Find research datasets worth reusing

opencc-by-4.0Jun 2021View details →

Cave amphipods reveal co-variation between morphology and trophic niche in a low-productivity environment

Datasets used to explore co-variation patterns between morphological traits and trophic niche in co-occurring Niphargus amphipods from five groundwater caves of the Dinaric Karst, Europe. We quantified gnathopod size and shape by means of morphometric measurements and assessed isotopic niche, trophic position, and carbon signatures using nitrogen (δ15N) and carbon (δ13C) stable isotopes. We provide morphometric and isotopic data for Niphargus specimens, and isotopic data for food resources sampled in the caves.

opencc-zeroJun 2021View details →

Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness

Invasive species pose increasing threats to global biodiversity and ecosystems. While previous studies have characterized successful invaders from ecological traits, characteristics related to evolutionary processes have rarely been investigated. Here we compared gene flow and local adaptation using demographic analyses and outlier tests in two co-occurring moth pests across their common native range of China, one of which (the peach fruit moth, Carposina sasakii) has maintained its native distribution, while the other (the oriental fruit moth, Grapholita molesta) has expanded its range globally during the past century. We found that both species showed a pattern of genetic differentiation and an evolutionary history consistent with a common southwestern origin and northward expansion in their native range. However, for the noninvasive species, genetic differentiation was closely aligned with the environment, and there was a relatively low level of gene flow, whereas in the invasive species, genetic differentiation was associated with geography. Genome scans indicated stronger patterns of climate-associated loci in the noninvasive species. While strong local adaptation and reduced gene flow across its native range may have decreased the invasiveness of C. sasakii, this requires further validation with additional comparisons of invasive and non-invasive species across their native range.

opencc-zeroJul 2021View details →

Increased room temperature ferromagnetism in Co-doped tetrahedral perovskite niobates

Dilute magnetic semiconductors (DMSs), such as (In, Mn)As and (Ga, Mn)As prototypes, are limited to III–V semiconductors with Curie temperatures (Tc) far from room temperature, thereby hindering their wide application. Here, one kind of DMS based on perovskite niobates is reported. BaMxNb(1-x)O3-δ (M=Fe, Co) powders are prepared by the composite-hydroxide-mediated method. The addition of M elements endows BaMxNb(1-x)O3-δ with local ferromagnetism. The tetragonal BaCoxNb(1-x)O3-δ nanocrystals can be obtained by Co doping, which shows strong saturation magnetization(Msat) of 2.22 emu/g, a remnant magnetization(Mr) of 0.084 emu/g, and a small coercive field(Hc) of 167.02 Oe at room temperature. The ab initio calculations indicate that Co doping could lead to a 64% local spin polarization at the Fermi level(EF) with net spin DOS of 0.89 electrons·eV-1, this result shows the possibility of maintaining strong ferromagnetism at room temperature. In addition, the trade-off effect between the defect band absorption and ferromagnetic properties of BaMxNb(1-x)O3-δ is verified experimentally and theoretically.

opencc-by-4.0Aug 2021View details →

Data for PM2.5/Ozone co-occurrence paper

This repository contains supporting data for the manuscript titled "Increasing co-occurrence of fine particulate matter and ozone extremes in the western United States" by Kalashnikov et al. (2021). Please contact me with any questions at dmitri.kalashnikov@wsu.edu. -Dmitri

opencc-by-4.0Aug 2021View details →

Data for: Simultaneous GPS-tracking of parents reveals a similar parental investment within pairs, but no immediate co-adjustment on a trip-to-trip basis

This repository contains data for the paper: Kavelaars et al. 2021. Simultaneous GPS-tracking of parents reveals a similar parental investment within pairs, but no immediate co-adjustment on a trip-to-trip basis. Movement Ecology. https://doi.org/10.1186/s40462-021-00279-1

opencc-by-4.0Sep 2004View details →

Fig. 1. A in Cytotaxonomic diagnosis of Trichomycterus diabolus (Teleostei: Trichomycteridae) with comments about its evolutionary relationships with co-generic species

Fig. 1. A specimen of Trichomycterus diabolus with 110 mm in total length. Photo by C. Oliveira.

opencc-by-4.0Dec 2020View details →

Galactic maps of H2, reconstructed from the CfA CO survey

Maps of galactic H2, reconstructed from the CfA CO survey (Dame et al., ApJ 547 (2001) 792) data, <a href="https://www.cfa.harvard.edu/rtdc/">downloaded from the SAO Radio Telescope Data Center</a>, using a Bayesian variational inference approach. Here, we provide the mean and standard deviation of the gas density (in cm-3) on a three-dimensional 512x512x16 grid, spanning -16 kpc < x < 16 kpc, 16 kpc < y < 16 kpc and -0.5 kpc < z < 0.5 kpc, both for the BEG03 and the SBM15 gas flow models: <ul> <li> H2_dens_mean_BEG03.fits </li> <li> H2_dens_stddev_BEG03.fits </li> <li> H2_dens_mean_SBM15.fits </li> <li> H2_dens_stddev_SBM15.fits </li> </ul> In addition, we also publish the mean and standard deviation of the mass surface density (in Msun pc-2) on a two-dimensional 512x512 grid, spanning -16 kpc < x < 16 kpc and 16 kpc < y < 16 kpc, again for both gas flow models: <ul> <li> H2_surf_mass_dens_mean_BEG03.fits </li> <li> H2_surf_mass_dens_stddev_BEG03.fits </li> <li> H2_surf_mass_dens_mean_SBM15.fits </li> <li> H2_surf_mass_dens_stddev_SBM15.fits </li> </ul> Throughout, we have assumed an CO-to-H2 conversion factor XCO=2 1020 molecules cm-2 (K km s-1)-1. Refer to the FITS headers for more detailed information and see <a href="https://arxiv.org/abs/2012.15770">arXiv:2012.15770</a> for a detailed description of the reconstruction as well as a comparison with earlier studies. When using the deprojected gas maps in your research work, please refer to this Zenodo dataset and the following publication P. Mertsch and A. Vittino, "Bayesian inference of three-dimensional gas maps: I. Galactic CO", <a href="https://arxiv.org/abs/2012.15770">arXiv:2012.15770</a>.

opencc-by-4.0Oct 2021View details →

Network analysis reveals rare disease signatures across multiple levels of biological organization - Co-expression dataset

The GTEx-derived co-expression data in 38 tissues generated in Buphamalai et.al., Network analysis reveals rare disease signatures across multiple levels of biological organization, Nature Communications 2021. Please see the publication's Methods section for details.

Data for: Innate immune function and antioxidant capacity of nestlings of an African raptor co-vary with the level of urbanization around breeding territories

Urban areas provide breeding habitats for many species. However, animals raised in urban environments face challenges such as altered food availability and quality, pollution, and pathogens assemblages. These challenges can affect physiological processes like immune function and antioxidant defences which are important for fitness. Here, we explore how levels of urbanisation influence innate immune function, immune response to a mimicked bacterial infection and antioxidant capacity of nestling Black Sparrowhawks Accipiter melanoleucus in South Africa. We also explore the effect of timing of breeding and rainfall on physiology since both can influence the environmental condition under which nestlings are raised. Finally, because urbanisation can influence immune function indirectly, we use path analyses to explore direct and indirect associations between urbanisation, immune function, and oxidative stress. We obtained measures of innate immunity (haptoglobin, lysis, agglutination and bactericidal capacity), indices of antioxidant capacity (total non-enzymatic antioxidant capacity (tAOX), and total glutathione from nestlings from 2015 - 2019. In addition, in 2018 and 2019, we mimicked a bacterial infection by injecting nestlings with lipopolysaccharide and quantified their immune response. Increased urban cover was associated with an increase in lysis and a decrease in tAOX, but not with any of the other physiological parameters. Furthermore, except for agglutination, no physiological parameters were associated with the timing of breeding. Lysis and bactericidal capacity, however, varied consistently with the annual rainfall pattern. Immune response to a mimicked a bacterial infection decreased with urban cover but not with the timing of breeding nor rainfall. Our path analyses suggested indirect associations between urban cover and some immune indices via tAOX but not via the timing of breeding. Our results show that early-life development in an urban environment is associated with variation in immune and antioxidant functions. The direct association between urbanisation and antioxidant capacity and their impact on immune function is likely an important factor mediating the impact of urbanisation on urban-dwelling animals. Future studies should explore how these results are linked to fitness and whether the responses are adaptive for urban-dwelling species.

Co-manipulation of soft-materials estimating deformation from depth images

Video describing our work on Co-manipulation of soft-materials estimating deformation from depth images

Data for "Resource use divergence facilitates the evolution of secondary syntopy in a continental radiation of songbirds (Meliphagoidea): insights from unbiased co-occurrence analyses"

These two files contain data needed to replicate analyses in the associated article. AUTHOR of data files: Vladimir Remes CONTACT: vlad.remes/at/gmail,com AUTHORS of the article: V. Remes, L. Harmackova DATE CREATED: 8 November 2022 ARTICLE: published in Ecography   The file named "data_syntopy.xlsx" has two sheets: "data": contains the data "legend": contains explanations of data columns The file was saved in MS Excel for Mac 16.65. The file named "tree_Mel.tre" is the phylogenetic tree in the parenthetic format used for the analyses. It has been pruned from the tree published by Marki et al. (2017) Mol Phyl Evol 107, 516–529. It was saved using the write.nexus function from the "ape" package for R software.

Helminth-associated changes in host immune phenotype connect top-down and bottom-up interactions during co-infection

Within-host parasite interactions can be mediated by the host and changes in host phenotypes often serve as indicators of the presence or intensity of parasite interactions. Parasites like helminths induce a range of physiological, morphological, and immunological changes in hosts that can drive bottom-up (resource-mediated) or top-down (immune-mediated) interactions with co-infecting parasites. Although top-down and bottom-up interactions are typically studied in isolation, the diverse phenotypic changes induced by parasite infection may serve as a useful tool for understanding if, and when, these processes act in concert. Using an anthelmintic treatment study of African buffalo (Syncerus caffer), we tracked changes in host immunological and morphological phenotypes during helminth-coccidia co-infection to investigate their role in driving independent and combinatorial bottom-up and top-down parasite interactions. We also examined repercussions for host fitness. Clearance of a blood-sucking helminth, Haemonchus, from the host gastrointestinal tract induced a systemic Th2 immune phenotype, while clearance of a tissue-feeding helminth, Cooperia, induced a systemic Th1 phenotype. Furthermore, the Haemonchus-associated systemic Th2 immune phenotype drove simultaneous top-down and bottom-up effects that increased coccidia shedding by changing the immunological and morphological landscapes of the intestine. Higher coccidia shedding was associated with lower host body condition, a lower chance of pregnancy, and older age at first pregnancy, suggesting that coccidia infection imposed significant condition and reproductive costs on the host. Our findings suggest that top-down and bottom-up interactions may commonly co-occur and that tracking key host phenotypes that change in response to infection can help uncover complex pathways by which parasites interact.

Interplay between Li and Na amid co-doped solution-processed Cu2ZnSn(S,Se)4 absorbers for solar cells

Alkali doping and alloying are well-known strategies to improve the performance of Cu2ZnSn(S,Se)4 (CZTSSe) absorber based thin film solar cells. The effects of individual light alkali elements such as Li and Na have been thoroughly investigated, with both dopants resulting in significant improvements in performance of CZTSSe solar cells. Here, the combined effects of Li and Na are investigated in a so-called co-doping approach to capture the benefits from both elements simultaneously. In order to do that, various concentrations of Li and Na between 0.0 M and 0.5 M are added to the solution used for spin coating of the precursor layer. After annealing under Se-enriched atmosphere, the two alkali elements displayed mutual dependency of in terms of their concentrations in the CZTSSe absorber layer. Furthermore, both, Li and Na showed signs of forming alloys with the CZTSSe phase. The efficiencies of the best Li-Na co-doped solar cells are above 10%, slightly above the Li baseline thanks to increased open-circuit-voltage and short-circuit current. A non-negligible Na incorporation was observed even in nominally Na-free devices, likely from indirect contamination from the SLG substrate. Further work is needed to better understand Na-poor compositions and draw conclusions relevant to Na-free substrates.

Identity and density of parasite exposures alter the outcome of co-infections: Implications for management

1) Although research has focused on density-dependent responses of hosts to single-parasite infections, hosts are exposed to numerous parasites simultaneously under natural conditions and if these exposures lead to infections, they can threaten host populations and ecosystem stability. Moreover, spatiotemporal variation in abundance of co-occurring parasites might influence host infection intensity. If interactions are consistent between different co-infecting parasites, then these patterns could give managers another tool to control disease spread and even predict problematic disease emergences. 2) We investigated how parasite density and identity alter within-host co-infection dynamics. To test this, we simultaneously exposed Cuban treefrogs (Osteopilus septentrionalis) as a model amphibian species to all pairwise combinations of three problematic parasites that commonly co-infect amphibians: the fungus Batrachochytrium dendrobatidis (Bd), the nematode Aplectana hamatospicula, and Ranavirus. Hosts were exposed to one parasite at a fixed dose and another parasite at a range of five doses. 3) Higher doses of Bd decreased Ranaviral and A. hamatospicula loads, but Bd load was not influenced by the dose of either parasite. Ranaviral load was negatively associated with A. hamatospicula dose, but A. hamatospicula load was not affected by Ranaviral dose. We found that all the pairwise co-infections were dependent on parasite density and that pairwise interactions were highly asymmetric – strong in one direction and weak in the other – consistent with interactions dominating food webs. 4) Synthesis and applications: We also revealed that the exposure dose of A. hamatospicula was positively associated with host tolerance to Bd infection and negatively associated with Ranaviral load in hosts. Ranavirus and Bd cause mass die-offs in amphibians, but A. hamatospicula does not. Therefore, in systems where these parasites coexist, maintaining or increasing densities of A. hamatospicula could reduce the negative effects of Bd and Ranavirus infections. Additionally, if these asymmetric and density dependent patterns from community ecology are applicable to other amphibian co-infections or co-infections in other systems, this should allow conservation organizations and resource managers to predict outbreaks and manage host declines associated with deadly parasites by modifying the abundance of co-infecting parasites that might be easier to manage.

Predator-prey co-occurrence in harvest blocks

Forest harvesting alters habitat, impacts wildlife, and disrupts ecosystem function. Across the boreal forest of Canada, forest harvesting affects ungulate prey species and their predators, with cascading impacts on other species, including threatened woodland caribou. We used camera and vegetation data and occupancy modeling to investigate what characteristics in and around forestry harvest blocks influenced the occupancy and co‐occurrence of primary prey (elk, moose, mule deer, white‐tailed deer) and predators (black bear, cougar, grizzly bear, wolf) in harvest blocks. Occupancy was linked to forage, the surrounding habitat and anthropogenic disturbance, and silviculture practices. Black and grizzly bear occupancy was influenced by the presence of deer, and bear–deer co‐occurrence was influenced by site‐specific silviculture practices and surrounding anthropogenic disturbance. In the context of caribou recovery, our results indicate that forestry within caribou ranges could consider site‐specific silviculture practices and landscape‐level planning to reduce use of harvest blocks by primary prey. Future caribou recovery efforts may also consider the roles of deer and bears in caribou predation risk. Our study provides the first insights into the impacts of forestry and silviculture on boreal forest predator–prey co‐occurrence and provides practical management applications to mitigate the impacts of anthropogenic activities on the boreal forest ecosystem into the future.

opencc-by-4.0Dec 2021View details →

Conceptualising Co-creation

This is a short video made in 'pecha-kucha’ style (March 2021), representing a fraction of the evidence so far found on co-creation, intended in a fun and accessible way for the Health CASCADE Consortium meeting in Ghent (April 2022). Evidence used in this video is informed by Katrina Messiha's early-stage narrative review and EU Deliverable (produced October-December, 2021) which is open-access, and can be accessed through this link: https://zenodo.org/record/6818098

opencc-by-4.0Oct 2022View details →

Appendix of Empirical Study of Co-Renamed Identifiers

This data contains four CSVs: Rename.csv, Rename_Ignore_Inflection.csv, Relation.csv, Relation_Ignore_Inflection.csv.   Rename.csv and Rename_Ignore_Inflection.csv contain renamings used in our study. The difference between these CSVs is whether we ignored inflections.  Each row represents a renaming. Columns descriptions are below. <ul> <li>repository: repository name</li> <li>commit: commit hash</li> <li>filepath: location of the renamed identifier</li> <li>oldname: identifier name before the renaming</li> <li>newname: identifier name after the renaming</li> <li>type: identifier type (Class, Method, Attribute, Parameter, Variable)</li> <li>operational_chunk: operational chunks of the renaming</li> <li>meaningful_rename_set_id: meaningful rename set IDs (independent for each repository)</li> </ul>   Relation.csv and Relation_Ignore_Inflection.csv contain relationships detected in our study. The difference between these CSVs is whether we ignored inflections.  Each row represents a relationship between renamed identifier 1 and renamed identifier 2. Columns descriptions are below. <ul> <li>repository: repository name</li> <li>meaningful_rename_set_id: meaningful rename set IDs (independent for each repository)</li> <li>commit: commit hash</li> <li>relation: type of relationship</li> <li>file{1,2}: location of the identifier</li> <li>oldname{1,2}: identifier name before the renaming</li> <li>newname{1,2}: identifier name after the renaming</li> <li>type{1,2}: identifier type (Class, Method, Attribute, Parameter, Variable)</li> </ul>

Co-creation Methods (Infographic)

Infographic showing things to consider when selecting methods for co-creation.

Co-creation Knowledge Database Infographic

A database of all literature on co-creation (infographic).

Fundamental Ethical Principles of Co-creation (Infographic)

An infographic showing the fundamental ethical principles of co-creation.