cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14823566
title: OPN results from Topological analysis of differential effects of ketamine and propofol anaesthesia on brain dynamics

description: Research has found that the vividness of conscious experience is related to brain dynamics. Despite both being anaesthetics, propofol and ketamine produce different subjective states: we explore the different effects of these two anaesthetics on the structure of dynamic attractors reconstructed from electrophysiological activity recorded from cerebral cortex of two macaques. We used two methods: the first embeds the recordings in a continuous high-dimensional manifold on which we use topological data analysis to infer the presence of higher-order dynamics. The second reconstruction, an ordinal partition network embedding, allows us to create a discrete state-transition network, which is amenable to information-theoretic analysis and contains rich information about state-transition dynamics. We find that the awake condition generally had the ‘richest’ structure, visiting the most states, the presence of pronounced higher-order structures, and the least deterministic dynamics. By contrast, the propofol condition had the most dissimilar dynamics, transitioning to a more impoverished, constrained, low-structure regime. The ketamine condition, interestingly, seemed to combine aspects of both: while it was generally less complex than the awake condition, it remained well above propofol in almost all measures. These results provide deeper and more comprehensive insights than what is typically gained by using point-measures of complexity.
DOI: 10.5281/zenodo.5013609
title: Interindividual differences influence multisensory processing during spatial navigation

description: The dataset contains the raw data from two experiments. We investigate the ability of spatial navigation using auditory, visual or audiovisual landmarks in the environment.
DOI: 10.5281/zenodo.5013608
title: Interindividual differences influence multisensory processing during spatial navigation

description: The dataset contains the raw data from two experiments. We investigate the ability of spatial navigation using auditory, visual or audiovisual landmarks in the environment.
DOI: 10.6084/m9.figshare.14823557
title: PHom results from Topological analysis of differential effects of ketamine and propofol anaesthesia on brain dynamics

description: Research has found that the vividness of conscious experience is related to brain dynamics. Despite both being anaesthetics, propofol and ketamine produce different subjective states: we explore the different effects of these two anaesthetics on the structure of dynamic attractors reconstructed from electrophysiological activity recorded from cerebral cortex of two macaques. We used two methods: the first embeds the recordings in a continuous high-dimensional manifold on which we use topological data analysis to infer the presence of higher-order dynamics. The second reconstruction, an ordinal partition network embedding, allows us to create a discrete state-transition network, which is amenable to information-theoretic analysis and contains rich information about state-transition dynamics. We find that the awake condition generally had the ‘richest’ structure, visiting the most states, the presence of pronounced higher-order structures, and the least deterministic dynamics. By contrast, the propofol condition had the most dissimilar dynamics, transitioning to a more impoverished, constrained, low-structure regime. The ketamine condition, interestingly, seemed to combine aspects of both: while it was generally less complex than the awake condition, it remained well above propofol in almost all measures. These results provide deeper and more comprehensive insights than what is typically gained by using point-measures of complexity.
DOI: 10.5281/zenodo.5013686
title: Identification of a Pathway for Electron Uptake in Shewanella oneidensis

description: Data for figures for "Identification of a Pathway for Electron Uptake in <em>Shewanella oneidensis</em>" <strong>Abstract</strong> Extracellular electron transfer (EET) could enable electron uptake into microbial metabolism for the synthesis of complex, energy dense organic molecules from CO<sub>2 </sub>and renewable electricity<sup>1-6</sup><sup> </sup>. Theoretically EET could do this with an efficiency comparable to H<sub>2</sub>-oxidation<sup>7,8</sup> but without the need for a volatile intermediate and the problems it causes for scale up<sup>9</sup>. However, significant gaps remain in understanding the mechanism and genetics of electron uptake. For example, studies of electron uptake in electroactive microbes have shown a role for the Mtr EET complex in the electroactive microbe <em>Shewanella oneidensis</em> MR-1<sup>10-14</sup>, though there is substantial variation in the magnitude of effect deletion of these genes has depending on the terminal electron acceptor used. This speaks to the potential for novel and/or differentially utilized genes involved in electron uptake. To address this, we screened gene disruption mutants for 3,667 genes, representing ≈ 99% of all non-essential genes, from the <em>S. oneidensis</em>whole genome knockout collection using a redox dye oxidation assay. Confirmation of electron uptake using electrochemical testing allowed us to identify five genes from <em>S.</em><em> oneidensis</em> that are indispensable for electron uptake from a cathode. Knockout of each gene eliminates extracellular electron uptake, yet in four of the five cases produces no significant defect in electron donation to an anode. This result highlights both distinct electron uptake components and an electronic connection between aerobic and anaerobic electron transport chains that allow electrons from the reversible EET machinery to be coupled to different respiratory processes in <em>S. oneidensis</em>. Homologs to these genes across many different genera suggesting that electron uptake by EET coupled to respiration could be widespread. These gene discoveries provide a foundation for: studying this phenotype in exotic metal-oxidizing microbes, genetic optimization of electron uptake in <em>S. oneidensis</em>; and genetically engineering electron uptake into a highly tractable host like <em>E. coli </em>to complement recent advances in synthetic CO<sub>2</sub> fixation<sup>15</sup>.
DOI: 10.5281/zenodo.5013574
title: Kingsbarns June 2021

description: PASS sample recorded in Kingsbarns, Scotland on June 21st 2021
DOI: 10.5281/zenodo.5013573
title: Kingsbarns June 2021

description: PASS sample recorded in Kingsbarns, Scotland on June 21st 2021
DOI: 10.5281/zenodo.5013704
title: Datasets used in the Lab Validation of the RADON Verification Tool

description: This repository contains the datasets that have been used to perform the lab validation of the RADON verification tool. In order to replicate the experiments, please unzip the file "validation-datasets.zip" and run the following command: <pre><code class="language-bash">./run_all.rb {path_to_VT} list.json</code></pre>
DOI: 10.5281/zenodo.3894901
title: Datasets used in the Lab Validation of the RADON Verification Tool

description: This repository contains the datasets that have been used to perform the lab validation of the RADON verification tool. In order to replicate the experiments, please unzip the file "validation-datasets.zip" and run the following command: <pre><code class="language-bash">./run_all.rb {path_to_VT} list.json</code></pre>
DOI: 10.5281/zenodo.3949769
title: Data set for all Bifurcation diagrams of 'Two-dimensional patterns in dip coating - first steps on the continuation path'

description: Data set for all bifurcation diagrams of 'Two-dimensional patterns in dip coating - first steps on the continuation path' by Phong-Minh Timmy Ly, Kevin David Joachim Mitas, Uwe Thiele, Svetlana V. Gurevich published as Physica D 409, 132485 (2020). DOI: 10.1016/j.physd.2020.132485 Specifically: Figures 1, 2, 5, 6 and 7
DOI: 10.5281/zenodo.3711931
title: Data set for all Bifurcation diagrams of 'Two-dimensional patterns in dip coating - first steps on the continuation path'

description: Data set for all bifurcation diagrams of 'Two-dimensional patterns in dip coating - first steps on the continuation path' by Phong-Minh Timmy Ly, Kevin David Joachim Mitas, Uwe Thiele, Svetlana V. Gurevich published as Physica D 409, 132485 (2020). DOI: 10.1016/j.physd.2020.132485 Specifically: Figures 1, 2, 5, 6 and 7
DOI: 10.5281/zenodo.5013680
title: Hyperspectral X-ray CT dataset of a single, iodine-stained lizard head sample

description: <strong>General Data description:</strong> This is a hyperspectral (energy-resolved) X-ray CT projection dataset of a lizard head sample, stained with an iodine contrast agent. It was acquired in a custom-built, laboratory micro-CT scanner with an energy-sensitive HEXITEC detector in the Henry Moseley X-ray Imaging Facility at The University of Manchester. The following data contains all the files necessary for reconstruction, after a hyperspectral scan was taken of a single, iodine-stained lizard head sample. The iodine contrast agent provided a spectral marker, measured by an energy-sensitive detector, which may be used for spatial mapping and segmentation of stained soft tissue regions. <strong>File descriptions:</strong> Contained are three MATLAB (.mat) data files, two HDF5 (.h5) files, and a single text (.txt) file. Lizard_head_scan_parameters.txt provides the full sample and detector geometry of the scan acquisition. lizard_head_sinogram_full.mat contains the full 4D sinogram constructed following flatfield normalisation of the raw projection data. The 4D array contains the total number of energy channels acquired during scanning, followed by vertical and horizontal pixel number, and finally total projections angles acquired. The data provided is prior to application of any post-processing filters. The full set of 200 energy channels are included. Energy_axis.mat provides a direct conversion between the energy channels, and the energies (in keV) that they correspond to, following a calibration procedure prior to scanning. FF.mat contains the 4D flatfield data acquired when no sample was present. This data was used to normalise the projection datasets, as the sinogram was constructed. The full set of 200 energy channels are included. Lizard_Sino_1_200.h5 contains the full 4D sinogram, with all 200 channels, but in an h5 format to enable easier data reading. Here the sinogram has also had a ring-reduction filter applied, using a wavelet-based Fourier filter which suppresses the presence of ring artefacts in every energy channel. Lizard_Sino_100_140.h5 contains a cropped version of the 4D sinogram, with 40 channels taken in the channel range 100 to 140, stored in an h5 format to enable easier data reading. These 40 channels are known to contain the key spectral information regarding the K-edge of the iodine contrast agent. Here the sinogram has also had a ring-reduction filter applied, using a wavelet-based Fourier filter which suppresses the presence of ring artefacts in every energy channel.
DOI: 10.5281/zenodo.5012925
title: SGB.Sep20

description: PhyloPhlAn metagenomic database "SGB.Sep20"
DOI: 10.5281/zenodo.5012924
title: SGB.Sep20

description: PhyloPhlAn metagenomic database "SGB.Sep20"
DOI: 10.5281/zenodo.5012080
title: SGB.Nov20

description: PhyloPhlAn metagenomic database "SGB.Nov20"
DOI: 10.5281/zenodo.5012079
title: SGB.Nov20

description: PhyloPhlAn metagenomic database "SGB.Nov20"
DOI: 10.5281/zenodo.5013135
title: SGB.Dec20

description: PhyloPhlAn metagenomic database "SGB.Dec20"
DOI: 10.5281/zenodo.5013768
title: SGB.Dec20

description: PhyloPhlAn metagenomic database "SGB.Dec20"
DOI: 10.5281/zenodo.5013134
title: SGB.Dec20

description: PhyloPhlAn metagenomic database "SGB.Dec20"
DOI: 10.5281/zenodo.5008842
title: Social media images from Peneda-Gerês National Park, Northern Portugal

description: This dataset contains images from the Peneda-Gerês National Park, Northern Portugal. The images were collected from the Flickr and Wikiloc platforms considering a time period from 2003 to 2017. In respect to the General Data Protection Regulation 2016/679, social media data protected by users’ rights was not downloaded nor analysed. Public data that would potentially contain personal information from social media users was kept anonymous through the study. Data was retrieved through the use of the freely available Flickr’s Application Programming Interface (API), indicating a time window and a bounding box with a pair of coordinates (in our case: minimum latitude: 41.653104; maximum lat.: 42.083595; min. longitude: -8.426270; max. lon.: -7.754076) around Peneda-Gerês. This information was then saved as an excel file with the following attributes: user-id, date taken, latitude, longitude, picture uniform resource locator (url). A first annotation, in the context of cultural ecosystem services (CES), was performed by dividing the photographs of the dataset into “Indoor” and “Outdoor” classes. Only the “Outdoor” pictures were included in this study, since CES are directly connected to nature and environment, which in turn are related to the outside/outdoor. The “Outdoor” images were further divided into two main classes, “Natural” and “Human”, depending on whether the image was dominated by natural or man-made elements. Lastly, a finer annotation for outdoor images was also provided, which encompasses the following six classes: “Species”, “Landscape”, “Nature”, “Human activities”, “Human structures” and “Posing”. “Species” pictures respectively pertained to close-up shots of animals or plants in the wild, translating CES pertaining to biodiversity appreciation. “Landscape” pictures show wide-open shots of nature in the wild, often with a visible horizon most often representing people’s enjoyment of landscape aesthetics. “Human activities” include pictures where people engage in by recreational activities, for instance related to sports such as ski or cycling. “Human structures” include those pictures where man-made structures dominate in the wild, e.g., historical monuments and churches, capturing situations of cultural heritage and spiritual enrichment. “Posing” refers to pictures with people looking at the camera, with recognizable faces, testifying social enjoyment and sense of identity. Finally, “Nature” pictures capture natural elements with no particular feature (such as species) but with an intermediate shot (differing from wide-open shots attributed to landscapes), expressing the appreciation of nature by people.
DOI: 10.5281/zenodo.5008841
title: Social media images from Peneda-Gerês National Park, Northern Portugal

description: This dataset contains images from the Peneda-Gerês National Park, Northern Portugal. The images were collected from the Flickr and Wikiloc platforms considering a time period from 2003 to 2017. In respect to the General Data Protection Regulation 2016/679, social media data protected by users’ rights was not downloaded nor analysed. Public data that would potentially contain personal information from social media users was kept anonymous through the study. Data was retrieved through the use of the freely available Flickr’s Application Programming Interface (API), indicating a time window and a bounding box with a pair of coordinates (in our case: minimum latitude: 41.653104; maximum lat.: 42.083595; min. longitude: -8.426270; max. lon.: -7.754076) around Peneda-Gerês. This information was then saved as an excel file with the following attributes: user-id, date taken, latitude, longitude, picture uniform resource locator (url). A first annotation, in the context of cultural ecosystem services (CES), was performed by dividing the photographs of the dataset into “Indoor” and “Outdoor” classes. Only the “Outdoor” pictures were included in this study, since CES are directly connected to nature and environment, which in turn are related to the outside/outdoor. The “Outdoor” images were further divided into two main classes, “Natural” and “Human”, depending on whether the image was dominated by natural or man-made elements. Lastly, a finer annotation for outdoor images was also provided, which encompasses the following six classes: “Species”, “Landscape”, “Nature”, “Human activities”, “Human structures” and “Posing”. “Species” pictures respectively pertained to close-up shots of animals or plants in the wild, translating CES pertaining to biodiversity appreciation. “Landscape” pictures show wide-open shots of nature in the wild, often with a visible horizon most often representing people’s enjoyment of landscape aesthetics. “Human activities” include pictures where people engage in by recreational activities, for instance related to sports such as ski or cycling. “Human structures” include those pictures where man-made structures dominate in the wild, e.g., historical monuments and churches, capturing situations of cultural heritage and spiritual enrichment. “Posing” refers to pictures with people looking at the camera, with recognizable faces, testifying social enjoyment and sense of identity. Finally, “Nature” pictures capture natural elements with no particular feature (such as species) but with an intermediate shot (differing from wide-open shots attributed to landscapes), expressing the appreciation of nature by people.
DOI: 10.17632/6zncsfvhkz.1
title: Data for: Topological aspects responsible for recrystallization evolution in an IF-steel sheet - investigation with cellular-automaton simulations

description: The datasets describe the microstructure of the cold-rolled IF-steel in the as-deformed state (input RVE), the recrystallized state (experimental), and during the recrystallization simulation (at specific time steps). All necessary data for the application and analysis discussed in the manuscript are included and defined in the relevant column titles. All datasets are in text file formats and can be read by orientation analysis software (e.g. EDAX OIM, MTEX) or individual scripts.
DOI: 10.5281/zenodo.3758479
title: Cross-platform mentions of the QAnon conspiracy theory

description: This dataset contains mentions of the QAnon conspiracy theory across the Web between 28 October 2017 and 1 November 2018. The following list details the data per platform and its collection process: <strong>4chan: </strong>Posts and comments on 4chan/pol/ mentioning "Q" or "QAnon". The data is collected through 4CAT, a data capturing and analysis tool that hosts all posts and comments made on 4chan/pol/ since 2014. <strong>8chan:</strong> Posts and comments on the /qresearch/ board and other smaller boards mentioning "Q" or "QAnon". The data is derived qanon.news, a grassroots archive. Considering its amateur nature, the dataset is likely not 100% complete, but still includes over 200,000 posts. <strong>Reddit:</strong> Comments made on politically-oriented subreddits mentioning "Q" or "QAnon". The data is gathered through the Pushshift API. <strong>YouTube:</strong> Videos mentioning QAnon or "Q" in the title or video decription. The data is collected via the YouTube v3 API using the search endpoint. Multiple keywords were queried ("qanon", "qanon 4chan", etc) to collect a large sample. False positives were then filtered out manually. <strong>Breitbart:</strong> Disqus comments on Breitbart.com mentioning QAnon or "Q". The data was gathered by crawling all of Breitbart.com in the timeframe and using the Disqus API. <strong>Online news media</strong>: Articles from English online news sources mentioning QAnon. The data is derived from Nexis Uni and ContextualWeb Search by searching for "QAnon". Irrelevant sources and false positives were filtered manually. The datasets include timestamps, text bodies, and platform-specific information like subreddits and channel titles. To collect data from 4chan, 8chan, Reddit, and Breitbart, we used the same SQL query, sampled 200 comments, and edited the query to so it would have sufficient number of true positives (&gt; 94%). The YouTube and online news media datasets are filtered manually. For Breitbart and Reddit, the data is anonymised by omitting author information. The online news media article text is omitted because of copyright concerns. See the article on First Monday for the full collection process.
DOI: 10.5281/zenodo.3758478
title: Cross-platform mentions of the QAnon conspiracy theory

description: This dataset contains mentions of the QAnon conspiracy theory across the Web between 28 October 2017 and 1 November 2018. The following list details the data per platform and its collection process: <strong>4chan: </strong>Posts and comments on 4chan/pol/ mentioning "Q" or "QAnon". The data is collected through 4CAT, a data capturing and analysis tool that hosts all posts and comments made on 4chan/pol/ since 2014. <strong>8chan:</strong> Posts and comments on the /qresearch/ board and other smaller boards mentioning "Q" or "QAnon". The data is derived qanon.news, a grassroots archive. Considering its amateur nature, the dataset is likely not 100% complete, but still includes over 200,000 posts. <strong>Reddit:</strong> Comments made on politically-oriented subreddits mentioning "Q" or "QAnon". The data is gathered through the Pushshift API. <strong>YouTube:</strong> Videos mentioning QAnon or "Q" in the title or video decription. The data is collected via the YouTube v3 API using the search endpoint. Multiple keywords were queried ("qanon", "qanon 4chan", etc) to collect a large sample. False positives were then filtered out manually. <strong>Breitbart:</strong> Disqus comments on Breitbart.com mentioning QAnon or "Q". The data was gathered by crawling all of Breitbart.com in the timeframe and using the Disqus API. <strong>Online news media</strong>: Articles from English online news sources mentioning QAnon. The data is derived from Nexis Uni and ContextualWeb Search by searching for "QAnon". Irrelevant sources and false positives were filtered manually. The datasets include timestamps, text bodies, and platform-specific information like subreddits and channel titles. To collect data from 4chan, 8chan, Reddit, and Breitbart, we used the same SQL query, sampled 200 comments, and edited the query to so it would have sufficient number of true positives (&gt; 94%). The YouTube and online news media datasets are filtered manually. For Breitbart and Reddit, the data is anonymised by omitting author information. The online news media article text is omitted because of copyright concerns. See the article on First Monday for the full collection process.
DOI: 10.5281/zenodo.3678199
title: News article mentions of 4chan from three weeks in 2017 and posts with links to these articles on 4chan/pol/

description: This upload includes two dataset. The first comprises articles that mentioning "4chan" in its post body as retreived by Nexis Uni. We identified the three weeks in which the highest spikes in terms of the amount of articles occured in 2017 (see the image mentions_nexis_uni_2017_weeks.png ) and extracted the articles that were published within these. The dataset includes the article source, the article title, and the sentences where they mention 4chan to analyse the framing. We deleted the article bodies for copyright reasons. Two columns indicate the URL to the article if it appeared online. Additionally, we added a column with URLs to archive.is links of the same articles, in case they were archived. The second dataset consists of posts on the imageboard 4chan/pol/ that refer to one of the aforementioned URLs.