Find research datasets worth reusing

opencc-by-4.0Dec 2018View details →

Fig. 4 in Wild bees (Anthophila) of Porto Santo (Madeira Archipelago) and their habitats: species diversity, distribution patterns and bee-plant network *

Fig. 4: Bipartite graph of the bee-plant network of Porto Santo.

opencc-by-4.0Aug 2021View details →

Observational Data for: Polarized information ecosystems can reorganize social networks via information cascades

General Information This contains the observational data for the publication: <blockquote> Tokita, Guess, and Tarnita (2021). Polarized information ecosystems can reorganize social networks via information cascades. Proceedings of the National Academies of Science of the United States. </blockquote> Please see the above peer-reviewed article that resulted from this data for more details. Please see the observational/ directory in the Github repository <a href="http://%28https//github.com/christokita/information-cascades)">https://github.com/christokita/information-cascades</a> for the code that analyzes the Twitter data and generates derived data. Data directly pertaining to the four news sources of interest are in the data/ directory, while data that is related to the 4,000 monitored news followers are in the data_derived/ directory. The main data file is in a zipped file. We also included a read me with a description of each directory and subdirectory of the data. Methods For each of our four news sources of interest (CBS News, USA Today, Vox, and the Washington Examiner), we used the Twitter API to sample 3,000 random Twitter users that followed that news source's account. We then used the tweetscores R package to estimate the ideology of each of the 12,000 sampled users. From the original pool of approximately 12,000 sampled users who follow a news outlet of interest, we monitored the follower networks of 1,000 liberal followers of CBS News, 1,000 conservative followers of USA Today, 1,000 liberal followers of Vox, and 1,000 conservative followers of the Washington Examiner. When selecting the 1,000 random users to monitor for a given news outlet, we first conducted filters based on self-reported geolocation and other Twitter profile attributes to reasonably filter down to US-based users who primarily tweet in English. We then pulled the complete follower network of each of our 4,000 monitored users at the beginning and end of a 6-week period from August to September 2020, allowing us to assess who unfollowed these users over this period of time. Finally, using the initial follower networks of each monitored user, we estimated the ideology of up to 50 random followers to create a baseline for the ideological composition of each user’s follower network.  Using the initial and final follower networks of each individual, we calculated the rate of unfollows by opposite-ideology users in their follower network. To determine whether an unfollow event was breaking a cross-ideology social tie, users and their unfollowers were classified simply as either liberal (ideology score < 0) or conservative (ideology score > 0). We excluded from analysis unfollowers for whom we could not estimate ideology, either because the account had been suspended, deleted, or made private, or because they did not follow any of the political, news, or cultural accounts needed to do the estimation. We then compared the proportion of unfollowers that were of the opposite ideology (i.e., conservative unfollowers if the focal user is liberal) against the estimated proportion of opposite-ideology followers in the focal user’s initial follower network. This allowed us to account for the fact that many user’s follower networks were not ideologically balanced and set the baseline expectation that if unfollows were random then the proportion of unfollows by opposite-ideology users should match the proportion of followers that were of the opposite ideology.   Abstract (for main paper) The precise mechanisms by which the information ecosystem polarizes society remain elusive. Focusing on political sorting in networks, we develop a computational model that examines how social network structure changes when individuals participate in information cascades, evaluate their behavior, and potentially rewire their connections to others as a result. Individuals follow proattitudinal information sources but are more likely to first hear and react to news shared by their social ties and only later evaluate these reactions by direct reference to the coverage of their preferred source. Reactions to news spread through the network via a complex contagion. Following a cascade, individuals who determine that their participation was driven by a subjectively “unimportant” story adjust their social ties to avoid being misled in the future. In our model, this dynamic leads social networks to politically sort when news outlets differentially report on the same topic, even when individuals do not know others’ political identities. Observational follow network data collected on Twitter support this prediction:We find that individuals in more polarized information ecosystems lose cross-ideology social ties at a rate that is higher than predicted by chance. Importantly, our model reveals that these emergent polarized networks are less efficient at diffusing information: Individuals avoid what they believe to be “unimportant” news at the expense of missing out on subjectively “important” news far more frequently. This suggests that “echo chambers”—to the extent that they exist—may not echo so much as silence.

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Individual-based networks reveal the highly skewed interactions of a frugivore mutualist with individual plants in a diverse community

While plant-animal interactions occur fundamentally at the individual level, the bulk of research examining the mechanisms that drive interaction patterns has focused on the species or population level. In seed-dispersal mutualisms between frugivores and plants, little is known about the role of space and individual-level variation among plants in structuring patterns of frugivore foraging and, thus, seed dispersal in a plant community. Here we use an animal perspective to examine how space and variation between individual plants affect movement and visitation by frugivores foraging on individual fruiting plants. To do this, we used a spatially explicit network approach informed by observations of the movement and foraging of a frugivorous lemur species (Eulemur rubriventer) amongst individual plants in a diverse plant community in Madagascar. The resulting hierarchical networks, in which a few individual plants received the bulk of the interactions, demonstrated how a generalist frugivore species could act as an individual-plant specialist within a plant community. The few individual plants that dominated interactions with the lemurs shaped the modular spatial structure of frugivory interactions in the community and facilitated visitation to near neighbors. This interaction structure was primarily driven by extrinsic factors, as lemur movements among plants were significantly influenced by the individual plant's spatial position and the species richness of fruiting plants in its immediate neighborhood. Individual plants in central spatial locations, with a rich fruiting neighborhood and large fruit crops, received the most visits. The observed drastic inequality in the interactions of a generalist frugivore within a highly diverse plant community highlights the importance of considering individual-level variation for essential ecosystem processes, such as seed dispersal.

opencc-zeroAug 2021View details →

opencc-by-4.0Aug 2021View details →

Networks for NicheNet (txt files)

NicheNet data source networks in txt format (cf https://zenodo.org/record/3260758)

Fig. 13 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 13. Distribution map of Ngirhaphium in Southeast Asia

Fig. 9 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 9. Distribution map of Ngirhaphium meieri, new species and Ngirhaphium thaicum, new species.

Fig. 7 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 7. Ngirhaphium meieri, new species, female habitus. Scale = 1 mm.

Fig. 6 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 6. Ngirhaphium meieri, new species, male habitus (photo: Abdulloh Samoh). Scale = 1 mm.

Fig. 3 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 3. Ngirhaphium thaicum, new species male habitus. Scale = 1 mm.

Fig. 4 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 4. Ngirhaphium thaicum, new species habitus female. Scale = 1 mm.

opencc-by-4.0Aug 2021View details →

data for Newbury et al Short term fitness effects of bipartite interactions shape network structure of mutualistic and antagonistic communities

speciescountdata.csv contains colony couts and plasmid detection from the main experiment. evonet.csv conatins colony counts of bacteria with and without plasmid pkjk5 from commuities where donors were  o/ p  ancestral/evolved.  AOPV.csv contains optical density data for species a,o,p and v. column 1 is time in hours. Then columns alternate between a, o, p, s, v, a+,o+,p+,s+,v+,s+,v+ (where + denotes plasmid carriage) until column 49. After which the same patten continues, but these were grown with tetracycline. s did not grow at all in the 96-well plate this data was taken from. This is likely due to experimental error, so an additional well plate was used just for s (S.scv). S.csv contains optical density data for species s. column 1 is time in hours. then there are  6 colulmns of s and 6 columns of s+ until column 49. After this the same pattern continues but bacteria were grown with tetracycline.

opencc-by-3.0-usMay 2021View details →

Investigating Fracture Network Deformation Using Noble Gas Release: Dataset

Data Description Data used in journal article: Investigating Fracture Network Deformation Using Noble Gas Release, 2021, W. Payton Gardner, Stephen J. Bauer, Scott Broome, Geofluids   <ol> <li>Noble gas quadrupole dynamic data are text files with time and logged current intensity for measured masses.  File suffix is .xlh – File names are descriptive.  Time stamps can be used to correlate with article figures</li> <li>He leak rate data – .xlsx (Microsoft Excel) format.  Figure in text can be found on its own worksheet.</li> <li>Air flow data -Microsoft Excel format.  Figures in text are in file.</li> </ol>

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Pollinator-mediated indirect effects on plant fecundity revealed by network indices

Indirect effects arise when one species influences how another species interacts with a third. Pollinator-mediated indirect effects are widespread in many plant communities and are often not restricted to plant species pairs. An analytical framework does not exist yet that allows for the evaluation of indirect effects through shared pollinators in a community context, as well as their consequences for plant fitness. We used network indices describing pollinator sharing to assess the extent to which plant species affect and are affected by others in a pollination network from a species-rich dune community. For 23 plant species, we explore how these indices relate to plant fecundity (seeds/flower) over two years. We further linked plant traits and indices to uncover functional aspects of pollinator-mediated indirect interactions. Species frequently visited by shared pollinators showed higher fecundity and exhibited traits that increase pollinator attraction and generalization. Conversely, species whose shared pollinators frequently visited other plants had lower fecundity and had more specialized traits. Thus, pollinator sharing benefited some species while others suffered reproductive disadvantages, consistent with competition. The framework developed here uses network tools to advance our understanding of how pollinator-mediated indirect interactions influence a species' relative reproductive success at the community-level.

opencc-zeroSep 2021View details →

Dataset : Identifying locations susceptible to micro-anatomical reentry using a spatial network representation of atrial fibre maps

<ul> <li>The three files in the dataset are:</li> </ul> 1) Healthy Sheep Atria Fibre Orientation Dataset 300µm 2) Heart Failure Sheep Atria Fibre Orientation Dataset 300µm 3) Human Atria Fibre Orientation Dataset 330µm <ul> <li>Data is stored as numpy binary files. Given below is an example .py script to open the flat datasets:</li> </ul>     import numpy as np     data = np.load("Human_330um.npy") <ul> <li>Volume and fibre orientation dataset stored in flat format as given below:</li> </ul>     i, j, k, v1, v2, v3, ...  repeated for each voxel           where (i, j, k) are voxel coordinates and (v1, v2, v3) are vector components corresponding to fibre orientation within that voxel.

Supplementary datasets for the paper of "Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization"

There are two eCLIP datasets (cell lines of K562 and HepG2). The eCLIP datasets were then divided into five categories for each cell line: low, medium 1, medium 2, high 1 and high 2 with peaks of >1,000 but <2,000, >2,000 but <4,000, >4,000 but <7,000, >7,000 but <10,000 and >10,000, respectively.

Dataset (n=1671) of the publication "Small-scale private forest owners and the European Natura 2000 conservation network: Perceived ecosystem services, management practices, and nature conservation attitudes"

The excel file contains the replies of small-scale private forest owners in Lower Saxony, Germany, to certain questions of a survey analyzed within the following publication: "Small-scale private forest owners and the European Natura 2000 conservation network: Perceived ecosystem services, management practices, and nature conservation attitudes”. The questions included in this dataset cover their objectives, management activities, attitudes and forest stand structures. Further details can be found in the second sheet of the file called “Code explanation”. More information about the methods of data collection can be found in the before-mentioned publication.

openSep 2021View details →

melian009/Mispark: Preliminary analysis mutualistic networks in space, rarefaction, sierra size and sampling individuals, species, and traits

Mutualistic networks in space, morphological traits and colors, or how to put all together to understand rare and common species in rapidly changing landscapes

Relativistic electron model in the outer radiation belt using a neural network approach

This dataset includes the models, dataset, and extra figures for the paper titled Relativistic electron model in the outer radiation belt using a neural network approach

Pressure signals acquired in a pipe network at the Water Engineering Laboratory of the University of Perugia, Italy

This dataset contains the pressure signals (i.e., the time-history of the pressure head, with t = 0 indicating the maneuver starting time) acquired in an HPDE network (with two 100 m x 100 m square loops) installed at the Water Engineering Laboratory of the University of Perugia, Italy. In this network, a short branch is installed. Tests refer to transients generated by the fast and total closure of a downstream end valve of such a branch.

Dataset Network Slicing - 5G

Dataset com métricas de redes com rótulo para três slices.