Find research datasets worth reusing

Supplementary data for the article: "Towards an widely applicable earthquake detection algorithm for fibreoptic and hybrid fibreoptic-seismometer networks"

Repository of supporting data associated with the article submitted to GJI, titled: "Towards an widely applicable earthquake detection algorithm for fibreoptic and hybrid fibreoptic-seismometer networks".   Contents include: <ol> <li>A full working example of modified QuakeMigrate version and seismic time-series data used to detect an earthquake.</li> <li>Earthquake catalogues for the three datasets described in the publication.</li> </ol>

Data and code for "Design Principles for Energy Transfer in the Photosystem II Supercomplex from Kinetic Transition Networks"

Data and code for "Design Principles for Energy Transfer in the Photosystem II Supercomplex from Kinetic Transition Networks".

opencc-by-nc-sa-4.0Jun 2024View details →

Supplementary data (CC BY-NC-SA 4.0): Germanium Distributions in Zeolites Derived from Neural Network Potentials

Content (Creative Commons Attribution Non Commercial Share Alike 4.0 International): This dataset contains supplementary data related to the Germanosilicate Project titled  "Germanium Distributions in Zeolites Derived from Neural Network Potentials". In various subfolders, it hosts database, simulations and post-processing calculations. Below is a brief overview of each subfolder: <ol> <li>Post_Processing_Calculation:  - Contains scripts and data for post-processing calculations such as coordination numbers,  - Pair distribution function, and various germanium distribution metrics. </li> <li>NNP_Simulation_DATA: - Stores simulation data for different zeolite structures along with setup files for neural network potentials (NNP) simulations. </li> <li>NNP_files_database: - NNP_files: NNP model files (compatible with <a href="https://github.com/atomistic-machine-learning/schnetpack/tree/schnetpack1.0">SchNetPack version 1.0</a>) - GeSiO_training.db: DFT (PBE+D3(BJ)) training database as SchNetPack1.0 database file readable by  <a href="https://wiki.fysik.dtu.dk/ase/index.html">Atomic Simulation Environment (ASE)</a> and SchNetPack version 1.0 </li> <li>DFT_vs_NNP_Data: - ASE traj files storing structures subsampled from MCBH runs along with energies/forces at the PBE+D3(BJ) ("*_dft.traj") and NNP level (*_nnp.traj) </li> <li>Zeolite_Structurers_ALL: - Holds data for various zeolite structures, including optimized structures for both single-cell and supercell configurations. </li> <li>GSOs_DATA: - The unoptimised Global Structure Optimas (GSOs) are provided - Optimised GSOs are stored inside folders for both various DFT and NNP methods</li> </ol>             Please refer to individual readme files in each subfolder for more detailed information.

Data Release: "A neural network emulator of the Advanced LIGO and Advanced Virgo selection function"

This dataset contains results presented in "A neural network emulator of the Advanced LIGO and Advanced Virgo selection function" (<a href="https://www.arxiv.org/abs/2408.16828">arXiv: 2408.16828</a>). The code used to generate this data and produce figures in the paper can be found at <a href="https://github.com/tcallister/learning-p-det/">https://github.com/tcallister/learning-p-det/</a>. Specific instructions about the workflow are provided in the <a href="https://tcallister.github.io/learning-p-det/">accompanying documentation</a>. The primary deliverable of this work is a trained neural network emulator for the compact binary selection function during the Advanced LIGO and Advanced Virgo O3 observing run. This emulator is made available in a standalone companion repository, <a href="https://github.com/tcallister/pdet">https://github.com/tcallister/pdet</a>. Additional information: <ul> <li>The files endo3_bbhpop-LIGO-T2100113-v12.hdf5, endo3_bnspop-LIGO-T2100113-v12.hdf5, and endo3_nsbhpop-LIGO-T2100113-v12.hdf5, used for network training, were created and released by the LIGO-Virgo-KAGRA Collaboration at <a href="../records/7890437">https://zenodo.org/records/7890437</a>.</li> <li>The file sampleDict_FAR_1_in_1_yr.pickle, used during hierarchical inference, was created via code in the repository <a href="https://github.com/tcallister/get-lvk-data">https://github.com/tcallister/get-lvk-data</a>.</li> <li>Inference results (popsummary_standardInjections.h5 and popsummary_dynamicInjections.h5) are provided in the popsummary results format; see <a href="https://git.ligo.org/christian.adamcewicz/popsummary">https://git.ligo.org/christian.adamcewicz/popsummary</a>.</li> </ul> Changelog: <ul> <li>v2: Added missing file sampleDict_FAR_1_in_1_yr.pickle</li> </ul>

Data from Demonstration of quantum network protocols over a 14-km urban fiber link

Datasets used to create all plots and results found in the paper "Data from Demonstration of quantum network protocols over a 14-km urban fiber link" from AG Eschner, Saarland University

openSep 2024View details →

The data for "Noise-Resilient Forward Transient Analysis for Pipe Burst Localization in Complex Pipe Networks: Theoretical Framework"

The data is for supporting our research paper titled "Noise-Resilient Forward Transient Analysis for Pipe Burst Localization in Complex Pipe Networks: Theoretical Framework".

opencc-by-4.0Sep 2024View details →

Raw data for Jin et. al "Intersectin1 promotes clathrin-mediated endocytosis by organizing and stabilizing endocytic protein interaction networks"

<h2>Intersectin1 promotes clathrin-mediated endocytosis by organizing and stabilizing endocytic protein interaction networks</h2>   Meiyan Jin1,2*, Yuichiro Iwamoto1, Cyna Shirazinejad1, David G. Drubin1,3** 1 Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA 2 Current Address: Department of Biology, University of Florida, Gainesville, Fl 32611, USA 3 Lead author * Correspondence: meiyan.jin@ufl.edu **Correspondence: drubin@berkeley.edu

opencc-by-4.0Oct 2024View details →

Communities in global tourism network and related data

1995-2021 Communities within Global Tourism Network and Population, Urban population, GDP, GDP per capita, Exports of goods and services, Air passengers carried, Number of world heritage, Number of representative intangible cultural heritage, War and conflict, Political violence and protest events, Geographical proximity.

opencc-by-4.0Oct 2024View details →

Data for "Learning Collective Cell Migratory Dynamics from a Static Snapshot with Graph Neural Networks"

This dataset contains snapshots of cell monolayers, represented as graphs, along with their corresponding average displacement measurements.

opencc-by-4.0Oct 2024View details →

Information diffusion assumptions can distort our understanding of social network dynamics (code and data)

This repository contains the data (<code>cascade_reconstruction.tar.gz</code>) and code (<code>code_repository.tar.gz</code>) for a paper titled "Information diffusion assumptions can distort our understanding of social network dynamics" by <a href="https://www.matthewdeverna.com/">Matthew R. DeVerna</a>, <a href="https://pierri.faculty.polimi.it/">Francesco Pierri</a>, <a href="https://rachithaiyappa.github.io/">Rachith Aiyappa</a>, <a href="https://diogofpacheco.github.io/">Diogo Pachecho</a>, <a href="https://jbryden.co.uk/home/">John Bryden</a>, and <a href="https://cnets.indiana.edu/fil">Filippo Menczer</a> . Please see the README.md file for important details! If you would like to report issues with the code, you can do so through an associated GitHub repository that houses the project's code, which can be found <a href="https://github.com/osome-iu/cascade_reconstruction">here</a>.

opencc-by-4.0Nov 2024View details →

ClimateNet Dataset as used in "Explaining neural networks for detection of tropical cyclones and atmospheric rivers in gridded atmospheric simulation data"

ClimateNet dataset as it was used by us for the study: "Explaining neural networks for detection of tropical cyclones and atmospheric rivers in gridded atmospheric simulation data" (https://gmd.copernicus.org/preprints/gmd-2024-60/).   For the original dataset refer to: https://portal.nersc.gov/project/ClimateNet/

opencc-zeroDec 2018View details →

Data from: Seeing is believing? comparing plant-herbivore networks constructed by field co-occurrence and DNA barcoding methods for gaining insights into network structures

Plant-herbivore interaction networks provide information about community organization. Two methods are currently used to document pairwise interactions among plants and insect herbivores. One is the traditional method that collects plant-herbivore interaction data by field observation of insect occurrence on host plants. The other is the increasing application of newly developed molecular techniques based on DNA barcodes to the analysis of gut contents. The second method is more appealing because it documents realized interactions. To construct complete networks, each technique of network construction is urgent to be assessed. We addressed this question by comparing the effectiveness and reliability of the two methods in constructing plant-Lepidoptera larval network in a 50 ha subtropical forest in China. Our results showed that the accuracy of diet identification by observation method increased with the number of observed insect occurrences on food plants. In contrast, the molecular method using three plant DNA markers were able to identify food residues for 35.6% larvae and correctly resolved 77.3% plant (diet) species. Network analysis showed molecular networks had three-fold more unique host plant species but fewer links than the traditional networks had. The molecular method detected plants that were not sampled by the traditional method, e.g., bamboos, bryophytes and lianas in the diets of insect herbivores. The two networks also possessed significantly different structural properties. Our study indicates the traditional observation of co-occurrence is inadequate, while molecular method can provide higher species resolution of ecological interactions.

opencc-zeroDec 2015View details →

Data from: Replicated landscape genetic and network analyses reveal wide variation in functional connectivity for American pikas

Landscape connectivity is essential for maintaining viable populations, particularly for species restricted to fragmented habitats or naturally arrayed in metapopulations and facing rapid climate change. The importance of assessing both structural connectivity (the physical distribution of favorable habitat patches) and functional connectivity (how species move among habitat patches) for managing such species is well understood. However, the degree to which functional connectivity for a species varies among landscapes, and the resulting implications for conservation, have rarely been assessed. We used a landscape genetics approach to evaluate resistance to gene flow and, thus, to determine how landscape and climate-related variables influence gene flow for American pikas (Ochotona princeps) in eight federally managed sites in the western United States. We used those empirically-derived, individual-based landscape resistance models in conjunction with predictive occupancy models to generate patch-based network models describing functional landscape connectivity. Metareplication across landscapes enabled identification of limiting factors for dispersal that would not otherwise have been apparent. Despite the cool microclimates characteristic of pika habitat, south-facing aspects consistently represented higher resistance to movement, supporting the previous hypothesis that exposure to relatively high temperatures may limit dispersal in American pikas. We found that other barriers to dispersal included areas with a high degree of topographic relief, such as cliffs and ravines, as well as streams and distances greater than one to four kilometers depending on the site. Using the empirically-derived network models of habitat patch connectivity, we identified habitat patches that were likely disproportionately important for maintaining functional connectivity, areas in which habitat appeared fragmented, and locations that could be targeted for management actions to improve functional connectivity. We concluded that climate change, besides influencing patch occupancy as predicted by other studies, may alter landscape resistance for pikas, thereby influencing functional connectivity through multiple pathways simultaneously. Spatial autocorrelation among genotypes varied across study sites and was largest where habitat was most dispersed, suggesting that dispersal distances increased with habitat fragmentation, up to a point. This study demonstrates how landscape features linked to climate can affect functional connectivity for species with naturally fragmented distributions, and reinforces the importance of replicating studies across landscapes.

opencc-zeroDec 2013View details →

Data from: Human-induced biotic invasions and changes in plankton interaction networks

1.Pervasive and accelerating changes to ecosystems due to human activities remain major sources of uncertainty in predicting the structure and dynamics of ecological communities. Understanding which biotic interactions within natural multitrophic communities are threatened or augmented by invasions of non-native species in the context of other environmental pressures is needed for effective management. 2.We used multivariate autoregressive models with detailed time-series data from largely freshwater and brackish regions of the upper San Francisco Estuary to assess the topology, direction and strength of trophic interactions following major invasions and establishment of non-native zooplankton in the early 1990s. We simultaneously compared the effects of fish and clam predation, environmental temperature, and salinity intrusion using time-series data from > 60 monitoring locations and spanning more than three decades. 3.We found changes in the networks of biotic interactions in both regions after the major zooplankton invasions. Our results imply an increased pressure on native herbivores; intensified negative interactions between herbivores and omnivores; and stronger bottom-up influence of juvenile copepods but weaker influence of phytoplankton as a resource for higher trophic levels following the invasions. We identified salinity intrusion as a primary pressure but showed relatively stronger importance of biotic interactions for understanding the dynamics of entire communities. 4.Synthesis and applications. Our findings highlight the dynamic nature of biotic interactions and provide evidence of how simultaneous invasions of exotic species may alter interaction networks in diverse natural ecosystems over large spatial and temporal scales. Efforts to restore declining fish stocks may be in vain without fully considering the trophic dynamics that limit the flow of energy to target populations. Focusing on multitrophic interactions that may be threatened by invasions rather than a limited focus on responses of individual species or diversity is likely to yield more effective management strategies.

opencc-zeroDec 2011View details →

Data from: Disentangling invasion processes in a dynamic shipping - boating network

The relative importance of multiple vectors to the initial establishment, spread, and population dynamics of invasive species remains poorly understood. This study used molecular methods to clarify the roles of commercial shipping and recreational boating in the invasion by the cosmopolitan tunicate, Botryllus schlosseri. We evaluated i) single vs. multiple introduction scenarios, ii) the relative importance of shipping and boating to primary introductions, iii) the interaction between these vectors for spread (i.e., the presence of a shipping-boating network), and iv) the role of boating in determining population similarity. Tunicates were sampled from 26 populations along the Nova Scotia, Canada, coast that were exposed to either shipping (i.e., ports), or boating (i.e., marinas) activities. A total of 874 individuals (~30 per population) from 5 ports and 21 marinas was collected and analyzed using both mitochondrial cytochrome c oxidase subunit I gene (COI) and 10 nuclear microsatellite markers. The geographical location of multiple hotspot populations indicates that multiple invasions have occurred in Nova Scotia. A loss of genetic diversity from port to marina populations suggests a stronger influence of ships than recreational boats on primary coastal introductions. Population similarity analysis reveals a clear dependence of marina populations on those that had been previously established in ports and connectivity due to a boating network better explains patterns in population similarities than does natural spread. We conclude that frequent primary introductions arise by ships and that secondary spread occurs gradually thereafter around individual ports, facilitated by recreational boating.

opencc-zeroDec 2016View details →

Data from: Sex-specific responses to territorial intrusions in a communication network: evidence from radio-tagged great tits

Signals play a key role in the ecology and evolution of animal populations, influencing processes such as sexual selection and conflict resolution. In many species, sexually selected signals have a dual function: attracting mates and repelling rivals. Yet, to what extent males and females under natural conditions differentially respond to such signals remains poorly understood, due to a lack of field studies that simultaneously track both sexes. Using a novel spatial tracking system, we tested whether or not the spatial behavior of male and female great tits (Parus major) changes in relation to the response of a territorial male neighbor to an intruder. We tracked the spatial behavior of male and female great tits (N = 44), 1 hr before and 1 hr after simulating territory intrusions, employing automatized Encounternet radio-tracking technology. We recorded the spatial and vocal response of the challenged males and quantified attraction and repulsion of neighboring males and females to the intrusion site. We additionally quantified the direct proximity network of the challenged male. The strength of a male's vocal response to an intruder induced sex-dependent movements in the neighborhood, via female attraction and male repulsion. Stronger vocal responders were older and in better body condition. The proximity networks of the male vocal responders, including the number of sex-dependent connections and average time spent with connections, did not change directly following the intrusion. The effects on neighbor movements suggest that the strength of a male's vocal response can provide relevant social information to both the males and the females in the neighborhood, resulting in both sexes adjusting their spatial behavior in contrasting ways, while the social proximity network remained stable. Moreover, our study underlines the importance of the "silent" eavesdroppers within communication networks for studying the dual functioning and evolution of sexually selected signals.

opencc-zeroDec 2015View details →

Data from: Stability and generalization in seed dispersal networks: a case study of frugivorous fish in Neotropical wetlands

When species within guilds perform similar ecological roles, functional redundancy can buffer ecosystems against species loss. Using data on the frequency of interactions between fish and fruit, we assessed whether co-occurring frugivores provide redundant seed dispersal services in three species-rich Neotropical wetlands. Our study revealed that frugivorous fishes have generalized diets; however, large-bodied fishes had greater seed dispersal breadth than small species, in some cases, providing seed dispersal services not achieved by smaller fish species. As overfishing disproportionately affects big fishes, the extirpation of these species could cause larger secondary extinctions of plant species than the loss of small specialist frugivores. To evaluate the consequences of frugivore specialization for network stability, we extracted data from 39 published seed dispersal networks of frugivorous birds, mammals and fish (our networks) across ecosystems. Our analysis of interaction frequencies revealed low frugivore specialization and lower nestedness than analyses based on binary data (presence–absence of interactions). In that case, ecosystems may be resilient to loss of any given frugivore. However, robustness to frugivore extinction declines with specialization, such that networks composed primarily of specialist frugivores are highly susceptible to the loss of generalists. In contrast with analyses of binary data, recently developed algorithms capable of modelling interaction strengths provide opportunities to enhance our understanding of complex ecological networks by accounting for heterogeneity of frugivore–fruit interactions.

opencc-zeroJun 2021View details →

Supporting Data and Code for "Managing to Climatology: Improving semi-arid agricultural risk management using crop models and a dense meteorological network"

Without reliable seasonal climate forecasts, farmers and managers in other weather-sensitive sectors might adopt practices that are optimal for recent climate conditions. To demonstrate this principle, crop simulation models driven by a dense meteorological network were used to identify climate-optimal planting dates for U.S. Southern High Plains (SHP) un-irrigated agriculture. This method converted large samples of SHP growing season weather outcomes into climate-representative cotton and sorghum yield distributions over a range of planting dates. Best planting dates were defined as those that maximized median cotton lint (April 24) and sorghum grain (July 1) yields. Those optimal yield distributions were then converted into corresponding profit distributions reflecting 2005-2019 commodity prices and fixed production costs. Both crop's profitability under variable price conditions and current SHP climate conditions were then compared based on median profits and loss probability, and through stochastic dominance analyses that assumed a slightly risk-averse producer.

opencc-zeroMay 2020View details →

Data from: Recurrent circuit dynamics underlie persistent activity in the macaque frontoparietal network

During delayed oculomotor response tasks, neurons in the lateral intraparietal area (LIP) and the frontal eye fields (FEF) exhibit persistent activity that reflects the active maintenance of behaviorally relevant information. Despite many computational models of the mechanisms of persistent activity, there is a lack of circuit-level data from the primate to inform the theories. To fill this gap, we simultaneously recorded ensembles of neurons in both LIP and FEF while macaques performed a memory-guided saccade task. A population encoding model revealed strong and symmetric long-timescale recurrent excitation between LIP and FEF. Unexpectedly, LIP exhibited stronger local functional connectivity than FEF, and many neurons in LIP had longer network and intrinsic timescales. The differences in connectivity could be explained by the strength of recurrent dynamics in attractor networks. These findings reveal reciprocal multi-area circuit dynamics in the frontoparietal network during persistent activity and lay the groundwork for quantitative comparisons to theoretical models.