Find research datasets worth reusing

opencc-by-4.0Feb 2023View details →

3D cloud effect bcXCO2 biases

These data files are associated with the AMT paper "Insights into 3D cloud radiative transfer effects for OCO-2" by Massie, Cronk, Merrelli, Schmidt, and Mauceri

opencc-zeroFeb 2023View details →

Data for: Sex-biased infections scale to population impacts for an emerging wildlife disease

Demographic factors are fundamental in shaping infectious disease dynamics. Aspects of populations that create structure, like age and sex, can affect patterns of transmission, infection intensity and population outcomes. However, studies rarely link these processes from individual to population-scale effects. Moreover, the mechanisms underlying demographic differences in disease are frequently unclear. Here, we explore sex-biased infections for a multi-host fungal disease of bats, white-nose syndrome, and link disease-associated mortality between sexes, the distortion of sex ratios, and the potential mechanisms underlying sex differences in infection. We collected data on host traits, infection intensity, and survival of five bat species at 42 sites across seven years. We found females were more infected than males for all five species. Females also had lower apparent survival over winter and accounted for a smaller proportion of populations over time. Notably, female-biased infections were evident by early hibernation and likely driven by sex-based differences in autumn mating behavior. Male bats were more active during autumn which likely reduced replication of the cool-growing fungus. Higher disease impacts in female bats may have cascading effects on bat populations beyond the hibernation season by limiting recruitment and increasing the risk of Allee effects.

opencc-zeroMar 2023View details →

Data from: Quantifying neighbour effects on tree growth: are common "competition" indices biased?

1. Interactions among neighbouring plants are key determinants of plant growth. To characterise the cumulative effect of all neighbours on the growth of a focal plant, neighbourhoods are often described by 'competition' indices. Common competition indices calculate the summed size of neighbour plants (focal-independent index) whilst others include the summed ratio of the neighbour size relative to focal plant size (focal-dependent). A frequently overlooked statistical artifact is that focal-dependent indices may lead to biased estimates of neighbourhood effects on plant growth when growth is size-dependent. 2. Here, we conduct a literature search to determine the most common index types used to explain neighbour effects on tree growth. We then assess the ability of two common index types – focal-dependent and focal-independent – to correctly infer neighbourhood effects in (1) observations of tree growth in an experimental forest in south-east Tasmania, Australia, and (2) an artificially created dataset where tree growth is unrelated to the neighbourhood. 3. Both indices detected the competitive neighbourhood effect on tree growth observed in our own dataset but differed in their conclusion regarding neighbour effects in the simulated data. Despite the simulated dataset being generated so there was no relationship between tree growth and their neighbourhood, the focal-dependent index detected strong, competitive neighbourhood effects when intrinsic growth was incorrectly related to tree size. In contrast, when we considered the focal-independent index as the neighbourhood metric, we correctly did not detect any neighbourhood effects in the simulated data regardless of how size-dependent growth was described. 4. Synthesis. 'Competition' indices are a useful method to characterise the cumulative neighbourhood effect on plant growth, however, we demonstrate that indices which include the size of the focal plant in their calculation can be biased by an inherent relationship between tree growth and initial size. Whilst this bias typically overstates the strength of competition in determining focal tree growth, we show that it can be mitigated by correctly describing intrinsic growth. We discuss the limitations of both index types, provide recommendations for performing statistical modelling, and outline how to check for accurate neighbour inference.

opencc-by-4.0Aug 2022View details →

DATA for Exploration of O-GlcNAc-transferase (OGT) glycosylation sites reveals a target sequence compositional bias

Mass spectrometry data for identification of glycosylation sites in CBP ID3 and EWS LCRn Perl based implementation of glycosylation Site Predictor OGTcomPred

opencc-by-4.0May 2023View details →

Review data for: SnowQM 1.0: A fast R Package for bias-correcting spatial fields of snow water equivalent using quantile mapping

Climatology of snow water equivalent of Switzerland between winters 1962 and 2021. Obtained using quartile mapping between a model using data assimilation since 1998 and a model without data assimilation. This version of the dataset corresponds to the publication revision time. The publication has been submitted to GMD Copernicus journal as: SnowQM 1.0: A fast R Package for bias-correcting spatial fields of snow water equivalent using quantile mapping

opencc-by-4.0Dec 2022View details →

Dataset for "Bias correction and statistical modeling of variable oceanic forcing of Greenland outlet glaciers" by Verjans et al.

Code and data products associated with "Bias correction and statistical modeling of variable oceanic forcing of Greenland outlet glaciers" by Verjans V., Robel A., Thompson A. F., and Seroussi H. Please see readme file for all the information. Contact: vverjans3@gatech.edu Author: Vincent Verjans

opencc-by-4.0Jun 2023View details →

Table 2. Studies on psychiatric side effects of fluoroquinolones. The risk of bias and study quality assessed with the Effective Public Health Practice Project's Quality Assessment Tool for Quantitative Studies (QATQS) was presented as the global rating for each publication (3 – weak).

Studies on psychiatric side effects of fluoroquinolones. The risk of bias and study quality assessed with the Effective Public Health Practice Project’s Quality Assessment Tool for Quantitative Studies (QATQS) was presented as the global rating for each publication (3 – weak).

opencc-zeroJun 2023View details →

Data for: Mechanisms that can cause population decline under heavily skewed male-biased adult sex ratios

<ol> <li>While adult sex ratio (ASR) is a crucial component for population management, there is still a limited understanding of how its fluctuation affects population dynamics. To demonstrate mechanisms that hinder population growth under a biased ASR, we examined changes in reproductive success with ASR using a decapod crustacean exposed to female-selective harvesting. </li> <li> We examined the effect of ASR on the spawning success of females. A laboratory experiment showed that the number of eggs carried by females decreased as the proportion of males in the mating groups increased. Although the same result was not observed in data collected over 25 years in the wild, the negative effect of ASR was suggested when success in carrying eggs was considered as a spawning success. These results indicate that a surplus of males results in females failing to carry eggs, probably due to sexual coercion, and the negative effect of ASR can be detected at the population level only when the bias increases because failure in spawning success occurs in part of population. </li> <li>We experimentally examined how male-biased sex ratios affected the maintenance of genetic diversity in a population. The diversity of paternity in a clutch increased with the number of candidate fathers. However, over 50% of a clutch was fertilised by a single male regardless of the sex ratio, and the degree of diversity was less than half of the highest diversity expected in each mating group. </li> <li>We also experimentally examined the mating ability of males during the breeding season. The experiment showed that multiple mating by males could not compensate for the risk that their genotypes would be lost when multiple males competed for one female. These results suggest that a male-biased ASR could trigger a decline of genetic diversity in a population.</li> <li>We show that ASR skewed by female-selective harvesting decreases reproductive success not only of males that have few mating opportunities but also of females. We discuss that we may still underestimate the significance of ASR on population persistence due to the difficulty of revealing the effect of ASR.</li> </ol>

opencc-zeroJul 2023View details →

Direct and indirect estimates of dispersal support strong juvenile philopatry and male-biased dispersal in a freshwater turtle species (Emys orbicularis)

Dispersal has major impacts on population dynamics, population genetics and evolution and is also critical for population management and conservation. Dispersal is frequently sex- and age-specific, but current knowledge is strongly taxonomically biased toward birds and mammals. Here, we provide estimates of dispersal in a threatened freshwater turtle species, the European pond turtle Emys orbicularis. Based on 15 years of Capture-Mark-Recapture (CMR) monitoring and DNA samples from 194 individuals, we quantified both demographic and genetic dispersal between three sites separated by 1.5 to 3.5 km. We also investigated the effect of age and sex on dispersal. Overall, direct (CMR) and indirect (genetic) approaches provided consistent results showing that the studied sites are well connected with a flow of about one to three dozen migrants per generation. Dispersal was both age- and sex-biased in this species, with frequent dispersal of adult males and a strong philopatry of juveniles (of both sexes) and adult females. The strong philopatry of juveniles contrasts with the recurrent higher dispersal rate in young birds and mammals and shows the relevance of investigating dispersal in various taxonomic groups. Our results also provide useful information for the conservation of European pond turtle populations.

opencc-zeroJul 2023View details →

Data from: Shifts in mutation bias promote mutators by altering the distribution of fitness effects

Recent experimental evidence demonstrates that shifts in mutational biases, for example increases in transversion frequency, can change the distribution of fitness effects of mutations (DFE). In particular, reducing or reversing a prevailing bias can increase the probability that a de novo mutation is beneficial. It has also been shown that mutator bacteria are more likely to emerge if the beneficial mutations they generate have a larger effect-size than observed in the wildtype. Here, we connect these two results, demonstrating that mutator strains that reduce or reverse a prevailing bias have a positively-shifted DFE, which in turn can dramatically increase their emergence probability. Since changes in mutation rate and bias are often coupled through the gain and loss of DNA repair enzymes, our results predict that the invasion of mutator strains will be facilitated by shifts in mutation bias that offer improved access to previously under-sampled beneficial mutations.

opencc-by-4.0Jul 2023View details →

Toileting behaviours of the UK public: insights for reducing gender bias wastewater-based epidemiology sampling strategies

Cross-sectional survey results from a toileting behaviour survey conducted between the 27th to the 28th of June 2022. Participants (n = 2109) were aged 18 years or older and were living in the UK. The survey consisted of 17 closed-ended questions, with 7 of the questions addressing specific demographic topics and 10 questions addressed toileting behaviour. The questionnaire was designed by a team consisting of environmental microbiologists, public health specialists, wastewater-based epidemiologists, and social scientists, based on the study objectives and incorporating information from previous studies on the same topic.  First, self-report questions were asked on typical frequency of urination and defecation, followed by self-reports of frequency of urination and defecation at a variety of locations including at home, at work, educational buildings, transport hubs, and in public toilets. The comfort in urination/defecation at these locations for defecation and urination was also measured. Other questions about toileting behaviour and health monitoring were measured by statements with a 5-point Likert scale (e.g., strongly disagree to strongly agree).

openother-openJul 2023View details →

Most global gauging stations present biased estimations of total catchment discharge

This dataset includes the data generated for the main figures, the codes of the Mabcd model used to simulate catchment hydrological processes in this study, and the neural network model (NN2) trained to evaluate the Budyko parameter ω.

opencc-by-4.0Jul 2023View details →

Dataset for "Research Trend of Behavioral Bias in Financial Market: A Bibliometric Analysis "

Dataset for Bibliometric research

opencc-by-4.0Jul 2023View details →

Data for "The DESI One-Percent Survey: Evidence for Assembly Bias from Low-Redshift Counts-in-Cylinders Measurements"

Summary statistics, covariance matrices, and MCMC results for each of our HOD samples. For links to the original data catalogs and instructions to reproduce the analysis, see the README at: <a href="https://github.com/AlanPearl/galtab/tree/main/galtab/paper2/">https://github.com/AlanPearl/galtab/tree/main/galtab/paper2/</a> In brief, the desi_observations/desi_obs_*.npz files contain information about each threshold/redshift sample. Data is loaded via `obs_data = np.load(filename, allow_pickle=True)`, and all available fields can be shown via `obs_data.keys()`. Most importantly, our target data and its corresponding covariance matrix can be accessed with the "mean" and "cov" keys, respectively. These arrays can be sliced into our three observables using the slice objects accessed with the "slice_n", "slice_wp", and "slice_cic" keys. The emcee MCMC chains for each sample can be found under desi_results/results_*/emcee_backend.h5. To access the chain data (i.e., to construct corner plots of our HOD parameters), you can either follow our paper plot notebooks linked in the README above, or see the <a href="https://emcee.readthedocs.io/en/stable/">emcee documentation</a>.

UKCP18 RCM precipitation and temperature bias corrected using non-parametric quantile mapping method

The UKCP18 RCM PPE (Met Office Hadley Centre, 2018) projections of precipitation and daily average temperature were bias adjusted using a non-parametric quantile mapping method based on empirical quantiles (Boe et al, 2007, Gudmundsson et al, 2012). The datasets cover the period from December 1980 to November 2080 and are intended for use in climate change impact assessments, where the bias correction helps reduce biases in multiple statistics while maintaining projected climatic changes. ------------------------------------------------- Met Office Hadley Centre (2018): UKCP18 Regional Projections on a 12km grid over the UK for 1980-2080. CEDA, 8 March 2022. <a href="https://catalogue.ceda.ac.uk/uuid/589211abeb844070a95d061c8cc7f604">https://catalogue.ceda.ac.uk/uuid/589211abeb844070a95d061c8cc7f604</a> Boe, J.; Terray, L.; Habets, F. & Martin, E. Statistical and dynamical downscaling of the Seine basin climate for hydro-meteorological studies. International Journal of Climatology, 2007, 27, 1643-1655, doi: 10.1002/joc.1602. Gudmundsson, L.; Bremnes, J. B.; Haugen, J. E. & Engen-Skaugen, T. Technical Note: Downscaling RCM precipitation to the station scale using statistical transformations - a comparison of methods. Hydrology and Earth System Sciences, 2012, 16, 3383-3390, doi:10.5194/hess-16-3383-2012. Paper Citation: We kindly ask users of this dataset to cite the paper that describes the dataset. The paper is published and can be accessed via the following link: <a href="https://doi.org/10.5194/essd-17-2113-2025" target="_new" rel="noopener">https://doi.org/10.5194/essd-17-2113-2025</a>. Please reference the paper as: Reyniers, N., Zha, Q., Addor, N., Osborn, T. J., Forstenhäusler, N., and He, Y.: Two sets of bias-corrected regional UK Climate Projections 2018 (UKCP18) of temperature, precipitation and potential evapotranspiration for Great Britain, Earth Syst. Sci. Data, 17, 2113–2133, https://doi.org/10.5194/essd-17-2113-2025, 2025.

Correction of 4sU induced quantification bias of Spt6 data set

This data set contains the GRAND-SLAM output of the Spt6 data set (https://zenodo.org/record/4275956) after correcting the 4sU induced quantification bias using the correction approach described <a href="https://www.biorxiv.org/content/10.1101/2023.04.21.537786v1">here</a> and implemented in the <a href="https://www.nature.com/articles/s41467-023-39163-4">grandR package</a>. The zip file contains the full GRAND-SLAM output, the *.tsv.gz file is the GRAND-SLAM output table. The RData file contains the grandR object as analyzed in the original original Spt6 data set (see respective zenodo repository).

Risk of Bias 2 Data: Cochrane MHFA Systematic Review

These files contain detailed information about how the authors reached their Risk of Bias 2 judgements for results included in the Cochrane review 'MHFA as a tool for improving mental health and well-being'

opencc-zeroDec 2022View details →

Data from: Past population control biases interpretations of contemporary genetic data: implications for future invasive Sitka black-tailed deer management in Haida Gwaii

Invasive species management practices often include genetic analyses to better inform decision-making and resource allocation. Yet, past management actions may artificially bias recovered patterns of genetic variation; for example, a population bottleneck caused by contemporary culling may mirror some patterns associated with historical isolation. Here, we aimed to disentangle the impacts of past management activities from natural processes for Sitka black-tailed deer (Odocoileus hemionus sitkensis), an invasive species that has been repeatedly culled on two islands, SGang Gwaay and Reef, within the Haida Gwaii archipelago (Canada). We applied a recently developed Genotyping-in-Thousands by sequencing panel to contemporary (e.g., blood, serum, tissue, muscle, feces) and archived deer samples, the latter collected prior to management activity within the system (c. 1997–1998), which allowed us to contextualize conflicting patterns of isolation and connectivity previously observed on SGang Gwaay and Reef. Successful genotyping (92.6%) and population genetic analysis of 292 individuals at 236 SNPs revealed signals of historical isolation on SGang Gwaay and Reef, provided evidence of a founder effect during initial colonization, and indicated an absence of ongoing gene flow. Furthermore, our spatiotemporal analyses consistently supported a priori predictions associated with bottlenecks within post-cull populations, such as within-island loss of genetic variation, elevated within-island kinship, and increased levels of among-island genetic differentiation. These findings are promising for future management of deer on SGang Gwaay and Reef, suggesting that eradications on these islands may be durable. More broadly, our work highlights the importance of understanding management history before interpreting contemporary population genetic data.

opencc-zeroAug 2023View details →

Exotic success following disturbance explained by weak native resilience and ruderal exotic bias

<ol> <li>Disturbance is a primary driver of exotic plant invasions, but why disturbance commonly favors exotics over natives is unresolved.</li> <li>To address this question, we conducted the first biogeographic study of disturbance across multiple plant species. We experimentally disturbed grasslands and added seeds of 34 plant species to plots in their native range and in two introduced ranges that differed in invasibility (susceptibility to invasion) to evaluate recruitment while examining potential influences of resource availability, native community recovery from disturbance (resilience), and life-history traits in local species pools.</li> <li>Species pools in the native (donor) range were more strongly skewed toward ruderal taxa than species pools in the introduced ranges. This bias in the donor pool was exacerbated by introduction filters that further selected for ruderal traits, strongly skewing exotic species pools in the introduced ranges toward ruderals. Sown species, which reflected these trait patterns, benefited from disturbance universally, but their disturbance response was 10-fold greater in the more invasible introduced range. This result was not explained by nutrient availability, which responded similarly to disturbance across ranges. Nor was it driven by background propagule pressure, which was minimal. Rather, the exaggerated disturbance effect in the more invasible introduced range appeared to be driven by weak recovery of the native plant community that allowed ruderal-biased exotics to proliferate.</li> <li>Overall, disturbance appeared to favored exotics because they were much more likely than natives to be ruderal. However, this trait bias only corresponded with an invader advantage in the more invasible range where weak community resilience was linked to slow-growing, stress-tolerant natives that failed to rapidly recover space and resources. In contrast, in the less invasible introduced range, highly competitive native perennials quickly filled the disturbance gap, demonstrating high community resilience that appeared to limit invader recruitment. </li> <li> Synthesis. Biogeographic influences on local species pools can facilitate invader success following disturbance, but final invasion outcomes are conditioned by native community resilience. </li> </ol>

Data for "Reducing Southern Ocean biases in the FOCI climate model"

Jupyter notebooks and time-averaged data needed to reproduce all plots in "Reducing Southern Ocean biases in the FOCI climate model" submitted to JAMES. Source code modifications needed to compile and run the model is also included. See attached README for more information.