some feral ungulate populations, including multiple horse populations, exhibit unusually male-biased ASR. For example, research suggests that the feral horse (Equus ferus caballus) population on Sable Island, Nova Scotia, Canada, may exhibit a male-biased ASR. Such exceptions to the rule provide a valuable opportunity to reveal the contributions of environmental context and trait differences to ASR bias.</p> <p>3. We aimed to test for bias in Sable Island horse ASR, identify the demographic drivers of bias, and explore its demographic and social consequences. To do this, we used life-history, movement, and group membership information for hundreds of horses followed through a long-term individual-based study between 2007 and 2018.</p> <p>4. Sable Island horse ASR is male-biased, and this skew has increased over time, reaching 62% male in 2018. Our life table response experiment suggested that ASR skew was driven predominantly by male-biased adult survival. Further analyses pointed to sex-biased survival being driven by reduced female survival post-reproduction. Male-biased ASR was associated with reduced harem sizes, an increase in the number of social groups on the island, and reduced reproduction in young females.</p> <p>5. Our results support the idea that male-biased ASR in feral ungulate populations may be caused by a combination of high population density and high reproductive output. We suggest that female-biased mortality may be caused by females continuing to reproduce at high density, and thus being more susceptible to resource shortages. Thus, our results highlight the strong context-dependence of ASR. Furthermore, our work indicates the potential for ASR to substantially alter a population's social organisation. Such changes in social structure could have knock-on consequences for demography by altering the formation/stability of social relationships, or competition for matings.</p>
The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements
<p>Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (<i>Helianthus annuus</i> L.), especially given its large genome size (∼3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain‐containing <i>Gypsy</i> LTR retrotransposons ('chromoviruses'), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.</p>
Data from: Aragonite bias exhibits systematic spatial variation in the late Cretaceous Western Interior Seaway, North America
Preferential dissolution of the biogenic carbonate polymorph aragonite promotes preservational bias in shelly marine faunas. Whilst field studies have documented the impact of preferential aragonite dissolution on fossil molluscan diversity, its impact on regional and global biodiversity metrics is debated. Epicontinental seas are especially prone to conditions which both promote and inhibit preferential dissolution, which may result in spatially extensive zones with variable preservation. Here we present a multi-faceted evaluation of aragonite dissolution within the late Cretaceous Western Interior Seaway of North America. Occurrence data of molluscs from two time intervals (Cenomanian-Turonian boundary, early Campanian) are plotted on new high-resolution paleogeographies to assess aragonite preservation within the seaway. Fossil occurrences, diversity estimates and sampling probabilities for calcitic and aragonitic fauna were compared in zones defined by depth and distance from the seaway margins. Apparent range sizes, which could be influenced by differential preservation potential of aragonite between separate localities, were also compared. Our results are consistent with exacerbated aragonite dissolution within specific depth zones for both time slices, with aragonitic bivalves additionally showing a statistically significant decrease in range size compared to calcitic fauna within carbonate-dominated Cenomanian-Turonian strata. However, we are unable to conclusively show that aragonite dissolution impacted diversity estimates. Therefore, whilst aragonite dissolution is likely to have affected the preservation of fauna in specific localities, time averaging and instantaneous preservation events preserve regional biodiversity. Our results suggest that the spatial expression of taphonomic biases should be an important consideration for paleontologists working on paleobiogeographic problems.
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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.