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1,663 results for “BIAS”
Nonrandom missing data can bias PCA inference of population genetic structure
<p>Population genetic studies in non-model systems increasingly use next-generation sequencing to obtain more loci, but such methods also generate more missing data that may affect downstream analyses. Here we focus on the Principal Component Analysis (PCA) which has been widely used to explore and visualize population structure with mean-imputed missing data. We simulated data of different population models with various total missingness (1%, 10%, 20%) introduced either randomly or biased among individuals or populations. We found that individuals biased with missing data would be dragged away from their real population clusters to the origin of PCA plots, making them indistinguishable from true admixed individuals and potentially leading to misinterpreted population structure. We also generated empirical data of the big brown bat (<i>Eptesicus fuscus</i>) using restriction site-associated DNA sequencing (RADseq). We filtered three data sets with 19.12%, 9.87%, and 1.35% total missingness, all showing nonrandom missing data with biased individuals dragged towards the PCA origin, consistent with results from simulations. We highlight the importance of considering missing data effects on PCA in non-model systems where nonrandom missing data are common due to varying sample quality. To help detect missing data effects, we suggest to 1) plot PCA with a color gradient showing per sample missingness, 2) interpret samples close to the PCA origin with extra caution, 3) explore filtering parameters with and without the missingness-biased samples, and 4) use complementary analyses (e.g., model-based methods) to cross-validate PCA results and help interpret population structure.</p>
Data and analysis for "A process-conditioned and spatially consistent method for reducing systematic biases in modeled streamflow"
<p>This contains all of the necessary data and code to reproduce the results of the manuscript submitted to the Journal of</p> <p>Hydrometeorology entitled "A process-conditioned and spatially consistent method for reducing systematic biases in modeled streamflow"</p>
Fig. 1 in Female-Biased Dispersal Activity of the River-Shore Stag Beetle,Nicagus japonicusNagel (Coleoptera: Lucanidae), in a Disrupted Habitat
Fig. 1. The ecology and habitat of Nicagus japonicus. a) Female, b) Several N. japonicus on the ground; male and female beetles are indicated by blue and red arrows, respectively, c) Riverside habitat in the Kinugawa River tributary near Dorobu, Japan; in 2012, many N. japonicus were observed on the sandy area of the riverside, d) Habitat completely disrupted in 2013 and only a few N. japonicus were observed in this area, e) Larvae feeding inside driftwood in the laboratory; arrows indicate larval feces packed in the tunnels, f) Larva (arrow) tunneling in the sand and pupating in contact with the bottom of a plastic cage.
Fig. 2 in Female-Biased Dispersal Activity of the River-Shore Stag Beetle,Nicagus japonicusNagel (Coleoptera: Lucanidae), in a Disrupted Habitat
Fig. 2. Daily maximum temperature at the Dorobu Weather Station in 2012 and 2013. Arrows indicate the days of the field surveys.
Phylogenetic signal and bias in paleontology
<p>An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant<span> taxa with a high proportion of missing </span><span>morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation. </span></p>
The observed mass distribution of Galactic black hole LMXBs is biased against massive black holes
<p>Jupyter Notebook plus necessary data files to recreate the figures, the numbers reported, and a table in the publication.</p> <p>Also available at: <a href="http://arxiv.org/abs/2104.03596">http://arxiv.org/abs/2104.03596</a></p> <p> </p>
No evidence for female kin association, indications for extragroup paternity, and sex‐biased dispersal patterns in wild western gorillas
Characterizing animal dispersal patterns and the rational behind individuals' transfer choices is a long-standing question of interest in evolutionary biology. In wild western gorillas (Gorilla gorilla), a one-male polygynous species, previous genetic findings suggested that, when dispersing, females might favor groups with female kin to promote cooperation, resulting in higher-than-expected within-group female relatedness. The extent of male dispersal remains unclear with studies showing conflicting results. To investigate male and female dispersal patterns and extra-group paternity, we analyzed long-term field observations, including female spatial proximity data, together with genetic data (10 autosomal microsatellites) on individuals from a unique set of four habituated western gorilla groups, and four additional extra-group males (49 individuals in total). The majority of offspring (25 of 27) were sired by the group male. For two offspring, evidence for extra-group paternity was found. Contrarily to previous findings, adult females were not significantly more related within groups than across groups. Consistently, adult female relatedness within groups did not correlate with their spatial proximity inferred from behavioral data. Adult females were similarly related to adult males from their group than from other groups. Using RST statistics, we found significant genetic structure and a pattern of isolation by distance, indicating limited dispersal in this species. Comparing relatedness among females and among males revealed that males disperse farer than females, as expected in a polygamous species. Our study on habituated western gorillas shed light on the dispersal dynamics and reproductive behavior of this polygynous species and challenge some of the previous results based on unhabituated groups.
Supplementary File_Antibiotics_Risk of Bias Excel Tool (Version 1)
<p>Supplementary material (Risk of Bias Excel Tool (Version 1)) for the Cochrane Review "Antibiotics for the treatment of COVID-19".</p>
Supplementary File_Antibiotics_Risk of Bias Excel Tool (Version 1)
<p>Supplementary material (Risk of Bias Excel Tool (Version 1)) for the Cochrane Review "Antibiotics for the treatment of COVID-19".</p>
Large Andreev Bound State Zero Bias Peaks in a Weakly Dissipative Environment
<p>This repository contains the raw data and processing Python scripts corresponding to the paper "Large Andreev bound state zero bias peaks in a weakly dissipative environment"</p>
Data for "Majorana-like Coulomb spectroscopy in the absence of zero bias peaks"
<p>This repository contains experimental data, scripts used for the data analysis, scripts used for the numerical calculation and the microscopy analysis for the following paper: "Majorana-like Coulomb spectroscopy in the absence of zero bias peaks".</p> <p>Authors: Marco Valentini, Maksim Borovkov, Elsa Prada, Sara Marti-Sanchez , Marc Botifoll , Andrea Hofmann, Jordi Arbiol, Ramon Aguado, Pablo San-Jose, Georgios Katsaros.</p>
Supplementary FIles for Cholesterol Biases the Conformational Landscape of the Chemokine Receptor CCR3: A MAS SSNMR-Filtered Molecular Dynamics Study
<p>This repository contains supplementary files for the initial submission of:</p> <p>Cholesterol Biases the Conformational Landscape of the Chemokine Receptor CCR3: A MAS SSNMR-Filtered Molecular Dynamics Study<br> Evan J. van Aalst, Corey J. McDonald, and Benjamin J. Wylie</p> <p>Files found in this repository include:<br> 1. Raw fids corresponding to the solid-state NMR spectra used in this work.<br> 2. The script, model structures, and predicted chemical shifts used in the COMPASS proof of concept.<br> 3. Input molecular dynamics files derived from CHARMM-GUI including all mdp files, initial model structure files, and the production script.<br> 4. Model structures per ns derived from MD trajectories with corresponding predicted chemical shift lists and associated experimental chemical shift lists.</p>
Supplementary Information for "Biased Borate Esterification during Nucleoside Phosphorylase-Catalyzed Reactions: Apparent Equilibrium Shifts and Kinetic Implications"
<p>This is the external Supplementary Information for our publication "Biased Borate Esterification during Nucleoside Phosphorylase-Catalyzed Reactions: Apparent Equilibrium Shifts and Kinetic Implications".</p> <p>The .zip files contains the raw data and metadata for all items (supplementary and main text) as well as the calculation results. This includes UV, HPLC, NMR, DFT and MD results. This revised version presents extended DFT results (now including dispersion contributions) as well as additional NMR data (now including analytical data for isolated 1f, among other data).</p> <p>To some extent, this work builds on and borrows from our previous publications on spectral unmixing (https://doi.org/10.3390/mps2030060, https://doi.org/10.1002/cbic.202000204), continuous reaction monitoring (https://doi.org/10.1021/acs.analchem.1c05356), and thermodynamic reaction control (https://doi.org/10.1002/adsc.201901230, https://doi.org/10.5281/zenodo.3568858, https://doi.org/10.1002/cphc.202000901, https://doi.org/10.1021/acscatal.1c02589).</p>
ActTemp+sMSA dataset of "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"
<p>PDB models generated with the protocol described in "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"</p>
Microsatellite genotypes and associated data for: Tetrasporophyte bias coupled with heterozygote deficiency in Antarctic Plocamium sp. (Rhodophyta)
<p>Meiosis and syngamy generate an alternation between two ploidy stages, but the timing of these two processes varies widely across taxa, thereby generating life cycle diversity. One hypothesis suggests that life cycles with long-lived haploid stages are correlated with selfing, asexual reproduction, or both. Though mostly studied in angiosperms, selfing and asexual reproduction are often associated with marginal habitats. Yet, in haploid-diploid macroalgae, these two reproductive modes have subtle, but unique consequences whereby predictions from angiosperms may not apply. Along the western Antarctic Peninsula, there is a thriving macroalgal community, providing an opportunity to explore reproductive system variation in haploid-diploid macroalgae at high latitudes where endemism is common. <em>Plocamium </em>sp. is a widespread and abundant red macroalga found within this ecosystem. We sampled twelve sites during 2017 and 2018 field seasons and used ten microsatellite loci to describe the reproductive system. Overall genotypic richness and evenness were high, suggesting sexual reproduction. Eight sites were dominated by tetrasporophytes, but there was strong heterozygote deficiency, suggesting intergametophytic selfing. We found slight differences in the prevailing reproductive mode among sites, possibly due to local conditions (e.g., disturbance) that may contribute to site-specific variation. It remains to be determined whether high levels of selfing are characteristic of macroalgae more generally at high latitudes or due to the haploid-diploid life cycle. Further investigations of algal life cycles will likely reveal the processes underlying the maintenance of sexual reproduction more broadly across eukaryotes, but more studies of natural populations are required.</p>
Multi-model ensemble bias-corrected precipitation dataset for historical and future climate (1961–2099) in China
<p>本文基于耦合模式比较项目第六阶段(CMIP6)的27个全球气候模式(GCM),采用随机森林(RF)模型和EQM方法整合27个大气监测模型的降水模拟数据,进一步修正中国综合月降水数据。修正后的降水资料在月降水量和极端降水量方面均明显优于原GCM降水资料。数据以 GeoTIFF 格式,其中嵌入了具有 1° 空间分辨率的地理配准信息。LST在GeoTIFF中的单位是mm。压缩文件被命名为历史文件.zip、SSP126.zip、SSP245.zip 和 SSP585.zip。压缩文件中的每个文件都命名为“yyyymm.tif”,其中“yyyy”和“mm”分别表示年份和月份。例如,文件“196101.tif”存储了 1961 年 1 月中国每月降水量。</p>
Female-biased sex allocation and lack of inbreeding avoidance in Cubitermes termites
<p>Sexually-reproducing organisms face a strong selective pressure to find a mate and ensure reproduction. An important criterion during mate-selection is to avoid closely-related individuals and subsequent potential fitness costs of resulting inbred offspring. Inbreeding avoidance can be active through kin recognition during mate choice, or passive through differential male and female-biased sex ratios, which effectively prevents sib-mating. In addition, sex allocation, or the resources allotted to male and female offspring, can impact mating and reproductive success. Here, we investigate mate choice, sex ratios, and sex allocation in dispersing reproductives (alates) from colonies of the termite <i>Cubitermes</i> <i>tenuiceps</i>. Termites have a short time to select a mate for life, which should intensify any fitness consequences of inbreeding. However, alates did not actively avoid inbreeding through mate choice via kin recognition based on genetic or environmental cues. Furthermore, the majority of colonies exhibited a female-biased sex ratio, and none exhibited a male-bias, indicating that differential bias does not reduce inbreeding. Sex allocation was generally female-biased, as females also were heavier, but the potential fitness effect of this costly strategy remains unclear. The bacterium <i>Wolbachia</i>, known in other insects to parasitically distort sex allocation toward females, was present within all alates. While <i>Wolbachia</i> is commonly associated with termites, parasitism has yet to be demonstrated, warranting further study of the nature of the symbiosis. Both the apparent lack of inbreeding avoidance and potential maladaptive sex allocation implies possible negative effects on mating and fitness.</p>
FIGURE 2 in New records of riverweeds (Podostemaceae) from the tropical Andes (Ecuador and Colombia): getting our feet wet to bypass collection bias in Neotropical rivers
FIGURE 2. Map of tropical South America with past records (blue) and the records published in this study (black) of Lophogyne aeruginosa (triangles) and Tristicha trifaria (cross marks).
Biased gene introgression and adaptation in face of chloroplast capture in Aquilegia
<p><span>Chloroplast capture</span><span>, a phenomenon that can occur through interspecific hybridization and introgression, has been frequently suggested as an explanation for cytonuclear discordance in plants. In theory, the captured donor chloroplasts may not cooperate with the recipient nuclear genome, especially chloroplast-targeted nuclear genes. However, relatively few studies have documented the mechanisms of cytonuclear coevolution and its potential species differentiation and possible functional differences in the face of chloroplast capture. To explore this crucial question, we chose the <em>Aquilegia</em> genus, which is known for having minimal sterility among the species, and we inferred that <em>A</em>. <em>amurensis</em> captured the plastome of <em>A</em>. <em>parviflora</em> based on cytonuclear discordance and gene flow between these two species. We focused on the introgression region and its differentiation with closely related species, especially its composition in a chloroplast capture scenario. We found that nuclear genes encoding cytonuclear enzyme complexes or organelle localized (CECs) were significantly enriched in the introgression regions, indicating that the CEC genes of chloroplast donor species were selectively retained and displaced the original CEC genes in chloroplast receptor species due to cytonuclear interactions during introgression. Notably, the intrinsic factor of cytonuclear compatibility may have a higher degree of evolutionary distance for the introgressed CEC genes between <em>A</em>. <em>amurensis</em> and <em>A</em>. <em>parviflora</em>. Introgression from <em>A</em>. <em>parviflora</em> promotes the differentiation of <em>A</em>. <em>amurensis</em> and <em>A</em>. <em>japonica</em>. Furthermore, we found that one of the overrepresented gene ontology terms in these introgressed genes was terpene synthase activity (GO: 0010333) in which more than one-third of the genes were CEC genes, showing that <em>A</em>. <em>amurensis</em> had similar release patterns for terpenes in flowers of <em>A</em>. <em>parviflora</em> when compared with <em>A</em>. <em>japonica</em>.</span> <span>Altogether, this study helps to clarify the mechanisms of cytonuclear coevolution, species differentiation and functional differences in face of chloroplast capture and highlights a critical role of chloroplast capture in adaptation.</span></p>
Datasets for origins of Southern Ocean warm sea surface temperature bias in CMIP6 models
<p>Datasets for origins of Southern Ocean warm sea surface temperature bias in CMIP6 models</p>
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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.