Find research datasets worth reusing

opencc-zeroDec 2017View details →

Data from: Sex bias in ability to cope with cancer: Tasmanian devils and facial tumour disease.

Knowledge of the ecological dynamics between hosts and pathogens during the initial stages of disease emergence is crucial to understanding the potential for evolution of new interspecific interactions. Tasmanian devil (Sarcophilus harrisii) populations have declined precipitously owing to infection by a transmissible cancer (devil facial tumour disease, DFTD) that emerged approximately 20 years ago. Since the emergence of DFTD, and as the disease spreads across Tasmania, the number of devil has dropped up to 90% across 80% of the species' distributional range. As a result, the disease is expected to act as a strong selective force on hosts to develop mechanisms of tolerance and/or resistance to the infection. We assessed the ability of infected devils to cope with infection, which translates into host tolerance to the cancer, by using the reaction norm of the individual body condition by tumour burden. We found that body condition of infected hosts is negatively affected by cancer progression. Males and females presented significant differences in their tolerance levels to infection, with males suffering declines of up to 25% of their body condition, in contrast to <5% in females. Sex-related differences in tolerance to cancer progression may select for changes in life history strategies of the host and could also alter the selective environment for the tumours.

opencc-by-nc-4.0Jun 2021View details →

Replication package for: "Concentration Bias in Intertemporal Choice"

This is the replication package for Dertwinkel-Kalt, Gerhardt, Riener, Schwerter, and Strang, “Concentration Bias in Intertemporal Choice,” Review of Economic Studies 89, no. 3 (2022): 1314–1334, <a href="https://doi.org/10.1093/restud/rdab043" target="_blank" rel="noopener">https://doi.org/10.1093/restud/rdab043</a>. The package includes the <a href="https://www.otree.org">oTree</a> code for running the consumption experiment and the <a href="https://www.ztree.uzh.ch/en.html">z-Tree</a> code for running the money experiment described in the article. It also includes the <a href="https://www.stata.com">Stata</a> code of all hypothesis tests and statistics reported in the article (figures, tables, numbers reported in the text) as well as the data on which the code runs. Moreover, it includes the <a href="https://www.r-project.org">R</a> code of the calibration exercise mentioned in Section 4.

opencc-zeroMar 2020View details →

Error, noise and bias in de novo transcriptome assemblies

De novo transcriptome assembly is a powerful tool, widely used over the last decade for making evolutionary inferences. However, it relies on two implicit assumptions: that the assembled transcriptome is an unbiased representation of the underlying expressed transcriptome, and that expression estimates from the assembly are good, if noisy approximations of the relative abundance of expressed transcripts. Using publicly available data for model organisms, we demonstrate that, across assembly algorithms and data sets, these assumptions are consistently violated. Bias exists at the nucleotide level, with genotyping error rates ranging from 30-83%. As a result, diversity is underestimated in transcriptome assemblies, with consistent under-estimation of heterozygosity in all but the most inbred samples. Even at the gene level, expression estimates show wide deviations from map-to-reference estimates, and positive bias at lower expression levels. Standard filtering of transcriptome assemblies improves the robustness of gene expression estimates but leads to the loss of a meaningful number of protein-coding genes, including many that are highly expressed. We demonstrate a computational method, length-rescaled CPM, to partly alleviate noise and bias in expression estimates. Researchers should consider ways to minimize the impact of bias in transcriptome assemblies.

Supplementary File_Ivermectin_Risk of Bias Excel Tool (Version 1)

Supplementary material (Risk of Bias Excel Tool (Version 1)) for the Cochrane Review "Ivermectin for preventing and treating COVID-19".

FESOM output supporting: Atmospheric wind biases: A challenge for simulating the Arctic Ocean in coupled models?

AWI-CM1 and FESOM1.4 simulation results used in the manuscript "Atmospheric wind biases: A challenge for simulating the Arctic Ocean in coupled models?".

opencc-zeroJul 2021View details →

Female Assamese macaques bias their affiliation to paternal and maternal kin

Forming strong social bonds can lead to higher reproductive success, increased longevity and/or increased infant survival in several mammal species. Given these adaptive benefits, understanding what determines partner preferences in social bonding is important. Maternal relatedness strongly predicts partner preference across many mammalian taxa. The role of paternal relatedness, however, has received relatively little attention, even though paternal and maternal kin share the same number of genes, and theoretically similar preferences would therefore be expected for paternal kin. Here, we investigate the role of maternal and paternal relatedness in female affiliation in Assamese macaques (Macaca assamensis), a species characterized by a relatively low male reproductive skew. We studied a wild population under natural conditions using extensive behavioral data and relatedness analyses based on pedigree reconstruction. We found stronger affiliative relationships and more time spent grooming between maternal kin and paternal half-sisters compared to non-kin, with no preference of maternal over paternal kin. Paternally related and non-related dyads did not form stronger relationships when they had less close maternal kin available, but we would need a bigger sample size to confirm this. As expected given the low reproductive skew, affiliative relationships between paternal half-sisters closer in age were not stronger than between paternal half-sisters with larger age differences, suggesting that the kin bias towards paternal kin was not mediated by age similarity. An alternative way through which paternal kin could get familiarized is mother- and/or father-mediated familiarity.

opencc-by-4.0Mar 2021View details →

Implementation of an adaptive bias-aware extended Kalman filter for sea-ice data assimilation in the HARMONIE-AROME numerical weather prediction system: numerical experiments

This data set provides the post-processed output of the numerical experiments performed to assess the possible effects of applying sea ice data assimilation within the surface analysis procedure of the HARMONIE-AROME NWP system. Results of five numerical experiments are provided: <ul> <li>HA-REF – reference experiment without sea ice data assimilation applied, and with blending for upper-air initialization</li> <li>HA-EKF – sensitivity experiment with sea ice data assimilation applied, and with blending for upper-air initialization</li> <li>3DVAR-REF – reference experiment without sea ice data assimilation applied, and with 3DVAR for the upper-air analysis</li> <li>3DVAR-EKF – sensitivity experiment with sea ice data assimilation applied, and with 3DVAR for the upper-air analysis</li> <li>3DVAR-EKF-TS – sensitivity experiment with sea ice data assimilation, and with 3DVAR for the upper-air analysis using coupled surface and atmospheric data assimilation procedures</li> </ul> For the HA-REF and HA-EKF experiments a subset of the gridded model output is provided; for the 3DVAR-REF, 3DVAR-EKF and 3DVAR-EKF-TS experiments a subset of the gridded model output and model data extracted at the positions of the SYNOP and TEMP stations within the model domain are provided. Additionally, in-situ observations, covering the same time period as the 3DVAR-REF, 3DVAR-EKF, 3DVAR-EKF-TS experiments, are provided.

opencc-zeroAug 2021View details →

Raw data and media: Tetraspanins are unevenly distributed across single extracellular vesicles and bias sensitivity to multiplexed cancer biomarkers

Raw datasets and media accompanying the manuscript: Tetraspanins are unevenly distributed across single extracellular vesicles and bias sensitivity to multiplexed cancer biomarkers, published in the Journal of Nanobiotechnology

opencc-by-4.0Sep 2021View details →

Risk of bias in observational studies using routinely collected data of comparative effectiveness research: a meta-research study

We performed a meta-research study by searching PubMed for comparative effectiveness observational studies evaluating therapeutic interventions using routinely collected data published in high impact factor journals from 01/06/2018 to 30/06/2020. We assessed the reporting of study design (i.e., eligibility, treatment assignment, and the start of follow-up). Risk of selection bias and immortal time bias was determined by assessing if the time of eligibility, treatment assignment and the start of follow-up were synchronised to mimic the randomisation following the target trial emulation framework.

opencc-zeroJan 2022View details →

Considering sampling bias in close-kin mark-recapture (CKMR) abundance estimates of Atlantic salmon

Genetic methods for the estimation of population size can be powerful alternatives to conventional methods. Close-kin mark-recapture (CKMR) is based on the principles of conventional mark-recapture, but instead of being physically marked, individuals are marked through their close kin. The aim of this study was to evaluate the potential of CKMR for the estimation of spawner abundance in Atlantic salmon and how age, sex, spatial, and temporal sampling bias may affect CKMR estimates. Spawner abundance in a wild population was estimated from genetic samples of adults returning in 2018 and of their potential offspring collected in 2019. Adult samples were obtained in two ways. First, adults were sampled and released alive in the breeding habitat during spawning surveys. Second, genetic samples were collected from out-migrating smolts PIT tagged in 2017 and registered when returning as adults in 2018. CKMR estimates based on adult samples collected during spawning surveys were somewhat higher than conventional counts. Uncertainty was small (CV<0.15), due to the detection of a high number of parent-offspring-pairs. Sampling of adults was age- and size-biased and correction for those biases resulted in moderate changes in the CKMR estimate. Juvenile dispersal was limited, but spatially balanced sampling of adults rendered CKMR estimates robust to spatially biased sampling of juveniles. CKMR estimates based on returning PIT tagged adults were approximately twice as high as estimates based on samples collected during spawning surveys. We suggest that estimates based on PIT tagged fish reflect the total abundance of adults entering the river, while estimates based on samples collected during spawning surveys reflect the abundance of adults present in the breeding habitat at the time of spawning. Our study showed that CKMR can be used to estimate spawner abundance in Atlantic salmon, with a moderate sampling effort, but a carefully designed sampling regime is required.

opencc-zeroOct 2021View details →

Size-driven preservational and macroecological biases in the latest Maastrichtian terrestrial vertebrate assemblages of North America

The end-Cretaceous (K/Pg) mass-extinction event is the most recent and well-understood of the "Big Five" and triggered establishment of modern terrestrial ecosystem structure. Despite the depth of research into this event, our knowledge of upper Maastrichtian terrestrial deposits globally relies primarily on assemblage-level data limited to a few well-sampled formations in North America, the Hell Creek and Lance formations. These assemblages disproportionally affect our interpretations of this important interval. Multiple investigations have quantified diversity patterns within these assemblages, but the potential effect of formation-level size-dependent taphonomic biases and their implications on extinction dynamics remains unexplored. Here, the relationship between taphonomy and body size of the Hell Creek and Lance formation dinosaurs and mammals are quantitatively analyzed. Small-bodied dinosaur taxa (< 70 kg) are consistently less complete, unlikely to be articulated, and delayed in their description relative to their large-bodied counterparts. Family-level abundance (particularly skeletons) is strongly tied to body mass, and the relative abundance of juveniles of large-bodied taxa similarly is underrepresented. Mammals show similar but non significant trends. The results are remarkably similar to those from the Campanian-aged Dinosaur Park Formation, suggesting a widespread strong taphonomic bias against the preservation of small taxa, which will result in their seemingly depauperate diversity within the assemblage. This taphonomically skewed view of diversity and abundance of small-bodied taxa amidst our best late Maastrichtian samples has significant implications for understanding speciation and extinction dynamics (e.g., size-dependent extinction selectivity) across the K/Pg Boundary.

opencc-by-4.0Nov 2021View details →

Risk of bias assessments and support for judgement with ROB 2 tool for the Cochrane Review: PEG-asparaginase treatment for acute lymphoblastic leukaemia in children: a network meta-analysis

Risk of bias assessments and support for judgement with ROB 2 tool for the Cochrane Review: PEG-asparaginase treatment for acute lymphoblastic leukaemia in children: a network meta-analysis

opencc-zeroNov 2022View details →

The potential bias of nitrogen deposition effects on primary productivity and biodiversity

Atmospheric nitrogen (N) deposition is composed of both inorganic N (IN) and organic N (ON), and these sources of N may exhibit different impacts on ecosystems. However, our understanding of the impacts of N deposition is largely based on experimental gradients of INs or more rarely ONs. Thus, the effects of N deposition on ecosystem productivity and biodiversity may be biased. We explored the differential impacts of different IN:ON ratios on aboveground net primary productivity (ANPP) and plant species richness in a typical temperate grassland with a long-term N addition experiment. Our results showed that N addition significantly increased ANPP and reduced species richness. While the IN:ON ratios showed no different effects on ANPP, more species loss occurred with increasing IN:ON ratios. Thus, the evaluation of N deposition on biodiversity might be overestimated if only IN is added or underestimated if only ON is added.

Floating-Gate MOS Transistor with Dynamic Biasing as a Radiation Sensor (raw data from journal article)

This upload contains raw data from the manuscript "Floating-Gate MOS Transistor with Dynamic Biasing as a Radiation Sensor". The manuscript was published in Sensors 20, no. 11 (2020): 3329; DOI: https://doi.org/10.3390/s20113329 The upload consists of .pdf file of the manuscript and .vsz files with raw data related to the figures in the manuscript. Each .vsz file is linked with raw data from the text files (.txt) and placed in a folder with the name and ordinal number of the figure in the publication. Additionally, a .pdf output file of the Veusz program (freely available) is placed in each folder. This work was supported in part by the European Union’s Horizon 2020 research and innovation programme (Grant No. 857558) and the Ministry of Education, Science and Technology Development of the Republic of Serbia (Project No. 43011).

opencc-zeroNov 2022View details →

Pooling robustness in distance sampling: Avoiding bias when there is unmodelled heterogeneity

Data from a two-visit line transect survey of four songbird species gathered in spring 2004. Study area size was 33.2 ha of woodland and parkland on the Montrave Estate near Leven in Fife, Scotland.

opencc-zeroDec 2022View details →

Wildlife documentaries present a diverse, but biased, portrayal of the natural world

1. Wildlife-documentary production has expanded over recent decades, while studies report reduced direct contact with nature. The role of documentaries and other electronic content in educating people about biodiversity is therefore likely to be growing increasingly important. This study investigated whether the content of wildlife documentaries is an accurate reflection of the natural world and whether conservation messaging in documentaries has changed over time. 2. We sampled an online film database (n = 105) to quantify the representation of taxa and habitats over time, and compared this with actual taxonomic diversity in the natural world. We assessed whether the precision with which an organism could be identified from the way it was mentioned varied between taxa or across time, and whether mentions of conservation and anthropogenic impacts on the natural world changed over time. 3. Mentions of organisms (n = 374) were very biased towards vertebrates (81.1% of mentions) relative to invertebrates (17.9% of mentions), despite vertebrates representing only 3.4% of described species, compared to 74.9% for invertebrates. Mentions were highly variable across groups and between time periods, particularly for insects, fish and reptiles. Plants had a consistently low representation across time periods. 4. A range of habitats was represented, the most common being tropical forest and the least common being deep ocean, but there was no change over time. 5. Mentions identifiable to species were significantly different between taxa, with 41.8% of mentions of vertebrates identifiable to species compared with just 7.5% of invertebrate mentions and 10% of plant mentions. This did not change over time. 6. Conservation was mentioned in 16.2% of documentaries overall but in almost 50% of documentaries in the current decade. Anthropogenic impacts were mentioned in 22.1% of documentaries and never before the 1970s. 7. Our results show that documentaries provide a diverse picture of nature with an increasing focus on conservation, with likely benefits for public awareness. However, they overrepresent vertebrate species, potentially directing public attention towards these taxa. We suggest widening the range of taxa featured to redress this and call for a greater focus on threats to biodiversity to improve public awareness.

opencc-by-4.0Dec 2021View details →

Exploring Holocene temperature trends and a potential summer bias in simulations and reconstructions: TransEBM1.2 simulation data and analysis

The TransEBM1.2 model code, transient climate simulation data of the last 26 ka and Python scripts to reproduce the analysis and Figures.

opencc-zeroJan 2023View details →

Biases and distribution patterns in hard-bodied microscopic animals (Acari: Halacaridae): Size doesn't matter, but generalism and sampling effort do

Aim The interplay between distribution ranges, species traits, and sampling and taxonomic biases remain elusive amongst microscopic animals. This ignorance obscures our understanding of the diversity patterns of a major component of biodiversity. Here, we used marine Halacaridae to explore whether differences between marine provinces can explain their distribution patterns or if differential sampling efforts across regions prevent any macroecological inference. Furthermore, we test if certain functional traits influence their distribution patterns. Location Europe. Results Whereas geographical variables provided a better explanation for differences in species composition, sampling effort and distance from marine biological stations accounted for the majority of differences in European Halacaridae richness. Species occurring in more habitats showed broader geographical ranges and accumulated more records. Species traits like body size affected the distribution of halacarid species. Main conclusions We propose that the sampling effort of halacarid mites in Europe might be explained by two different cognitive biases: the convenience of selecting certain sampling localities compared to others, and the tendency of zoologists to scrutinize habitats where their target organisms are more common.

Risk of bias assessments and support for judgement with ROB 2 tool for the Cochrane Review: Remdesivir for the treatment of COVID-19

Updated Risk of bias assessments and support for judgement with ROB 2 tool for the Cochrane Review: Remdesivir for the treatment of COVID-19.