cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5f254
title: MassIVE MSV000087972 - Proteomic analysis of Angelman mouse models
title: Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by the loss of neuronal E3 ligase UBE3A. Restoring UBE3A levels is a potential disease-modifying therapy for AS and has recently entered clinical trials. There is paucity of data regarding the molecular changes downstream of UBE3A, hampering elucidation of disease therapeutics and biomarkers. Notably, UBE3A plays an important role in the nucleus but its targets have yet to be elucidated. Using proteomics, we assessed changes during postnatal cortical development in an AS mouse model. Pathway analysis revealed dysregulation of proteasomal and tRNA synthetase pathways at all postnatal brain developmental stages, while synaptic proteins were altered in adults. We confirmed pathway alterations in an adult AS rat model across multiple brain regions and highlighted region-specific differences. The top hits were altered in human AS patient neurons, supporting disease translation. UBE3A reinstatement in AS mice resulted in near complete and partial rescue of the proteome alterations in adolescence and adults respectively, supporting the notion that early restoration of UBE3A expression provides is a promising therapeutic option. We show that Transketolase (TKT), one of the most abundantly altered proteins, is a direct UBE3A substrate and is elevated in the neuronal nucleus of rat brains and human iPSC derived neurons. Taken together, our study provides a comprehensive map of UBE3A driven changes in AS across development and species, and corroborates UBE3A reinstatement as a viable therapeutic option.
DOI: 10.5281/zenodo.5184720
title: Integrated automatic design process for robot swarms

description: Demonstration of the Integrated automatic process for robot swarms in three missions: Aggregation, Foraging, and Migration.<br> The dataset contains the following:<br> 1. SML (Swarm Mission Language) related files: <br> - specification files used to create missions,<br> - generated files to be used by an optimization method <br> 2. AUTOMODE related files:<br> - the log files running AUTOMODE - an optimization method that generates control software for different missions<br> - generated control software <br> 3. Demonstration:<br> - snapshots and videos of running the missions on real robots
DOI: 10.5281/zenodo.5184719
title: Integrated automatic design process for robot swarms

description: Demonstration of the Integrated automatic process for robot swarms in three missions: Aggregation, Foraging, and Migration.<br> The dataset contains the following:<br> 1. SML (Swarm Mission Language) related files: <br> - specification files used to create missions,<br> - generated files to be used by an optimization method <br> 2. AUTOMODE related files:<br> - the log files running AUTOMODE - an optimization method that generates control software for different missions<br> - generated control software <br> 3. Demonstration:<br> - snapshots and videos of running the missions on real robots
DOI: 10.25919/tdvj-6e78
title: Targeted proteomics analysis on Lyssa virus samples

description: Targeted protein quantitation from Lyssa virus treated- and Mock infected cells by LC-MRM-MS.
DOI: 10.21227/zx3d-d450
title: ptb-diagnostic-ecg-database-1.0.0

description: The database contains 549 records from 290 subjects (aged 17 to 87, mean 57.2; 209 men, mean age 55.5, and 81 women, mean age 61.6; ages were not recorded for 1 female and 14 male subjects). Each subject is represented by one to five records. There are no subjects numbered 124, 132, 134, or 161. Each record includes 15 simultaneously measured signals: the conventional 12 leads (i, ii, iii, avr, avl, avf, v1, v2, v3, v4, v5, v6) together with the 3 Frank lead ECGs (vx, vy, vz). Each signal is digitized at 1000 samples per second, with 16 bit resolution over a range of ± 16.384 mV. On special request to the contributors of the database, recordings may be available at sampling rates up to 10 KHz.
DOI: 10.6084/m9.figshare.15155688
title: MATLAB code for the Monte Carlo light simulations using ValoMC from Multiphysics modelling of photon, mass and heat transfer in coral microenvironments

description: Coral reefs are constructed by calcifying coral animals that engage in a symbiosis with dinoflagellate microalgae harboured in their tissue. The symbiosis takes place in the presence of steep and dynamic gradients of light, temperature and chemical species that are affected by the structural and optical properties of the coral and their interaction with incident irradiance and water flow. Microenvironmental analyses have enabled quantification of such gradients and bulk coral tissue and skeleton optical properties, but the multi-layered nature of corals and its implications for the optical, thermal and chemical microenvironment remains to be studied in more detail. Here, we present a multiphysics modelling approach, where three-dimensional Monte Carlo simulations of the light field in a simple coral slab morphology with multiple tissue layers were used as input for modelling the heat dissipation and photosynthetic oxygen production driven by photon absorption. By coupling photon, heat and mass transfer, the model predicts light, temperature and O<sub>2</sub> gradients in the coral tissue and skeleton, under environmental conditions simulating e.g. tissue contraction/expansion, symbiont loss via coral bleaching or different distributions of coral host pigments. The model reveals basic structure–function mechanisms that shape the microenvironment and ecophysiology of the coral symbiosis in response to environmental change.
DOI: 10.6084/m9.figshare.15155694.v1
title: MATLAB code for the figure plots from Multiphysics modelling of photon, mass and heat transfer in coral microenvironments

description: Coral reefs are constructed by calcifying coral animals that engage in a symbiosis with dinoflagellate microalgae harboured in their tissue. The symbiosis takes place in the presence of steep and dynamic gradients of light, temperature and chemical species that are affected by the structural and optical properties of the coral and their interaction with incident irradiance and water flow. Microenvironmental analyses have enabled quantification of such gradients and bulk coral tissue and skeleton optical properties, but the multi-layered nature of corals and its implications for the optical, thermal and chemical microenvironment remains to be studied in more detail. Here, we present a multiphysics modelling approach, where three-dimensional Monte Carlo simulations of the light field in a simple coral slab morphology with multiple tissue layers were used as input for modelling the heat dissipation and photosynthetic oxygen production driven by photon absorption. By coupling photon, heat and mass transfer, the model predicts light, temperature and O<sub>2</sub> gradients in the coral tissue and skeleton, under environmental conditions simulating e.g. tissue contraction/expansion, symbiont loss via coral bleaching or different distributions of coral host pigments. The model reveals basic structure–function mechanisms that shape the microenvironment and ecophysiology of the coral symbiosis in response to environmental change.
DOI: 10.6084/m9.figshare.15155694
title: MATLAB code for the figure plots from Multiphysics modelling of photon, mass and heat transfer in coral microenvironments

description: Coral reefs are constructed by calcifying coral animals that engage in a symbiosis with dinoflagellate microalgae harboured in their tissue. The symbiosis takes place in the presence of steep and dynamic gradients of light, temperature and chemical species that are affected by the structural and optical properties of the coral and their interaction with incident irradiance and water flow. Microenvironmental analyses have enabled quantification of such gradients and bulk coral tissue and skeleton optical properties, but the multi-layered nature of corals and its implications for the optical, thermal and chemical microenvironment remains to be studied in more detail. Here, we present a multiphysics modelling approach, where three-dimensional Monte Carlo simulations of the light field in a simple coral slab morphology with multiple tissue layers were used as input for modelling the heat dissipation and photosynthetic oxygen production driven by photon absorption. By coupling photon, heat and mass transfer, the model predicts light, temperature and O<sub>2</sub> gradients in the coral tissue and skeleton, under environmental conditions simulating e.g. tissue contraction/expansion, symbiont loss via coral bleaching or different distributions of coral host pigments. The model reveals basic structure–function mechanisms that shape the microenvironment and ecophysiology of the coral symbiosis in response to environmental change.
DOI: 10.6084/m9.figshare.15155688.v1
title: MATLAB code for the Monte Carlo light simulations using ValoMC from Multiphysics modelling of photon, mass and heat transfer in coral microenvironments

description: Coral reefs are constructed by calcifying coral animals that engage in a symbiosis with dinoflagellate microalgae harboured in their tissue. The symbiosis takes place in the presence of steep and dynamic gradients of light, temperature and chemical species that are affected by the structural and optical properties of the coral and their interaction with incident irradiance and water flow. Microenvironmental analyses have enabled quantification of such gradients and bulk coral tissue and skeleton optical properties, but the multi-layered nature of corals and its implications for the optical, thermal and chemical microenvironment remains to be studied in more detail. Here, we present a multiphysics modelling approach, where three-dimensional Monte Carlo simulations of the light field in a simple coral slab morphology with multiple tissue layers were used as input for modelling the heat dissipation and photosynthetic oxygen production driven by photon absorption. By coupling photon, heat and mass transfer, the model predicts light, temperature and O<sub>2</sub> gradients in the coral tissue and skeleton, under environmental conditions simulating e.g. tissue contraction/expansion, symbiont loss via coral bleaching or different distributions of coral host pigments. The model reveals basic structure–function mechanisms that shape the microenvironment and ecophysiology of the coral symbiosis in response to environmental change.
DOI: 10.6084/m9.figshare.14607882
title: Global Pollinator Contribution Dataset and Associated Metadata and Analyses

description: This is the dataset and associated metadata and analysis for Rodger et al. "Widespread vulnerability of plant seed production to pollinator declines."<br>
DOI: 10.5281/zenodo.5184447
title: Comparative genomics reveals evolution traits, mating strategies and pathogenicity-related genes variation of Botryosphaeriaceae

description: <em>Botryosphaeriaceae</em>, as a major family of the largest class of kingdom fungi <em>Dothideomycetes</em>, encompasses phytopathogens, saprobes, and endophytes. Many members of this family are opportunistic phytopathogens with a wide host range and worldwide geographical distribution, and can infect many economically important plants, including food crops and bio-material plants. To date, however, little is known about the family evolutionary characterization, mating strategies, and pathogenicity-related genes variation from a comparative genome perspective. Here, we conducted the first large-scale whole-genome comparison of 271 <em>Dothideomycetes</em>, including 19 species in <em>Botryosphaeriaceae</em>. The comparative genome analysis provided a clear classification of <em>Botryosphaeriaceae</em> in <em>Dothideomycetes</em> and indicated that <em>Botryosphaeriaceae</em> pathogenicity evolution undergoes multiple times. Mating strategies analysis demonstrated at least 3 transitions were found within <em>Botryosphaeriaceae</em> from heterothallism to homothallism. Additionally, pathogenicity-related genes contents in different species within <em>Botryosphaeriaceae</em> varied greatly, indicating that a secondary lineage expansion occurs in speciation. These findings cast new insights into evolution traits, mating strategies and pathogenicity-related genes variation of <em>Botryosphaeriaceae</em>.
DOI: 10.6084/m9.figshare.15155709.v1
title: Supplemental Table 1 from Biomechanics of pollen pellet removal by the honey bee

description: The test speed and constant stress, sigma_0, applied by the UTM for every pellet sample.
DOI: 10.6084/m9.figshare.15155709
title: Supplemental Table 1 from Biomechanics of pollen pellet removal by the honey bee

description: The test speed and constant stress, sigma_0, applied by the UTM for every pellet sample.
DOI: 10.6084/m9.figshare.15134943
title: OSM1-4+8+10_chapter_five

description: Data belonging to chapter 5. This contains modelled physico-chemical properties of rpoB, PCR and KASP based genotyping results and Cx values.
DOI: 10.6084/m9.figshare.15134943.v2
title: OSM1-4+8+10_chapter_five

description: Data belonging to chapter 5. This contains modelled physico-chemical properties of rpoB, PCR and KASP based genotyping results and Cx values.
DOI: 10.6084/m9.figshare.15134943.v1
title: OSM1-4+8+10_chapter_five

description: Data belonging to chapter 5. This contains modelled physico-chemical properties of rpoB, PCR and KASP based genotyping results and Cx values.
DOI: 10.5281/zenodo.5184733
title: Assessing QT interval in COVID-19 patients:safety of hydroxychloroquine-azithromycin combination regimen

description: Dataset from the article Bernardini A, Ciconte G, Negro G, Rondine R, Mecarocci V, Viva T, Santini F, de Innocentiis C, Giannelli L, Witkowska E, Locati ET, Castelvecchio S, Marrocco-Trischitta MM, Vicedomini G, Menicanti L, Pappone C. Assessing QT interval in COVID-19 patients:safety of hydroxychloroquine-azithromycin combination regimen. Int J Cardiol. 2021 Feb 1;324:242-248. doi: 10.1016/j.ijcard.2020.09.038. Epub 2020 Sep 19. PMID: 32956782; PMCID: PMC7501148. <strong>Abstract</strong> <strong>Background: </strong>Hydroxychloroquine (HCQ) and azithromycin (AZT) have been proposed for COVID-19 treatment. Data available in the literature reported a potential increased risk of fatal arrhythmias under these therapies. The aim of this study was to assess the effects of these drugs on QT interval and outcome in a COVID-19 population. <strong>Method: </strong>A total of 112 consecutive COVID-19 patients were included in this analysis and were divided in 3 groups according to the receiving therapeutic regimens: 19 (17%) patients in Group 1 (no treatment), 40 (36%) in Group 2 (HCQ only), 53 (47%) in Group 3 (HCQ/AZT). <strong>Results: </strong>A prolonged QTc interval was found in 61% of patients treated with HCQ alone or in combination with AZT, but only 4 (4%) patients showed a QTc &gt; 500 ms. HCQ/AZT combination determined a greater increase of QTc duration compared to the other two strategies (Group 3 452 ± 26.4 vs Group 2 436.3 ± 28.4 vs Group 1 424.4 ± 24.3 ms, respectively; p &lt; 0.001). Multivariate analysis demonstrated that HCQ/AZT combination (OR 9.02, p = 0.001) and older age (OR 1.04, p = 0.031) were independent predictors of QTc prolongation. The risk increased with age (incremental utility analysis p = 0.02). Twenty patients (18%) died, and no cardiac arrest neither arrhythmic fatalities were documented. <strong>Conclusions: </strong>The HCQ/AZT combination therapy causes a significantly increase of QT interval compared to HCQ alone. Older patients under such regimen are at higher risk of experiencing QT prolongation. The use of such drugs may be considered as safe relating to arrhythmic risk in the treatment of COVID-19 patients as no arrhythmic fatalities occurred.
DOI: 10.5281/zenodo.5184732
title: Assessing QT interval in COVID-19 patients:safety of hydroxychloroquine-azithromycin combination regimen

description: Dataset from the article Bernardini A, Ciconte G, Negro G, Rondine R, Mecarocci V, Viva T, Santini F, de Innocentiis C, Giannelli L, Witkowska E, Locati ET, Castelvecchio S, Marrocco-Trischitta MM, Vicedomini G, Menicanti L, Pappone C. Assessing QT interval in COVID-19 patients:safety of hydroxychloroquine-azithromycin combination regimen. Int J Cardiol. 2021 Feb 1;324:242-248. doi: 10.1016/j.ijcard.2020.09.038. Epub 2020 Sep 19. PMID: 32956782; PMCID: PMC7501148. <strong>Abstract</strong> <strong>Background: </strong>Hydroxychloroquine (HCQ) and azithromycin (AZT) have been proposed for COVID-19 treatment. Data available in the literature reported a potential increased risk of fatal arrhythmias under these therapies. The aim of this study was to assess the effects of these drugs on QT interval and outcome in a COVID-19 population. <strong>Method: </strong>A total of 112 consecutive COVID-19 patients were included in this analysis and were divided in 3 groups according to the receiving therapeutic regimens: 19 (17%) patients in Group 1 (no treatment), 40 (36%) in Group 2 (HCQ only), 53 (47%) in Group 3 (HCQ/AZT). <strong>Results: </strong>A prolonged QTc interval was found in 61% of patients treated with HCQ alone or in combination with AZT, but only 4 (4%) patients showed a QTc &gt; 500 ms. HCQ/AZT combination determined a greater increase of QTc duration compared to the other two strategies (Group 3 452 ± 26.4 vs Group 2 436.3 ± 28.4 vs Group 1 424.4 ± 24.3 ms, respectively; p &lt; 0.001). Multivariate analysis demonstrated that HCQ/AZT combination (OR 9.02, p = 0.001) and older age (OR 1.04, p = 0.031) were independent predictors of QTc prolongation. The risk increased with age (incremental utility analysis p = 0.02). Twenty patients (18%) died, and no cardiac arrest neither arrhythmic fatalities were documented. <strong>Conclusions: </strong>The HCQ/AZT combination therapy causes a significantly increase of QT interval compared to HCQ alone. Older patients under such regimen are at higher risk of experiencing QT prolongation. The use of such drugs may be considered as safe relating to arrhythmic risk in the treatment of COVID-19 patients as no arrhythmic fatalities occurred.
DOI: 10.5281/zenodo.5184741
title: Dataset for: Hydrological processes in East African tropical montane headwater catchments influenced by land use

description: This dataset contains high-resolution (10-minute interval) data for nitrate (concentration and load), precipitation and discharge at four measurement stations (NF, SHA, TTP, OUT) in the South West Mau, Kenya, as well as trace element data and stable isotopes of water for rainfall and stream water samples. The data was used to investigate the influence of land use on hydrological processes through time series analysis (Jacobs et al. 2018a), end member mixing analysis and estimation of the young water fraction (Jacobs et al. 2018b).
description: {"references": ["Jacobs, S.R., Weeser, B., Guzha, A.C., Rufino, M.C., Butterbach-Bahl, K., Windhorst, D., Breuer, L. (2018a): Using high-resolution data to assess land use impact on nitrate dynamics in East African tropical montane catchments. Water Resour. Res. 54, 1812\u20131830. DOI: https://doi.org/10.1002/2017WR021592", "Jacobs, S.R., Timbe, E., Weeser, B., Rufino, M.C., Butterbach-Bahl, K., Breuer, L. (2018b): Assessment of hydrological pathways in East African montane catchments under different land use. Hydrology and Earth System Sciences 22, 4981\u20135000. DOI: https://doi.org/10.5194/hess-22-4981-2018"]}
DOI: 10.5281/zenodo.5184740
title: Dataset for: Hydrological processes in East African tropical montane headwater catchments influenced by land use

description: This dataset contains high-resolution (10-minute interval) data for nitrate (concentration and load), precipitation and discharge at four measurement stations (NF, SHA, TTP, OUT) in the South West Mau, Kenya, as well as trace element data and stable isotopes of water for rainfall and stream water samples. The data was used to investigate the influence of land use on hydrological processes through time series analysis (Jacobs et al. 2018a), end member mixing analysis and estimation of the young water fraction (Jacobs et al. 2018b).
description: {"references": ["Jacobs, S.R., Weeser, B., Guzha, A.C., Rufino, M.C., Butterbach-Bahl, K., Windhorst, D., Breuer, L. (2018a): Using high-resolution data to assess land use impact on nitrate dynamics in East African tropical montane catchments. Water Resour. Res. 54, 1812\u20131830. DOI: https://doi.org/10.1002/2017WR021592", "Jacobs, S.R., Timbe, E., Weeser, B., Rufino, M.C., Butterbach-Bahl, K., Breuer, L. (2018b): Assessment of hydrological pathways in East African montane catchments under different land use. Hydrology and Earth System Sciences 22, 4981\u20135000. DOI: https://doi.org/10.5194/hess-22-4981-2018"]}
DOI: 10.6084/m9.figshare.14604368.v1
title: Human Development by Gender and National Culture: A Comparative Analysis

description: The differences between female and male human development indicators are evidence that the general scenario (whole population) presents a blurred analytical viewpoint. Female schooling and life expectancy have advanced, but income is far from keeping pace. For women, legislation does not seem to be enough without the cultural legitimisation; for men, the cultural dependency on psychopathologies derived from the subjective expectations of masculinity is more evident. However, no study has apparently analysed the influence of national culture (NC) on human development (HD), by comparing the General, Female, and Male scenarios. This research sought to fill this gap by applying univariate and multivariate techniques to the data from 59 countries, using the Hofstede cultural dimensions as independent variables, HD indicators as dependent variables, and democracy, agricultural dependence, and urbanisation as controls. The influence of culture is a reality in all scenarios, but differs according to gender. For women, <i>individualism appears to be a more powerful ally, and</i> masculinity <i>and uncertainty avoidance</i> more harmful factors than for men; for men, <i>power distance</i> and <i>indulgence</i> have a greater impact than on women. Considering HD as a whole, an autonomous thinking society that rejects unjustifiable inequalities seems to be the most important cultural enabler.
DOI: 10.6084/m9.figshare.14604368
title: Human Development by Gender and National Culture: A Comparative Analysis

description: The differences between female and male human development indicators are evidence that the general scenario (whole population) presents a blurred analytical viewpoint. Female schooling and life expectancy have advanced, but income is far from keeping pace. For women, legislation does not seem to be enough without the cultural legitimisation; for men, the cultural dependency on psychopathologies derived from the subjective expectations of masculinity is more evident. However, no study has apparently analysed the influence of national culture (NC) on human development (HD), by comparing the General, Female, and Male scenarios. This research sought to fill this gap by applying univariate and multivariate techniques to the data from 59 countries, using the Hofstede cultural dimensions as independent variables, HD indicators as dependent variables, and democracy, agricultural dependence, and urbanisation as controls. The influence of culture is a reality in all scenarios, but differs according to gender. For women, <i>individualism appears to be a more powerful ally, and</i> masculinity <i>and uncertainty avoidance</i> more harmful factors than for men; for men, <i>power distance</i> and <i>indulgence</i> have a greater impact than on women. Considering HD as a whole, an autonomous thinking society that rejects unjustifiable inequalities seems to be the most important cultural enabler.
DOI: 10.25919/2czc-7w32
title: Quantitation of tropomyosin, troponin and myosin from cricket (Acheta domesticus)

description: Targeted proteomics assay was developed to monitor the protein extraction protocol efficiency and sample processing effect for three allergens (tropomyosin, troponin and myosin) from cricket.