cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7093538
title: Application of fragment based virtual screening towards inhibition of bacterial <i>N-</i>acetyglucosaminidase<sup>$</sup>

description: A structure-based approach is applied for the development of inhibitors of bacterial <i>N-</i>acetyglucosaminidase (autolysin). Autolysins are enzymes involved in the degradation of peptidoglycan and therefore participate in bacterial cell growth and different lysis phenomena. Several studies indicate that by the inhibition of autolysins, and consequently of bacterial cell division, antibacterial activity can be obtained, thus paving the road to a novel group of therapeutics against human pathogens. As crystal structures of the autolysin E (AtlE)–ligand complexes were obtained in our laboratories, fragment-based virtual screening was the method of choice for the initial studies. Fragment libraries from various databases were merged to increase the number of compounds for the virtual screening. Twenty-four commercially available virtual hits were selected and subjected to quantitative analysis of binding interactions using the surface plasmon resonance technique. Twelve fragments showed fragment–AtlE interactions. For F1, the top hit of the virtual screening, a <i>K</i><sub>D</sub> of 228 µM was determined, while other fragments displayed non-stoichiometric binding. Blind docking of potential binders uncovers three possible allosteric sites. Ligands of <i>N-</i>acetyglucosaminidase identified in our study represent valuable information for the further development of AtlE inhibitors, which could in future represent antibacterial agents acting by a novel mode of action.
DOI: 10.6084/m9.figshare.7093538.v1
title: Application of fragment based virtual screening towards inhibition of bacterial <i>N-</i>acetyglucosaminidase<sup>$</sup>

description: A structure-based approach is applied for the development of inhibitors of bacterial <i>N-</i>acetyglucosaminidase (autolysin). Autolysins are enzymes involved in the degradation of peptidoglycan and therefore participate in bacterial cell growth and different lysis phenomena. Several studies indicate that by the inhibition of autolysins, and consequently of bacterial cell division, antibacterial activity can be obtained, thus paving the road to a novel group of therapeutics against human pathogens. As crystal structures of the autolysin E (AtlE)–ligand complexes were obtained in our laboratories, fragment-based virtual screening was the method of choice for the initial studies. Fragment libraries from various databases were merged to increase the number of compounds for the virtual screening. Twenty-four commercially available virtual hits were selected and subjected to quantitative analysis of binding interactions using the surface plasmon resonance technique. Twelve fragments showed fragment–AtlE interactions. For F1, the top hit of the virtual screening, a <i>K</i><sub>D</sub> of 228 µM was determined, while other fragments displayed non-stoichiometric binding. Blind docking of potential binders uncovers three possible allosteric sites. Ligands of <i>N-</i>acetyglucosaminidase identified in our study represent valuable information for the further development of AtlE inhibitors, which could in future represent antibacterial agents acting by a novel mode of action.
DOI: 10.6084/m9.figshare.7028348
title: Modelling methods and cross-validation variants in QSAR: a multi-level analysis<sup>$</sup>

description: Prediction performance often depends on the cross- and test validation protocols applied. Several combinations of different cross-validation variants and model-building techniques were used to reveal their complexity. Two case studies (acute toxicity data) were examined, applying five-fold cross-validation (with random, contiguous and Venetian blind forms) and leave-one-out cross-validation (CV). External test sets showed the effects and differences between the validation protocols. The models were generated with multiple linear regression (MLR), principal component regression (PCR), partial least squares (PLS) regression, artificial neural networks (ANN) and support vector machines (SVM). The comparisons were made by the sum of ranking differences (SRD) and factorial analysis of variance (ANOVA). The largest bias and variance could be assigned to the MLR method and contiguous block cross-validation. SRD can provide a unique and unambiguous ranking of methods and CV variants. Venetian blind cross-validation is a promising tool. The generated models were also compared based on their basic performance parameters (<i>r</i><sup>2</sup> and <i>Q</i><sup>2</sup>). MLR produced the largest gap, while PCR gave the smallest. Although PCR is the best validated and balanced technique, SVM always outperformed the other methods, when experimental values were the benchmark. Variable selection was advantageous, and the modelling had a larger influence than CV variants.
DOI: 10.6084/m9.figshare.7028348.v1
title: Modelling methods and cross-validation variants in QSAR: a multi-level analysis<sup>$</sup>

description: Prediction performance often depends on the cross- and test validation protocols applied. Several combinations of different cross-validation variants and model-building techniques were used to reveal their complexity. Two case studies (acute toxicity data) were examined, applying five-fold cross-validation (with random, contiguous and Venetian blind forms) and leave-one-out cross-validation (CV). External test sets showed the effects and differences between the validation protocols. The models were generated with multiple linear regression (MLR), principal component regression (PCR), partial least squares (PLS) regression, artificial neural networks (ANN) and support vector machines (SVM). The comparisons were made by the sum of ranking differences (SRD) and factorial analysis of variance (ANOVA). The largest bias and variance could be assigned to the MLR method and contiguous block cross-validation. SRD can provide a unique and unambiguous ranking of methods and CV variants. Venetian blind cross-validation is a promising tool. The generated models were also compared based on their basic performance parameters (<i>r</i><sup>2</sup> and <i>Q</i><sup>2</sup>). MLR produced the largest gap, while PCR gave the smallest. Although PCR is the best validated and balanced technique, SVM always outperformed the other methods, when experimental values were the benchmark. Variable selection was advantageous, and the modelling had a larger influence than CV variants.
DOI: 10.6084/m9.figshare.7048082
title: Development of models to predict fish early-life stage toxicity from acute <i>Daphnia magna</i> toxicity<sup>$</sup>

description: Herein, we propose models for predicting fish early-life stage (ELS) toxicity from acute <i>Daphnia magna</i> toxicity and various molecular descriptors. Specifically, eight models were developed with fathead minnow (<i>Pimephales promelas</i>) data and were validated against Japanese medaka (<i>Oryzias latipes</i>) data because the quantity of available Japanese medaka data is much smaller than the quantity of fathead minnow data. The training data set for the models consisted of ELS fathead minnow toxicity data for 77 chemicals; data for 67 of the 77 chemicals originated from the OPP Pesticide Ecotoxicity Database of the US Environmental Protection Agency. The training data were biased toward pesticides. A simple quantitative activity–activity relationship (QAAR) model based on the correlation between fish ELS and acute <i>Daphnia magna</i> toxicities showed good predictivity for the chemicals in the external validation data set relative to the predictivities of the other models in this study. However, goodness-of-fit and robustness were better for quantitative structure–activity–activity relationship (QSAAR) models that included molecular descriptors (such as pesticide-related atoms and substructures as well as molecular weight and three-dimensional-structure-based parameters). A battery approach involving the use of both the QAAR and the QSAARs might enhance the reliability of the estimated values and prevent underestimates.
DOI: 10.6084/m9.figshare.7048082.v2
title: Development of models to predict fish early-life stage toxicity from acute <i>Daphnia magna</i> toxicity<sup>$</sup>

description: Herein, we propose models for predicting fish early-life stage (ELS) toxicity from acute <i>Daphnia magna</i> toxicity and various molecular descriptors. Specifically, eight models were developed with fathead minnow (<i>Pimephales promelas</i>) data and were validated against Japanese medaka (<i>Oryzias latipes</i>) data because the quantity of available Japanese medaka data is much smaller than the quantity of fathead minnow data. The training data set for the models consisted of ELS fathead minnow toxicity data for 77 chemicals; data for 67 of the 77 chemicals originated from the OPP Pesticide Ecotoxicity Database of the US Environmental Protection Agency. The training data were biased toward pesticides. A simple quantitative activity–activity relationship (QAAR) model based on the correlation between fish ELS and acute <i>Daphnia magna</i> toxicities showed good predictivity for the chemicals in the external validation data set relative to the predictivities of the other models in this study. However, goodness-of-fit and robustness were better for quantitative structure–activity–activity relationship (QSAAR) models that included molecular descriptors (such as pesticide-related atoms and substructures as well as molecular weight and three-dimensional-structure-based parameters). A battery approach involving the use of both the QAAR and the QSAARs might enhance the reliability of the estimated values and prevent underestimates.
DOI: 10.5281/zenodo.7763280
title: A Lexicon of Emotions in Turkish

description: A Turkish lexicon of emotions prepared for dictionary function of MaxQDA software. This lexicon has been prepared as a part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No.896311”
DOI: 10.5281/zenodo.7763279
title: A Lexicon of Emotions in Turkish

description: A Turkish lexicon of emotions prepared for dictionary function of MaxQDA software. This lexicon has been prepared as a part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No.896311”
DOI: 10.5281/zenodo.5913226
title: COLET: A Dataset for Cognitive workLoad estimation based on Eye-Tracking

description: Cognitive workload is an important component in performance psychology, ergonomics, and human factors. Unfortunately, benchmarks and publicly available datasets are scarce, making it difficult to establish new approaches and comparative studies. In this work, COLET-COgnitive workLoad state estimation based on Eye-Tracking dataset is presented. Forty-seven (47) individuals' eye movements were monitored as they solved puzzles involving visual search tasks of varying complexity and duration. The authors give an in-depth study of the participants' performance during the experiments while eye and gaze features were derived from low-level eye recorded metrics, and their relationships with the experiment tasks were investigated. Finally, the results from the classification of cognitive workload levels solely based on eye and gaze data, by employing and testing a set of machine learning algorithms are provided. The dataset is made available to the public. Please cite the following work: Ktistakis, E., Skaramagkas, V., Manousos, D., Tachos, N. S., Tripoliti, E., Fotiadis, D. I., & Tsiknakis, M. (2022). Colet: A dataset for cognitive workload estimation based on eye-tracking. <em>Computer Methods and Programs in Biomedicine</em>, 106989. https://doi.org/10.1016/j.cmpb.2022.106989
DOI: 10.5281/zenodo.5913227
title: COLET: A Dataset for Cognitive workLoad estimation based on Eye-Tracking

description: Cognitive workload is an important component in performance psychology, ergonomics, and human factors. Unfortunately, benchmarks and publicly available datasets are scarce, making it difficult to establish new approaches and comparative studies. In this work, COLET-COgnitive workLoad state estimation based on Eye-Tracking dataset is presented. Forty-seven (47) individuals' eye movements were monitored as they solved puzzles involving visual search tasks of varying complexity and duration. The authors give an in-depth study of the participants' performance during the experiments while eye and gaze features were derived from low-level eye recorded metrics, and their relationships with the experiment tasks were investigated. Finally, the results from the classification of cognitive workload levels solely based on eye and gaze data, by employing and testing a set of machine learning algorithms are provided. The dataset is made available to the public.<br> <br> IMPORTANT NOTE: This is version 0. The next version which will contain the eye-tracking data is going to be uploaded after the article's publication.
description: This is version 0. The next version which will contain the eye-tracking data is going to be uploaded after the article's publication.
DOI: 10.5281/zenodo.6401065
title: COLET: A Dataset for Cognitive workLoad estimation based on Eye-Tracking

description: Cognitive workload is an important component in performance psychology, ergonomics, and human factors. Unfortunately, benchmarks and publicly available datasets are scarce, making it difficult to establish new approaches and comparative studies. In this work, COLET-COgnitive workLoad state estimation based on Eye-Tracking dataset is presented. Forty-seven (47) individuals' eye movements were monitored as they solved puzzles involving visual search tasks of varying complexity and duration. The authors give an in-depth study of the participants' performance during the experiments while eye and gaze features were derived from low-level eye recorded metrics, and their relationships with the experiment tasks were investigated. Finally, the results from the classification of cognitive workload levels solely based on eye and gaze data, by employing and testing a set of machine learning algorithms are provided. The dataset is made available to the public. Please cite the following work: Ktistakis, E., Skaramagkas, V., Manousos, D., Tachos, N. S., Tripoliti, E., Fotiadis, D. I., & Tsiknakis, M. (2022). Colet: A dataset for cognitive workload estimation based on eye-tracking. <em>Computer Methods and Programs in Biomedicine</em>, 106989. https://doi.org/10.1016/j.cmpb.2022.106989
DOI: 10.5281/zenodo.6801166
title: COLET: A Dataset for Cognitive workLoad estimation based on Eye-Tracking

description: Cognitive workload is an important component in performance psychology, ergonomics, and human factors. Unfortunately, benchmarks and publicly available datasets are scarce, making it difficult to establish new approaches and comparative studies. In this work, COLET-COgnitive workLoad state estimation based on Eye-Tracking dataset is presented. Forty-seven (47) individuals' eye movements were monitored as they solved puzzles involving visual search tasks of varying complexity and duration. The authors give an in-depth study of the participants' performance during the experiments while eye and gaze features were derived from low-level eye recorded metrics, and their relationships with the experiment tasks were investigated. Finally, the results from the classification of cognitive workload levels solely based on eye and gaze data, by employing and testing a set of machine learning algorithms are provided. The dataset is made available to the public. Please cite the following work: Ktistakis, E., Skaramagkas, V., Manousos, D., Tachos, N. S., Tripoliti, E., Fotiadis, D. I., & Tsiknakis, M. (2022). Colet: A dataset for cognitive workload estimation based on eye-tracking. <em>Computer Methods and Programs in Biomedicine</em>, 106989. https://doi.org/10.1016/j.cmpb.2022.106989
DOI: 10.5281/zenodo.7766785
title: COLET: A Dataset for Cognitive workLoad estimation based on Eye-Tracking

description: Cognitive workload is an important component in performance psychology, ergonomics, and human factors. Unfortunately, benchmarks and publicly available datasets are scarce, making it difficult to establish new approaches and comparative studies. In this work, COLET-COgnitive workLoad state estimation based on Eye-Tracking dataset is presented. Forty-seven (47) individuals' eye movements were monitored as they solved puzzles involving visual search tasks of varying complexity and duration. The authors give an in-depth study of the participants' performance during the experiments while eye and gaze features were derived from low-level eye recorded metrics, and their relationships with the experiment tasks were investigated. Finally, the results from the classification of cognitive workload levels solely based on eye and gaze data, by employing and testing a set of machine learning algorithms are provided. The dataset is made available to the public. Please cite the following work: Ktistakis, E., Skaramagkas, V., Manousos, D., Tachos, N. S., Tripoliti, E., Fotiadis, D. I., & Tsiknakis, M. (2022). Colet: A dataset for cognitive workload estimation based on eye-tracking. <em>Computer Methods and Programs in Biomedicine</em>, 106989. https://doi.org/10.1016/j.cmpb.2022.106989
DOI: 10.6084/m9.figshare.17129555
title: RSL data

description: RSL data for Lutregala, Wapengo and Tarra salt marshes
DOI: 10.6084/m9.figshare.17129555.v1
title: RSL data

description: RSL data for Lutregala, Wapengo and Tarra salt marshes
DOI: 10.6084/m9.figshare.17129597
title: Age data

description: Age data for <b>Relative sea-level changes in southeastern Australia during the 19<sup>th</sup> and 20<sup>th</sup> centuries</b><b></b>
DOI: 10.6084/m9.figshare.17129597.v1
title: Age data

description: Age data for <b>Relative sea-level changes in southeastern Australia during the 19<sup>th</sup> and 20<sup>th</sup> centuries</b><b></b>
DOI: 10.4121/15177759
title: Data supplementary to the paper 'Influence of slope incline on the ejection of two-phase soil splashed material'

description: The results are related with experiments of soil splash phenomenon on simulated slope samples affected by single drop impact. The dataset contains 1) raw data with measured quantitites (mass of ejected material) and 2) Supplementary Material for the paper (detailed statistical analysis).<br>More details are available in README file.
DOI: 10.4121/15177759.v2
title: Data supplementary to the paper 'Influence of slope incline on the ejection of two-phase soil splashed material'

description: The results are related with experiments of soil splash phenomenon on simulated slope samples affected by single drop impact. The dataset contains 1) raw data with measured quantitites (mass of ejected material) and 2) Supplementary Material for the paper (detailed statistical analysis).<br>More details are available in README file.
DOI: 10.5281/zenodo.7766897
title: Test data upload

description: Test upload
DOI: 10.5281/zenodo.7766896
title: Test data upload

description: Test upload
DOI: 10.22008/fk2/ox5crv/gmcojn
title: ResultatGridFiler.zip

description: zip file containing scenario and results related to GEUS report 2023/12. All grid files are in geotiff covering all Denmark in 500m resolution.
DOI: 10.22008/fk2/ox5crv/76ii46
title: ResultatShape.gdb.zip

description: zip file containing a geodatabase with shape and tables related to GEUS report 2023/12. The geodatabase is in ESRI gdb format.
DOI: 10.25345/c5959cj1n
title: MassIVE MSV000091541 - different ipomea species nectar metabolomics data analysis
title: different ipomea species nectar metabolomics data analysis from southern india tamilnadu
DOI: 10.5281/zenodo.7764802
title: Net-zero CO2 emissions scenarios for Switzerland

description: This dataset accompanies the relevant article in Communications Earth and Environment. It contains the key assumptions used in the energy system modelling with the Swiss TIMES energy systems model (STEM) for assessing net-zero carbon dioxide emissions scenarios for Switzerland. In addition, contains extensive results from STEM for each one of the core scenarios and variants assessed in the study.
DOI: 10.5281/zenodo.7764801
title: Net-zero CO2 emissions scenarios for Switzerland

description: This dataset accompanies the relevant article in Communications Earth and Environment. It contains the key assumptions used in the energy system modelling with the Swiss TIMES energy systems model (STEM) for assessing net-zero carbon dioxide emissions scenarios for Switzerland. In addition, contains extensive results from STEM for each one of the core scenarios and variants assessed in the study.
DOI: 10.5281/zenodo.7764917
title: Net-zero CO2 emissions scenarios for Switzerland

description: This dataset accompanies the relevant article in Communications Earth and Environment. It contains the key assumptions used in the energy system modelling with the Swiss TIMES energy systems model (STEM) for assessing net-zero carbon dioxide emissions scenarios for Switzerland. In addition, contains extensive results from STEM for each one of the core scenarios and variants assessed in the study.
DOI: 10.25345/c55d8nq7w
title: MassIVE MSV000091542 - Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimers as HIV-1 vaccine candidates
title: Site-specific analysis of UFO-based immunogens designed to elicit bnAbs, RAW file upload
DOI: 10.5281/zenodo.7015310
title: Glycosylated models for: The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2

description: Glycosylated models (as PDB files) of the sarbecovirus spike proteins used in the study: The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2.
DOI: 10.5281/zenodo.7015311
title: Glycosylated models for: The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2

description: Glycosylated models (as PDB files) of the sarbecovirus spike proteins used in the study: The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2.
DOI: 10.5281/zenodo.7636233
title: Glycosylated models for: The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2

description: Glycosylated models (as PDB files) of the sarbecovirus spike proteins used in the study: The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2.
DOI: 10.5445/ir/1000151148
title: Supplementary animations "On the clustering of low-aspect-ratio oblate spheroids settling in ambient fluid"
DOI: 10.5445/ir/1000155816
title: Research data to "Monitoring of osmotic swelling induced filling degree changes in WOW double emulsions using Raman technologies"

description: Due to their nested structure, double emulsions have the potential to encapsulate value-adding substances until their application, making them of interest to various industries. However, the complex, nested structure negatively affects the stability of double emulsions. Still there is a lack of suitable measurement technology to fundamentally understand the cause of the instability mechanisms taking place. This study presents a novel measurement method to continuously track filling degree changes due to water diffusion in a water-in-oil-in-water (W1/O/W2) double emulsion droplet. The measurement method is based on the Raman effect and provides both photometric and spectrometric data. No sample preparation is required, and the measurement does not affect the double emulsion droplet.
DOI: 10.23729/a8f035e7-a652-4854-b4d4-b806c7e4bb60
title: MinExTarget

description: One rock sample imaged for the MinExTarget project (http://projects.gtk.fi/minextarget). Report is in writing at the moment. Preview dataset found at https://doi.org/10.23729/fb45981d-ddc9-4a43-b96f-1d76f3e3126a . To obtain data, please contact fairdata-pas@gtk.fi .