cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20131321
title: Additional file 9 of Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis)

description: Additional file 9: Table S4. Clusters of contiguous clade-specific genes. Clusters were identified amongst sets of genes deemed specific of the focal clade based on detection by either Pantagruel or GET_HOMOLOGUES pipelines. a) Clusters of genes specific to All. vitis species complex (present in all All. vitis sensu stricto, All. ampelinum and Allorhizobium sp. Av2, and in no other Allorhizobium spp.). b) Clusters of genes specific to All. vitis sensu stricto (present in all five tested strains and in none of All. ampelinum). c) Clusters of genes specific to All. ampelinum (present in all eight tested strains and in none of All. vitis sensu stricto).
DOI: 10.6084/m9.figshare.20131315
title: Additional file 7 of Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis)

description: Additional file 7: Table S2. Pairwise OGRI comparisons amongst 14 All. vitis species complex strain genomes towards species delimitation. a) ANIb comparisons. b) ANIm comparisons. c) orthoANIu comparisons. d) fastANI comparisons. e) dDDH comparisons.
DOI: 10.17043/sjostrom-2022-davidsmosse-1
title: Chemical and mineral composition of peat and soils samples, Halland province, southwestern Sweden
DOI: 10.6084/m9.figshare.20131670
title: SI for Muli-Jinpingshan thrust

description: AHe, AFT and ZFT ages
DOI: 10.6084/m9.figshare.20131670.v2
title: SI for Muli-Jinpingshan thrust

description: AHe, AFT and ZFT ages
DOI: 10.6084/m9.figshare.20131670.v1
title: Muli tables.docx

description: AHe, AFT and ZFT ages
DOI: 10.4119/unibi/2963964
title: Data Publication for: Effort−Reward Imbalance at Work and Prescription Drug Misuse - Prospective Evidence from Germany

description: This study examines how work stress affects the misuse of prescription drugs to augment mental performance without medical necessity (i.e., cognitive enhancement). Based on the effort−reward imbalance model, it can be assumed that a misalignment of effort exerted and rewards received increases prescription drug misuse, especially if employees overcommit. To test these assump-tions, we conducted a prospective study using a nationwide web-based sample of the working population in Germany (N = 11,197). Effort, reward, and overcommitment were measured at t1 and the 12 month frequency of prescription drug misuse for enhancing cognitive performance was measured at a one-year follow-up (t2). The results show that 2.6% of the respondents engaged in such drug misuse, of which 22.7% reported frequent misuse. While we found no overall associa-tion between misuse frequency and effort, reward, or their imbalance, overcommitment was sig-nificantly associated with a higher misuse frequency. Moreover, at low levels of overcommitment, more effort and an effort−reward imbalance discouraged future prescription drug misuse, while higher overcommitment, more effort, and an imbalance increased it. These findings suggest that a stressful work environment is a risk factor for health-endangering behavior, and thereby under-lines the importance of identifying groups at risk of misusing drugs.
DOI: 10.25421/yorksj.20089349
title: Excel Data File (A longitudinal examination of executive function, visual attention, and soccer penalty performance)

description: This is the Excel file for the PhD study of Jack Brimmell entitled: A longitudinal examination of executive function, visual attention, and soccer penalty performance.
DOI: 10.25421/yorksj.20089349.v2
title: Excel Data File (A longitudinal examination of executive function, visual attention, and soccer penalty performance)

description: This is the Excel file for the PhD study of Jack Brimmell entitled: A longitudinal examination of executive function, visual attention, and soccer penalty performance.
DOI: 10.25421/yorksj.20089349.v1
title: Excel Data File

description: This is the Excel file for the PhD study of Jack Brimmell entitled: A longitudinal examination of executive function, visual attention, and soccer penalty performance.
DOI: 10.6084/m9.figshare.19873927
title: Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus

description: <em>Aspergillus fumigatus</em> is both an environmental saprobe and an opportunistic human fungal pathogen. Knowledge of genomic variation across <em>A. fumigatus </em>isolates is essential for understanding the evolution of pathogenicity, virulence, and resistance to antifungal drugs. Here, we investigated 206 <em>A. fumigatus</em> isolates (133 clinical and 73 environmental isolates) aiming to identify genes with variable presence across isolates and test whether this variation was related to the clinical or environmental origin of isolates. The PanOrtho genome of <em>A. fumigatus </em>constitutes 13,085 ortholog groups, of which 7,773 (59.4%) are shared by all isolates (CORE) and 5,312 (40.6%) vary in their gene presence across isolates (ACCESSORY plus singletons). Despite differences in the distribution of orthologs across all isolates, no significant differences were observed among clinical versus environmental isolates when accounting for phylogeny. Orthologs that differ in their distribution across isolates tend to occur in low frequency and/or be restricted to specific isolates; thus, the degree of genomic conservation between orthologs of <em>A. fumigatus </em>is high. These results suggest that differences in the distribution of orthologs within <em>A. fumigatus </em>cannot be associated with the clinical or environmental origin of isolates.
DOI: 10.6084/m9.figshare.19873927.v1
title: Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus

description: <em>Aspergillus fumigatus</em> is both an environmental saprobe and an opportunistic human fungal pathogen. Knowledge of genomic variation across <em>A. fumigatus </em>isolates is essential for understanding the evolution of pathogenicity, virulence, and resistance to antifungal drugs. Here, we investigated 206 <em>A. fumigatus</em> isolates (133 clinical and 73 environmental isolates) aiming to identify genes with variable presence across isolates and test whether this variation was related to the clinical or environmental origin of isolates. The PanOrtho genome of <em>A. fumigatus </em>constitutes 13,085 ortholog groups, of which 7,773 (59.4%) are shared by all isolates (CORE) and 5,312 (40.6%) vary in their gene presence across isolates (ACCESSORY plus singletons). Despite differences in the distribution of orthologs across all isolates, no significant differences were observed among clinical versus environmental isolates when accounting for phylogeny. Orthologs that differ in their distribution across isolates tend to occur in low frequency and/or be restricted to specific isolates; thus, the degree of genomic conservation between orthologs of <em>A. fumigatus </em>is high. These results suggest that differences in the distribution of orthologs within <em>A. fumigatus </em>cannot be associated with the clinical or environmental origin of isolates.
DOI: 10.5281/zenodo.5506647
title: Data collection for article "Quantifying Local Ecosystem Service Outcomes by Modelling Their Supply, Demand and Flow in Myanmar's Forest Frontier Landscape"

description: This dataset contains the nine ecosystem service models (in .neta format) underlying the publication "Quantifying Local Ecosystem Service Outcomes by Modelling Their Supply, Demand and Flow in Myanmar’s Forest Frontier Landscape". The ecosystem models were implemented using the commercial software Netica (version 6.05) for constructing and analysing Bayesian Networks.
DOI: 10.5281/zenodo.5506646
title: Data collection for article "Quantifying Local Ecosystem Service Outcomes by Modelling Their Supply, Demand and Flow in Myanmar's Forest Frontier Landscape"

description: This dataset contains the nine ecosystem service models (in .neta format) underlying the publication "Quantifying Local Ecosystem Service Outcomes by Modelling Their Supply, Demand and Flow in Myanmar’s Forest Frontier Landscape". The ecosystem models were implemented using the commercial software Netica (version 6.05) for constructing and analysing Bayesian Networks.
DOI: 10.34740/kaggle/dsv/3850404
title: AutoXGB
DOI: 10.5281/zenodo.6697321
title: Dataset for the Manuscript: Demonstration of optically-driven plasmonic nanomotors designed by deep learning networks

description: This repository contains the data corresponding to the manuscript "Demonstration of the optically-driven plasmonic nanomotor designed by deep learning networks." It consists of 5 parts: Machine learning, Numerical analysis, Rotation measurement, Scattering measurement, and Supplementary information. The code for the machine learning algorithm is available at "https://github.com/mintaechung/Nanomotor_Predictor_Generator." <strong>'Machine_learning.zip'</strong>: Correlation between optical torques calculated by SIE and predicted by trained CNN, Objective loss functions at the 1st iteration, and the torque distribution of the initial randomset and the output of the nanorotor generator after the 3rd iteration. <strong>'Numerical_analysis.zip'</strong>: MATLAB codes to retrieve 'Moments', 'Field intensity distribution', 'Poynting vectors', and 'Torques'. <strong>'Rotation_measurement.zip'</strong>: Raw videos, Intensity profiles of ROI, Rotation measurement results. <strong>'Scattering_measurement.zip'</strong>: Scattering intensity measurement with reference light. <strong>'Supplementary_Info.zip'</strong>: Random geometry generation, Optical torques of 6 blades, Expanded structure, Shrinkage, Polarization independence, Angular momentum, and Machine learning progress.
description: Funding from the European Research Council (ERC-2015-AdG-695206 Nanofactory)
DOI: 10.5281/zenodo.6637950
title: Dataset for the Manuscript: Demonstration of optically-driven plasmonic nanomotors designed by deep learning networks

description: This repository contains the data corresponding to the manuscript "Demonstration of the optically-driven plasmonic nanomotor designed by deep learning networks." It consists of 5 parts: Machine learning, Numerical analysis, Rotation measurement, Scattering measurement, and Supplementary information. The code for the machine learning algorithm is available at "https://github.com/mintaechung/Nanomotor_Predictor_Generator." <strong>'Machine_learning.zip'</strong>: Correlation between optical torques calculated by SIE and predicted by trained CNN, Objective loss functions at the 1st iteration, and the torque distribution of the initial randomset and the output of the nanorotor generator after the 3rd iteration. <strong>'Numerical_analysis.zip'</strong>: MATLAB codes to retrieve 'Moments', 'Field intensity distribution', 'Poynting vectors', and 'Torques'. <strong>'Rotation_measurement.zip'</strong>: Raw videos, Intensity profiles of ROI, Rotation measurement results. <strong>'Scattering_measurement.zip'</strong>: Scattering intensity measurement with reference light. <strong>'Supplementary_Info.zip'</strong>: Random geometry generation, Optical torques of 6 blades, Expanded structure, Shrinkage, Polarization independence, Angular momentum, and Machine learning progress.
description: Funding from the European Research Council (ERC-2015-AdG-695206 Nanofactory)
DOI: 10.5281/zenodo.6697342
title: CoFly-WeedDB: A UAV image dataset for weed detection and species identification

description: The CoFly-WeedDB contains 201 RGB images (~436MB) from the attached camera of DJI Phantom Pro 4 from a cotton field in Larissa, Greece during the first stages of plant growth. The RGB images were collected while the Unmanned Aerial Vehicle (UAV) was performing a coverage mission over the field's area. During the designed mission, the camera angle was adjusted to -87°, vertically with the field. The flight altitude and speed of the UAV were equal to 5m and 3m/s, respectively, aiming to provide a close and clear view of the weed instances. All images have been annotated by expert agronomists using the LabelMe annotation tool, providing the exact boundaries of 3 types of common weeds in this type of crop, namely (i) Johnson grass, (ii) Field bindweed, and (iii) Purslane. The dataset can be used alone and in combination with other datasets to develop AI-based methodologies for automatic weed segmentation and classification purposes.
description: This research has been financed by the European Regional Development Fund of the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH - CREATE - INNOVATE (T1EDK-00636).
DOI: 10.5281/zenodo.6695805
title: Dataset and R script for Collection and Processing of Behavioural Data of the Olive Fruit Fly, Bactrocera oleae, when Exposed to Olive Twigs Treated with Different Commercial Products

description: We provide raw data and R script for analysis of data published in: 1) Daher, E.; Cinosi, N.; Chierici, E.; Rondoni, G.; Famiani, F.; Conti, E. Field and Laboratory Efficacy of Low-Impact Commercial<br> Products in Preventing Olive Fruit Fly, Bactrocera oleae, Infestation. Insects 2022, 13, 213. https://doi.org/10.3390/insects13020213 2) Daher, E.; Chierici, E.; Cinosi, N.; Rondoni, G.; Famiani, F.; Conti, E. Collection and Processing of Behavioural Data of the Olive Fruit Fly, <em>Bactrocera oleae</em>, when Exposed to Olive Twigs Treated with Different Commercial Products. <em>Data </em><strong>2022</strong>, <em>7</em>,
DOI: 10.5281/zenodo.6695804
title: Dataset and R script for Collection and Processing of Behavioural Data of the Olive Fruit Fly, Bactrocera oleae, when Exposed to Olive Twigs Treated with Different Commercial Products

description: We provide raw data and R script for analysis of data published in: 1) Daher, E.; Cinosi, N.; Chierici, E.; Rondoni, G.; Famiani, F.; Conti, E. Field and Laboratory Efficacy of Low-Impact Commercial<br> Products in Preventing Olive Fruit Fly, Bactrocera oleae, Infestation. Insects 2022, 13, 213. https://doi.org/10.3390/insects13020213 2) Daher, E.; Chierici, E.; Cinosi, N.; Rondoni, G.; Famiani, F.; Conti, E. Collection and Processing of Behavioural Data of the Olive Fruit Fly, <em>Bactrocera oleae</em>, when Exposed to Olive Twigs Treated with Different Commercial Products. <em>Data </em><strong>2022</strong>, <em>7</em>,
DOI: 10.21227/w45r-mb55
title: Conversion Loss Simulation Data

description: This dataset is created for neural network-based surrogate modeling of the power conversion losses. The dataset includes two sets of training and test data (for AC/DC and DC/DC converters respectively) for the neural network. The raw data is generated using PLECS Blockset Packages in MATLAB-Simulink environment.
DOI: 10.24417/bmdc.be:dataset:2720
title: 3D voxel model of the Hinder Banks

description: Three-dimensional voxel model of the geological subsurface of the Hinderbanks containing information on probabilities of lithological classes (2: clay, 3: silt, 5: fine sand, 6: medium sand, 7: coarse sand and 8: gravel) and stratigraphy (1: Upper Holocene Nearshore, 2: Upper Holocene Offshore, 3: Lower Holocene, 4: Pleistocene and 5: Paleogene), estimated percentages of lithoclasses (clay, silt, mud, fine sand, medium sand, coarse sand, gravel and shells), and uncertainties (borehole density, entropie, positional quality, sampling quality and vintage).
DOI: 10.5281/zenodo.6320571
title: Escherichia coli 13k assemblies PopPUNK database

description: # _Escherichia coli_ 13k reference<br> ## PopPUNK database files<br> ## v1.0.0 (1 March 2022)<br> ### Description<br> This tarball contains the PopPUNK v2.4.0 [1] database files of a<br> clustering for the 13435 _E. coli_ assemblies from three studies<br> [2-4]. A file matching the clustering with the multilocus sequence<br> types [5] (identified using mlst v2.19.0 [6]) is provided in<br> `ecoli_sequence_information.tsv`. The corresponding assemblies and a Themisto v2.1.0 [7] pseudoalignment<br> index are also available as separate uploads in Zenodo. __Note:__ the `esc_ra9772aa_as` entry in the PopPUNK files does not<br> have a corresponding assembly nor is it included in the Themisto<br> pseudoalignment index or the `ecoli_sequence_information.tsv`<br> file. This is because the entry for this sequence was corrupted in the<br> original run of PopPUNK. ### Files<br> - `pop_db`: the PopPUNK sketch files.<br> - `pop_fit_dbscan`: the initial DBSCAN fit for the sketch.<br> - `pop_fit_refined`: the final refined version of the DBSCAN fit.<br> - `pop_fit_refined_viz`: microreact visualisation files from the refined fit.<br> - `ecoli_sequence_information.tsv`: a tab-separated text file containing the MLST types and the PopPUNK clusters. ### References<br> - [1] Lees J et al., _Fast and flexible bacterial genomic epidemiology with PopPUNK._ https://doi.org/10.1101/gr.241455.118<br> - [2] Horesh G et al., _A comprehensive and high-quality collection of Escherichia coli genomes and their genes._ https://doi.org/10.1099/mgen.0.000499<br> - [3] Gladstone R et al., _Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study._ https://doi.org/10.1016/S2666-5247(21)00031-8<br> - [4] Shao Y et al., _Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth._ https://doi.org/10.1038/s41586-019-1560-1<br> - [5] Jolley K et al., _Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications._ https://doi.org/10.12688/wellcomeopenres.14826.1<br> - [6] Seemann T, _mlst_ _GitHub._ https://github.com/tseemann/mlst<br> - [7] Mäklin T et al., _Bacterial genomic epidemiology with mixed samples._ https://doi.org/10.1099/mgen.0.000691
DOI: 10.5281/zenodo.6320570
title: Escherichia coli 13k assemblies PopPUNK database

description: # _Escherichia coli_ 13k reference<br> ## PopPUNK database files<br> ## v1.0.0 (1 March 2022)<br> ### Description<br> This tarball contains the PopPUNK v2.4.0 [1] database files of a<br> clustering for the 13435 _E. coli_ assemblies from three studies<br> [2-4]. A file matching the clustering with the multilocus sequence<br> types [5] (identified using mlst v2.19.0 [6]) is provided in<br> `ecoli_sequence_information.tsv`. The corresponding assemblies and a Themisto v2.1.0 [7] pseudoalignment<br> index are also available as separate uploads in Zenodo. __Note:__ the `esc_ra9772aa_as` entry in the PopPUNK files does not<br> have a corresponding assembly nor is it included in the Themisto<br> pseudoalignment index or the `ecoli_sequence_information.tsv`<br> file. This is because the entry for this sequence was corrupted in the<br> original run of PopPUNK. ### Files<br> - `pop_db`: the PopPUNK sketch files.<br> - `pop_fit_dbscan`: the initial DBSCAN fit for the sketch.<br> - `pop_fit_refined`: the final refined version of the DBSCAN fit.<br> - `pop_fit_refined_viz`: microreact visualisation files from the refined fit.<br> - `ecoli_sequence_information.tsv`: a tab-separated text file containing the MLST types and the PopPUNK clusters. ### References<br> - [1] Lees J et al., _Fast and flexible bacterial genomic epidemiology with PopPUNK._ https://doi.org/10.1101/gr.241455.118<br> - [2] Horesh G et al., _A comprehensive and high-quality collection of Escherichia coli genomes and their genes._ https://doi.org/10.1099/mgen.0.000499<br> - [3] Gladstone R et al., _Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study._ https://doi.org/10.1016/S2666-5247(21)00031-8<br> - [4] Shao Y et al., _Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth._ https://doi.org/10.1038/s41586-019-1560-1<br> - [5] Jolley K et al., _Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications._ https://doi.org/10.12688/wellcomeopenres.14826.1<br> - [6] Seemann T, _mlst_ _GitHub._ https://github.com/tseemann/mlst<br> - [7] Mäklin T et al., _Bacterial genomic epidemiology with mixed samples._ https://doi.org/10.1099/mgen.0.000691
DOI: 10.5281/zenodo.5675203
title: Kilombero and Ulanga Antiretroviral Cohort (KIULARCO) study: Causes of death and associated factors over a decade of follow-up in a cohort of HIV-infected adults in rural Tanzania

description: These are a subset of pseudo-anonymised data from the Kilombero and Ulanga Antiretroviral Cohort (KIULARCO), which were used to analyse causes of death and associated factors among adults. The dataset contains one row for each of the 9871 participants included in this analysis, described further in the data dictionary. KIULARCO has been described in detail previously (see references).
description: {"references": ["Vanobberghen F, Letang E, Gamell A, Mnzava DK, Faini D, Luwanda LB, et al. A decade of HIV care in rural Tanzania\u202f: Trends in clinical outcomes and impact of clinic optimisation in an open , prospective cohort. PLoS One. 2017;69:1\u201317", "Letang E, Vedastus KA, Anna G, Herry M, George S, Bonaventure LL, et al. Cohort profile\u202f: The Kilombero and Ulanga Antiretroviral Cohort (KIULARCO). Swiss Med Wkly. 2017; July:1\u20139"]}
DOI: 10.5281/zenodo.4646669
title: Kilombero and Ulanga Antiretroviral Cohort (KIULARCO) study: Causes of death and associated factors over a decade of follow-up in a cohort of HIV-infected adults in rural Tanzania

description: These are a subset of pseudo-anonymised data from the Kilombero and Ulanga Antiretroviral Cohort (KIULARCO), which were used to analyse causes of death and associated factors among adults. The dataset contains one row for each of the 9871 participants included in this analysis, described further in the data dictionary. KIULARCO has been described in detail previously (see references).
description: {"references": ["Vanobberghen F, Letang E, Gamell A, Mnzava DK, Faini D, Luwanda LB, et al. A decade of HIV care in rural Tanzania\u202f: Trends in clinical outcomes and impact of clinic optimisation in an open , prospective cohort. PLoS One. 2017;69:1\u201317", "Letang E, Vedastus KA, Anna G, Herry M, George S, Bonaventure LL, et al. Cohort profile\u202f: The Kilombero and Ulanga Antiretroviral Cohort (KIULARCO). Swiss Med Wkly. 2017; July:1\u20139"]}
DOI: 10.5281/zenodo.6697651
title: oncoEnrichRDB

description: Data repository for oncoEnrichR R package
DOI: 10.5281/zenodo.6697732
title: supplementary data on the faunal remains from Nahal Rahaf 2

description: S1 = archaeozoological database of the faunal remains from Nahal Rahaf 2 S2 = osteometric data on the faunal remains from Nahal Rahaf 2, measurements follow von den Driesch (1976) S3 = skeletal element representation data S4 = comparable UP sites.
DOI: 10.5281/zenodo.6697731
title: supplementary data on the faunal remains from Nahal Rahaf 2

description: S1 = archaeozoological database of the faunal remains from Nahal Rahaf 2 S2 = osteometric data on the faunal remains from Nahal Rahaf 2, measurements follow von den Driesch (1976) S3 = skeletal element representation data S4 = comparable UP sites.