Find research datasets worth reusing

Data from: Median-Joining Networks and Bayesian phylogenies often do not tell the same story

Inferring phylogenies among intraspecific individuals often yields unresolved relationships (i.e., polytomies). Consequently, methods that compute distance-based abstract networks, like Median-Joining Networks (MJNs), are thought to be more appropriate tools for reconstructing such relationships than traditional trees. Median-Joining Networks visualize all routes of relationships in the form of cycles, if needed, when traditional approaches cannot resolve them. However, the MJN method is a distance-based phenetic approach that does not involve character transformations and makes no reference to ancestor-descendant relationships. Although philosophical and theoretical arguments challenging the implication that MJNs reflect phylogenetic signal in the traditional sense have been presented elsewhere, an empirical comparison with a character-based approach is needed given the increasing popularity of MJN analysis in evolutionary biology. Here, we use the conservative Approximately Unbiased (AU) test to compare 85 cases of branching patterns of cycle-free MJNs and Bayesian Inference (BI) phylogenies using datasets from 55 empirical studies. By rooting the MJN analyses to provide directionality, we report substantial disagreement between computed MJNs and posterior distributions on BI phylogenies. The branching patterns in MJNs and BI phylogenies show significantly different relationships in 37.6% of cases. Among the relationships that do not significantly differ, 96.2% show alternative sets of relationships. Our results indicate that the two methods provide different measures of relatedness in a phylogenetic sense. Finally, our analyses also support previous observations of the statistical hypothesis testing by reconfirming the over-conservativeness of the Shimodaira-Hasegawa test versus the AU test.

SI_III_4_Spatialized metabolomic annotation combining MALDI imaging and molecular network

Ces documents regroupent les données supplémentaires générés lors du développement méthdologique pour la création de réseaux moléculaires par MALDI-FT-ICR IMS. Un .ppt regroupe l'ensemble des cartographies ioniques spécifiques à chaque ion.

openmit-licenseApr 2024View details →

A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods

This repository contains all the datasets used for benchmarking drug repositioning methods based on heterogeneous networks, including drug-drug similarity, disease-disease similarity, and drug-disease associations. The repository consists of: <ol> <li>Name or keyword information for drugs and diseases information contained in the dataset</li> <li>Inputs needed for different drug repositioning methods: multiple drug similarity matrices,multiple disease similarity matrices, and drug-disease associations matrices.</li> </ol>     <blockquote> Please cite us : Yinghong Li, Yinqi Yang, Zhuohao Tong, Yu Wang, Qin Mi, Mingze Bai, Guizhao Liang, Bo Li, Kunxian Shu, A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods, Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae172, <a href="https://doi.org/10.1093/bib/bbae172">https://doi.org/10.1093/bib/bbae172</a> </blockquote>

opencc-by-nc-4.0Jan 2024View details →

Combining graph neural networks and computer vision methods for cell nuclei classification in lung tissue

Database of the article "Combining graph neural networks and computer vision methods for cell nuclei classification in lung tissue ".

opencc-by-4.0Dec 2022View details →

The upgrade of Waveform Dataset in Continuous Mode by improved Montefeltro Seismic Network (MF) in Central-Northern Italy from 2021 to 2022

The temporary seismic network of Montefeltro (FDSN Network code: 1S), which covers from December 2018 a geographic area between the regions of Emilia-Romagna and the Marches in central-northern Italy, was implemented with a new seismic station (ISC Station code: MF05) located in the surroundings of the town of Perticara (RN), Italy. The new station increases the coverage in the northern sector of the above described area and the recording by the local network combined with that of the National Seismic Network allows to obtain a better resolution in the relocation of events occurred in the area. After this station addition, the array of Montefeltro seismic network actually consists of four stations with the last one equipped by dynamic digitizer (Gaia2 data acquisition unit) and three component extended band seismometer (Lennartz 3D/5s sensor). The local mobile network records seismic data in continuous mode at 100 sps.Data availability for all the stations (registered in ISC) of the network 1S during the time period 2021-2022 is tabled and uploaded in an apart pdf file.   Seismic Instruments and Dataless information: Station code    Sensor                     Recorder MF01               Lennartz 3D/5s        Sara SL06 MF03               Guralp CMG/20s     Reftek 130 MF04               Guralp CMG/30s     Reftek 130 MF05               Lennartz 3D/5s        INGV Gaia2The dataless files are separately provided. The dataless format contains a complete and comprehensive history of metadata for seismic networks and their stations, including geographic coordinates and response information.List for the dataless files of the Montefeltro seismic network MF01              1S_MF01.dless MF03              1S_MF03.dless MF04              1S_MF04.dless MF05              1S_MF05.dlessThe complete dataset of this study is also uploaded in the Zenodo repository. The repository contains a zip file for each recording year, subdivided by stations belonging to the network 1S, and a single zip file for the dataless files.

Network embedding for understanding the National Park System through the lenses of news media, scientific communication and biogeography

The United States national parks encompass a variety of biophysical and historical resources important for national cultural heritage. Yet how these resources are socially constructed often depends upon the beholder. Parks tend to be conceptualized according to their (fixed) geographic context, so our understanding of this system of systems is dominated by this geographic lens. To expose the systemic structure that exists beyond their geographic embedding, we analyze three representations of the national park system using park-park similarity networks according to their co-occurrence in: (a) ~423,000 news media articles; (b) ~11,000 research publications; and (c) ~60,000 species inhabiting parks. We quantify structural variation between network representations by leveraging similarity measures at different scales: park-level (park-park correlations) and system-level (network communities' consistency). Because parks are governed and experienced at multiple scales, cross-network comparison informs how management should account for the varying objectives and constraints that dominate at each scale. Our results identify an interesting paradox: whereas park-level correlations depend strongly on the representative lens, the network communities are remarkably robust and consistent with the underlying geographic embedding. Our data-driven methodology is generalizable to other geographically embedded socio-environmental systems and supports the holistic analysis of systems-level structure that may elude other approaches.

Forest restoration treatments indirectly diversify pollination networks via floral- and temperature-mediated effects

In North American conifer forests a variety of federally initiated thinning programs are implemented to restore pre-European settlement forest structures, but these changes may impact ecosystem function via impacts on sensitive biotic communities. Across the wildland-urban interface of the Front Range region of Colorado, agencies associated with the 'Collaborative Forest Landscape Restoration Program' (CFLRP) have implemented thinning treatments across thousands of hectares of ponderosa pine forest; here we leverage these treatments as an experimental framework to examine thinning effects on a pollinator community. We measured variation in forest structure and sampled bee community assemblages using multiple methods (trapping and netting) to compare bee biodiversity and patterns of floral visitation by bees (bee-flower networks) between mechanically thinned stands that were 3–10 years post-treatment and non-thinned stands. Three key findings emerged: (1) Native bee abundance, richness, and diversity were 120, 53, and 37% greater, respectively, in thinned stands. Nestedness, richness, and abundance of bee-flower interactions were all substantially higher in thinned stands, and there was increased functional redundancy in bee assemblages after thinning. (2) Structural equation modelling indicated that variation in temperature and floral abundance were mediated by canopy openness and were correlated with bee richness and abundance, thereby indirectly driving variation in bee-flower interactions. (3) Four floral species (Penstemon virens, Cerastium arvense, Erysimum capitatum, and Geranium caespitosum) were identified as key connectors in bee-flower interaction networks, though these were not necessarily the most abundant flowering plants. Our analyses indicate that native bee α-diversity and bee-flower interactions positively responded to thinning treatments, and these effects were indirectly driven by canopy removal. We conclude that CFLRP treatments have conservation value for native bee communities. Further monitoring is warranted to evaluate the longevity of these effects.

Experimental evidence that network topology can accelerate the spread of beneficial mutations

Whether and how the spatial arrangement of a population influences adaptive evolution has puzzled evolutionary biologists. Theoretical models make conflicting predictions about the probability a beneficial mutation will become fixed in a population for certain topologies like stars, in which "leaf" populations are connected through a central "hub." To date, these predictions have not been evaluated under realistic experimental conditions. Here, we test the prediction that topology can change the dynamics of fixation both in vitro and in silico by tracking the frequency of a beneficial mutant under positive selection as it spreads through networks of different topologies. Our results provide empirical support that metapopulation topology can increase the likelihood that a beneficial mutation spreads, broadens the conditions under which this phenomenon is thought to occur, and points the way towards using network topology to amplify the effects of weakly favored mutations under directed evolution in industrial applications.

Data for: Does capital account liberalization drive the systemic importance of mainland China stock market? A network perspective

Even though Chinese government has launched a series of capital account liberalization schemes to promote the systemic importance of mainland China stock market, the mainland China market still remains relatively marginal in the global stock markets, that is, China’s capital account liberalization does not seem to work as expected. This paper measures the systemic importance of mainland China stock market based on dynamic tail correlation networks, and further analyzes the impact of China’s capital account liberalization on it. Empirical results manifest that, capital account liberalization indeed contributes to improving the systemic importance of mainland China stock market. Besides, the systemic importance is also significantly and positively affected by economic policy uncertainty and direct investment. More specially, investor sentiment in mainland China stock market has the apparent impact on systemic importance only when extreme events occur.

Data for Vasari Social Network

Results for Vasari Social Network

Files to run scripts in <a href="https://github.com/ISE-FIZKarlsruhe/vasari_network">https://github.com/ISE-FIZKarlsruhe/vasari_network</a> for generating a social network weighted with Pointwise Mutual Information (PMI) from The Lives of The Artists (1568) by Giorgio Vasari. The input data for running the source code is available <a href="https://doi.org/10.5281/zenodo.8395369">here</a>. The centralities/ directory contains 10 files reporting the highest centraility scores in the extracted network. The network is extracted dynamically from a 10 volumes edition of the book. This means that a network is created for each volume. However, every network is the evolution of his precedent since it includes the information extracted from the previous volumes of the book. The numerical division of the results (from 0 to 9) reflects this dynamic extraction.

opencc-zeroOct 2023View details →

DLC networks from: Application of a novel deep learning based 3D videography workflow to bat flight data

Studying the detailed biomechanics of flying animals relies on producing accurate three-dimensional coordinates for key anatomical landmarks. Traditionally, this is achieved through manual digitization of animal videos, a labor-intensive task that grows more so with increasing frame rates and numbers of cameras. In this study, we present a workflow that combines deep learning-powered automatic digitization with intelligent filtering and correction of mislabeled points using 3D information. We tested our workflow using a particularly challenging scenario – bat flight. First, we documented bats flying steadily in a wind tunnel. We compared the results from manually digitizing bats with markers applied to anatomical landmarks against using our automatic workflow on the same bats without markers. In our second test case, we compared manual digitization against our automated workflow for bats exhibiting complex maneuvers in a large flight arena. We found that the variation between the 3D coordinates from our workflow and those from manual digitization was less than a millimeter larger than the variation between 3D coordinates resulting from two different human digitizers. The reduced reliance on manual digitization stemming from this work has the potential to significantly increase the scalability of studies into the detailed biomechanics of animal flight.

opencc-by-4.0Mar 2022View details →

A gap in primate default mode network organization (Atlases and Script)

Code deposit in Python for the article: "A gap in primate default mode network organization" published in Cell Report. + Dictionary learning-based functional atlas in four primate species (mouse lemurs, marmosets, macaques, and humans) BOLD images were acquired in mouse lemurs, marmosets, macaques, and humans Each functional atlas was made using a dictionary learning analysis with 7 components on pre-treated BOLD images. Each component was concatenated and labeled to create each atlas. The atlases were broken into functional regions automatically and manually. For each species: DL7cpts_DicL_yung.nii.gz ==> output of the dictionary learning dict_learning_7compos_concat.nii.gz ==> functional atlas dict_learning_7compos_concat_break.nii.gz ==> functional atlas segmented automatically into functional regions or dict_learning_7compos_concat_break_handseg.nii.gz ==> functional atlas segmented automatically and manually into functional regions if used for publication please cite:  An evolutionary gap in primate default mode network organization Clement M Garin, Yuki Hori, Stefan Everling, Christopher T Whitlow, Finnegan Calabro, Beatriz Luna, Mathilda Froesel, Maëva Gacoin, Suliann Ben Hamed, Marc Dhenain, Christos Constantinidis Apr 2022 Cell Report 39, 2, 110669 DOI: <a href="https://doi.org/10.1016/j.celrep.2022.110669">10.1016/j.celrep.2022.110669</a>

opencc-by-nc-4.0May 2022View details →

Extracted Information for the Systematic Review of Survey Scales for Measuring Information Privacy Concerns on Social Network Sites

The data set is part of a systematic literature review of survey scales for measuring information privacy concerns (IPCs) used in research on social network sites (SNSs). The results of this systematic literature review are available in Bartol, J., Vehovar, V., & Petrovčič, A. (2023). Systematic review of survey scales measuring information privacy concerns on social network sites. Telematics and Informatics, 102063. https://doi.org/10.1016/j.tele.2023.102063 The article also includes a detailed description of the methods used in generating this data set.

openmit-licenseOct 2023View details →

Data from Genome scale metabolic network modelling for metabolic profile predictions

Data used to produce figures 4, 5 and 6 in the paper Genome scale metabolic network modelling for metabolic profile predictions.

opencc-by-4.0Dec 2022View details →

Indicators of Social Sustainability obtained from Sustainability in Aquaculture Research Network

Indicators of social sustainability obtained for the 8 systems of LTS studied. Monoc. = monoculture; sub-trop. = subtropical; IMTA = integrated multi trophic aquaculture; PHY = person-hour per year; PH = person-hour, “-“ = no data.

opencc-by-4.0Dec 2022View details →

Indicators of Economic Sustainability obtained from Sustainability in Aquaculture Research Network

Indicators of economic sustainability obtained for the 8 systems of LTS studied. Monoc. = monoculture; sub-trop. = subtropical; IMTA = integrated multi trophic aquaculture; “-“ = no data.

opencc-by-4.0Oct 2023View details →

Exploring the anti-glioma mechanism of the active components of Cortex Periplocae based on network pharmacology and iTRAQ proteomics in vitro

Hierarchical clustering analysis of candidate proteins was illustrated in heat map, which showed obvious differences between CP-induced cells and controls (Fig. 6). Each column is a sample and each rowindicates a differentially expressed protein. Log values (log2expression) of significantly differentially expressed proteins in different samples are displayed in heat maps in different colors. GreenandRedrepresent up-regulation and down-regulation, respectively. The gray part represents no quantitative information of the proteins. T1, T2 and T3 means the CP-treated U251 cells group and C2, C2 and C3 means control group (n=3).

opencc-zeroOct 2023View details →

Data from: Integrating variation in bacterial-fungal co-occurrence network with soil carbon dynamics

Bacteria and fungi are core microorganisms in diverse ecosystems, and their cross-kingdom interactions are considered key determinants of microbiome structure and ecosystem functioning. However, how bacterial-fungal interactions mediate soil organic carbon (SOC) dynamics remains largely unexplored in the context of artificial forest ecosystems. Here, we characterized soil bacterial and fungal communities in four successive planting of Eucalyptus and compared them to a neighboring evergreen broadleaf forest. Carbon (C) mineralization combined with five C-degrading enzymatic activities was investigated to determine the effects of successive planting of Eucalyptus on SOC dynamics. Our results indicated that successive planting of Eucalyptus significantly altered the diversity and structure of soil bacterial and fungal communities and increased the negative bacterial-fungal associations. The bacterial diversity significantly decreased in all Eucalyptus plantations compared to the evergreen forest, while the fungal diversity showed the opposite trend. The ratio of negative bacterial-fungal associations increased with successive planting of Eucalyptus due to the decrease in SOC, ammonia nitrogen (NH4+−N), nitrate nitrogen (NO3−−N), and available phosphorus (AP). Structural equation modeling indicated that the potential cross-kingdom competition, based on the ratio of negative bacterial-fungal correlations, was significantly negatively associated with the diversity of total bacteria and keystone bacteria, thereby increasing C-degrading enzymatic activities and C mineralization. Synthesis and applications: Our results highlight the regulatory role of the negative bacterial-fungal association in enhancing the correlation between bacterial diversity and C mineralization. This suggests that promoting short-term successive planting in the management of Eucalyptus plantations can mitigate the impact of this association on SOC decomposition. Taken together, our study advances the understanding of bacterial-fungal negative associations to mediate carbon mineralization in Eucalyptus plantations, giving us a new insight into SOC cycling dynamics in artificial forests.