cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7848575
title: SCA-2023: A two-part dataset for benchmarking the methods of image precompensation for users with refractive errors

description: The recent practices of demonstrating various static and video images to users by means of digital, processor-controlled, often self-luminous devices (computer monitors, smartphone and tablet screens, etc.) have spurred the development of various methods for improving the perception of such images through their computer processing. In particular, this applies to the task of precompensating images shown to users with various anomalies of refraction of the eyes (e.g. myopia or astigmatism) in situations where they are not equipped with glasses or other corrective devices. Researchers have proposed a considerable number of such precompensation methods, but to this day there has been no way to accurately compare their quality. We propose an original dataset, which we called “SCA-2023”, of images specially designed for this purpose. Its most important feature is the fact that it includes not only a set of ground-truth images for implementing the precompensation transform, but also a separate set of images characterizing specific types and degrees of manifestation of the refractive errors. The benchmarking procedure itself includes applying the precompensation transformation to a certain image from the first part of the dataset, computer simulation of the so-called retinal image (distribution of light on the retina of an imaginary observer) based on the selection of the “distorting eye” from the second part of the dataset, and evaluating the similarity of this image to the ground-truth image, using any of the commonly used similarity metrics for this purpose.
DOI: 10.5281/zenodo.7849058
title: replicAnt - Plum2023 - 3D Models - Unreal Engine 5

description: This dataset contains the 3D models used to generate all synthetic data presented in the <em>replicAnt - generating annotated images of animals in complex environments using Unreal Engine </em>manuscript. The models have been generated with the open-source photogrammetry platform <em>scAnt</em> peerj.com/articles/11155/ and have been pre-processed and converted into Unreal Engine 5 compatible .uasset files, to be used with the associated <em>replicAnt</em> project available from https://github.com/evo-biomech/replicAnt. <strong>Abstract:</strong> Deep learning-based computer vision methods are transforming animal behavioural research. Transfer learning has enabled work in non-model species, but still requires hand-annotation of example footage, and is only performant in well-defined conditions. To overcome these limitations, we created <em>replicAnt</em>, a configurable pipeline implemented in Unreal Engine 5 and Python, designed to generate large and variable training datasets on consumer-grade hardware instead. <em>replicAnt</em> places 3D animal models into complex, procedurally generated environments, from which automatically annotated images can be exported. We demonstrate that synthetic data generated with <em>replicAnt</em> can significantly reduce the hand-annotation required to achieve benchmark performance in common applications such as animal detection, tracking, pose-estimation, and semantic segmentation; and that it increases the subject-specificity and domain-invariance of the trained networks, so conferring robustness. In some applications, <em>replicAnt</em> may even remove the need for hand-annotation altogether. It thus represents a significant step towards porting deep learning-based computer vision tools to the field. <strong>Funding</strong> This study received funding from Imperial College’s President’s PhD Scholarship (to Fabian Plum), and is part of a project that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 851705, to David Labonte). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
DOI: 10.5281/zenodo.7849059
title: replicAnt - Plum2023 - 3D Models - Unreal Engine 5

description: This dataset contains the 3D models used to generate all synthetic data presented in the <em>replicAnt - generating annotated images of animals in complex environments using Unreal Engine </em>manuscript. The models have been generated with the open-source photogrammetry platform <em>scAnt</em> peerj.com/articles/11155/ and have been pre-processed and converted into Unreal Engine 5 compatible .uasset files, to be used with the associated <em>replicAnt</em> project available from https://github.com/evo-biomech/replicAnt. <strong>Abstract:</strong> Deep learning-based computer vision methods are transforming animal behavioural research. Transfer learning has enabled work in non-model species, but still requires hand-annotation of example footage, and is only performant in well-defined conditions. To overcome these limitations, we created <em>replicAnt</em>, a configurable pipeline implemented in Unreal Engine 5 and Python, designed to generate large and variable training datasets on consumer-grade hardware instead. <em>replicAnt</em> places 3D animal models into complex, procedurally generated environments, from which automatically annotated images can be exported. We demonstrate that synthetic data generated with <em>replicAnt</em> can significantly reduce the hand-annotation required to achieve benchmark performance in common applications such as animal detection, tracking, pose-estimation, and semantic segmentation; and that it increases the subject-specificity and domain-invariance of the trained networks, so conferring robustness. In some applications, <em>replicAnt</em> may even remove the need for hand-annotation altogether. It thus represents a significant step towards porting deep learning-based computer vision tools to the field. <strong>Funding</strong> This study received funding from Imperial College’s President’s PhD Scholarship (to Fabian Plum), and is part of a project that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 851705, to David Labonte). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
DOI: 10.4121/21763220
title: River plastic measurements in the Rhine, Odaw and Mekong 2021-2022

description: We measured floating plastic in the Rhine (Netherlands to Switzerland), Odaw (Ghana) and Mekong (Cambodia) rivers using visual counting from bridges. We also measured riverbank and terrestrial plastic density in the Odaw river through physical sampling and classification.<br>We measured river plastic pollution in three rivers across relevant gradients, including geography, hydrology, and plastic pollution levels. In the Rhine basin (Switzerland, France, Germany, the Netherlands) we showed that urban areas and tributaries may act as entry points of plastic pollution. For the Odaw basin (Ghana) we compared floating, terrestrial and riverbank plastics, identifying source and accumulation zones. Finally, in the Mekong river (Cambodia) we quantified the contribution of the city of Phnom Penh to plastic pollution through quantifying the plastic mass balance in the Mekong-Tonle Sap-Bassac region.<br>
DOI: 10.4121/21763220.v1
title: River plastic measurements in the Rhine, Odaw and Mekong 2021-2022

description: We measured floating plastic in the Rhine (Netherlands to Switzerland), Odaw (Ghana) and Mekong (Cambodia) rivers using visual counting from bridges. We also measured riverbank and terrestrial plastic density in the Odaw river through physical sampling and classification.<br>We measured river plastic pollution in three rivers across relevant gradients, including geography, hydrology, and plastic pollution levels. In the Rhine basin (Switzerland, France, Germany, the Netherlands) we showed that urban areas and tributaries may act as entry points of plastic pollution. For the Odaw basin (Ghana) we compared floating, terrestrial and riverbank plastics, identifying source and accumulation zones. Finally, in the Mekong river (Cambodia) we quantified the contribution of the city of Phnom Penh to plastic pollution through quantifying the plastic mass balance in the Mekong-Tonle Sap-Bassac region.<br>
DOI: 10.6084/m9.figshare.22110681
title: Derivation and internal validation of a clinical prediction score to predict major effect or death in acute metamfetamine toxicity

description: Metamfetamine use can cause serious complications or death. We aimed to derive and internally validate a clinical prediction score to predict major effect or death in acute metamfetamine toxicity. We performed secondary analysis of 1,225 consecutive cases reported from all local public emergency departments to the Hong Kong Poison Information Centre between 1 January 2010 and 31 December 2019. We split the entire dataset chronologically into derivation (first 70% of cases) and validation (the remaining 30% of cases) cohorts. Univariate analysis was conducted, followed by multivariable logistic regression in the derivation cohort to identify independent predictors of major effect or death. We developed a clinical prediction score based on the regression coefficients of the independent predictors in the regression model and compared its discriminatory performance with five existing early warning scores in the validation cohort. The MASCOT (Male, Age, Shock, Consciousness, Oxygen, Tachycardia) score was derived based on the six independent predictors: male gender (1 point), age (≥35 years, 1 point), shock (mean arterial pressure &lt;65 mmHg, 3 points), consciousness (Glasgow Coma Scale &lt;13, 2 points), need for supplemental oxygen (1 point), and tachycardia (pulse rate &gt;120 beats/min, 1 point). The score ranges from 0–9, with a higher score indicating higher risk. The area under the receiver operating characteristic curve of the MASCOT score was 0.87 (95% CI 0.81–0.93) in the derivation cohort and 0.91 (95% CI 0.81–1.00) in the validation cohort, with a discriminatory performance comparable with existing scores. The MASCOT score enables quick risk stratification in acute metamfetamine toxicity. Further external validation is warranted before wider adoption.
DOI: 10.6084/m9.figshare.22110681.v1
title: Derivation and internal validation of a clinical prediction score to predict major effect or death in acute metamfetamine toxicity

description: Metamfetamine use can cause serious complications or death. We aimed to derive and internally validate a clinical prediction score to predict major effect or death in acute metamfetamine toxicity. We performed secondary analysis of 1,225 consecutive cases reported from all local public emergency departments to the Hong Kong Poison Information Centre between 1 January 2010 and 31 December 2019. We split the entire dataset chronologically into derivation (first 70% of cases) and validation (the remaining 30% of cases) cohorts. Univariate analysis was conducted, followed by multivariable logistic regression in the derivation cohort to identify independent predictors of major effect or death. We developed a clinical prediction score based on the regression coefficients of the independent predictors in the regression model and compared its discriminatory performance with five existing early warning scores in the validation cohort. The MASCOT (Male, Age, Shock, Consciousness, Oxygen, Tachycardia) score was derived based on the six independent predictors: male gender (1 point), age (≥35 years, 1 point), shock (mean arterial pressure &lt;65 mmHg, 3 points), consciousness (Glasgow Coma Scale &lt;13, 2 points), need for supplemental oxygen (1 point), and tachycardia (pulse rate &gt;120 beats/min, 1 point). The score ranges from 0–9, with a higher score indicating higher risk. The area under the receiver operating characteristic curve of the MASCOT score was 0.87 (95% CI 0.81–0.93) in the derivation cohort and 0.91 (95% CI 0.81–1.00) in the validation cohort, with a discriminatory performance comparable with existing scores. The MASCOT score enables quick risk stratification in acute metamfetamine toxicity. Further external validation is warranted before wider adoption.
DOI: 10.34943/8899ca59-6c0c-4732-8567-f1308e6e1ed4
title: ODP 1026 Broadband Seismometer Deployed 2010-10-06

description: The Guralp CMG-IT Broadband Seismometer 2533 was deployed on 2010-10-06 at ODP 1026. ODP 1026 is a borehole site used to pinpoint an area within Cascadia. This device is a Broadband Seismometer. Broadband Seismometers measure seismic waves over a broad frequency range depending on the device (e.g. 0.00278 Hz - 250 Hz). A broadband seismometer facilitates measurement of seismic events in the widest frequency band possible. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.3886/e183161
title: Data and Code for: Information, Mobile Communication, and Referral Effects

description: This paper uses the universe of cellphone records from a Chinese telecommunication provider for a northern Chinese city to examine the role of information exchange in urban labor markets. We provide the first direct evidence of increased communication among referral pairs around job changes. Information provided by social contacts mitigates information asymmetry and improves labor market performance.
DOI: 10.3886/e183161v1
title: Data and Code for: Information, Mobile Communication, and Referral Effects

description: This paper uses the universe of cellphone records from a Chinese telecommunication provider for a northern Chinese city to examine the role of information exchange in urban labor markets. We provide the first direct evidence of increased communication among referral pairs around job changes. Information provided by social contacts mitigates information asymmetry and improves labor market performance.
DOI: 10.5281/zenodo.7220573
title: Source data belonged to "Establishing structure-property linkages for wicking time predictions in porous polymeric membranes using a data-driven approach"

description: This record contains all the necessary data to obtain the results of the study "Establishing structure-property linkages for wicking time predictions in porous polymeric membranes using a data-driven approach"
DOI: 10.5281/zenodo.7220572
title: Source data belonged to "Establishing structure-property linkages for wicking time predictions in porous polymeric membranes using a data-driven approach"

description: This record contains all the necessary data to obtain the results of the study "Establishing structure-property linkages for wicking time predictions in porous polymeric membranes using a data-driven approach"
DOI: 10.18462/iif.nitec51.04.2023
title: Renewable energy today - A quick overview. 51st Informatory Note on Refrigeration Technologies.
DOI: 10.5281/zenodo.7849576
title: ICDAR 2021 Historical Document Classification Test Dataset for Task 3 - Location

description: Test set for the location classification task of the ICDAR 2021 Historical Document Classification.
DOI: 10.5281/zenodo.7849575
title: ICDAR 2021 Historical Document Classification Test Dataset for Task 3 - Location

description: Test set for the location classification task of the ICDAR 2021 Historical Document Classification.
DOI: 10.6084/m9.figshare.22665535.v1
title: Accounting for central place foraging constraints in habitat selection studies

description: "CP-dependent_landscape.asc" is the file corresponding to the CP-dependent landscape "CP-independent_landscape.asc" is the file corresponding to the CP-independent landscape HABITAT_SELECTION_pseudo-code.sim is the code used to simulate a biased correlated random walk for the conditional logistic regression analysis.
DOI: 10.5281/zenodo.7747186
title: Multidimensional specialization and generalization are pervasive in soil prokaryotes with generalists dominating communities and specialists more central in networks

description: Project folder to run analyses in the manuscript "<strong>Multidimensional specialization and generalization are pervasive in soil prokaryotes with generalists dominating communities and specialists more central in networks</strong>" with necessary raw and processed data. Manuscript abstract: Habitat specialization underpins biological processes from species distributions to speciation. However, organisms are often described as specialists or generalists based on a single niche axis, despite facing complex, multidimensional environments. Here, we analyzed 236 prokaryotic communities across the United States demonstrating for the first time that 90% of &gt;1,200 prokaryotes followed one of two trajectories: specialization on all niche axes (multidimensional specialization) or generalization on all axes (multidimensional generalization). We then documented that this pervasive multidimensional specialization/generalization had a wide range of ecological and evolutionary consequences. First, multidimensional specialization and generalization are highly conserved with very few transitions between these two trajectories. Second, multidimensional generalists dominated communities because they were 73 times more abundant than specialists. Lastly, multidimensional specialists played important roles in community structure with ~220% more connections in microbiome networks. These results indicate that multidimensional generalization and specialization are evolutionarily stable with multidimensional generalists supporting larger populations and multidimensional specialists playing important roles within communities likely stemming from their overrepresentation among pollutant detoxifiers and nutrient cyclers. Taken together, we demonstrate that the vast majority of soil prokaryotes are restricted to one of two multidimensional niche trajectories, multidimensional specialization or multidimensional generalization, which then has far-reaching consequences for evolutionary transitions, microbial dominance, and community roles.
DOI: 10.5519/qd.3rzfho4a
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (6 records)
DOI: 10.5281/zenodo.7747185
title: Multidimensional specialization and generalization are pervasive in soil prokaryotes with generalists dominating communities and specialists more central in networks

description: Project folder to run analyses in the manuscript "<strong>Multidimensional specialization and generalization are pervasive in soil prokaryotes with generalists dominating communities and specialists more central in networks</strong>" with necessary raw and processed data. Manuscript abstract: Habitat specialization underpins biological processes from species distributions to speciation. However, organisms are often described as specialists or generalists based on a single niche axis, despite facing complex, multidimensional environments. Here, we analyzed 236 prokaryotic communities across the United States demonstrating for the first time that 90% of &gt;1,200 prokaryotes followed one of two trajectories: specialization on all niche axes (multidimensional specialization) or generalization on all axes (multidimensional generalization). We then documented that this pervasive multidimensional specialization/generalization had a wide range of ecological and evolutionary consequences. First, multidimensional specialization and generalization are highly conserved with very few transitions between these two trajectories. Second, multidimensional generalists dominated communities because they were 73 times more abundant than specialists. Lastly, multidimensional specialists played important roles in community structure with ~220% more connections in microbiome networks. These results indicate that multidimensional generalization and specialization are evolutionarily stable with multidimensional generalists supporting larger populations and multidimensional specialists playing important roles within communities likely stemming from their overrepresentation among pollutant detoxifiers and nutrient cyclers. Taken together, we demonstrate that the vast majority of soil prokaryotes are restricted to one of two multidimensional niche trajectories, multidimensional specialization or multidimensional generalization, which then has far-reaching consequences for evolutionary transitions, microbial dominance, and community roles.
DOI: 10.6084/m9.figshare.19187471
title: Annotation files

description: Largemouth bass genome annotation
DOI: 10.6084/m9.figshare.19187471.v1
title: genome annotation

description: largemouth bass genome annotation
DOI: 10.15156/bio/2912106
title: Pseudohydnum alignments for Spirin et al.

description: Alignment files used as a basis for phylogenetic trees in Spirin V, Malysheva V, Viner I, Dudka V, Grebenc T, Miettinen M: Taxonomy and multigene phylogeny of Pseudohydnum (Auriculariales, Basidiomycota)
DOI: 10.5281/zenodo.7846221
title: FLUTE: a Python GUI for interactive phasor analysis of FLIM data

description: This repository contains the Fluorescence lifetime imaging microscopy (FLIM) data relative to the following publication <em>"FLUTE: a Python GUI for interactive phasor analysis of FLIM data" </em>https://www.biorxiv.org/content/10.1101/2023.03.31.534529v1 <em><strong>Fluorescein.tif</strong> </em>stack contains the fluorescence intensity decay of fluorescein solution with a known lifetime of 4ns, used as calibration. <strong><em>Embryo.tif</em></strong> file contains the fluorescence intensity decay of a zebrafish embryo at 3 days post fertilisation. Both files have been acquired with the following parameters: temporal bin number = 56 laser repetition rates = 80 MHz bin width = 0.223ns
DOI: 10.15156/bio/sh393487.07fu
title: SH393487.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh393488.07fu
title: SH393488.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.