cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4680454
title: Test Dataset for Whole Slide Image Registration

description: Mouse duodenum fixed in 4% PFA overnight at 4°C, processed for paraffin infiltration using a standard histology procedure and cut at 4 microns were dewaxed, rehydrated, permeabilized with 0.5% Triton X-100 in PBS 1x and stained with Azide - Alexa Fluor 555 (Thermo Fisher) to detect EdU and DAPI for nuclei. The images were taken using a Leica DM5500 microscope with a 40X N.A.1 objective (black&white camera: DFC350FXR2, pixel dimension: 0.161 microns). Next, the slide was unmounted and stained using the fully automated Ventana Discovery xT autostainer (Roche Diagnostics, Rotkreuz, Switzerland). All steps were performed on automate with Ventana solutions. Sections were pretreated with heat using the CC1 solution under mild conditions. The primary rat anti BrDU (clone: BU1/75 (ICR1), Serotec, diluted 1:300) was incubated 1 hour at 37°C. After incubation with a donkey anti rat biotin diluted 1:200 (Jackson ImmunoResearch Laboratories), chromogenic revelation was performed with DabMap kit. The section was counterstained with Harris hematoxylin (J.T. Baker) before a second round of imaging on DM5500 PL Fluotar 40X N.A.1.0 oil (color camera: DFC 320 R2, pixel dimension: 0.1725 microns). Before acquisition, a white-balance as well as a shading correction is performed according to Leica LAS software wizard. The fluorescence and DAB images were converted in ome.tiff multiresolution file with the kheops Fiji Plugin. Sampled prepared in the EPFL histology core facility by Nathalie Müller and Gian-Filippo Mancini. Associated documents: https://c4science.ch/w/bioimaging_and_optics_platform_biop/teaching/dab-intensity/ https://imagej.net/plugins/bdv/warpy/warpy This document contains a full QuPath project with an example of registered image.
DOI: 10.5281/zenodo.5674521
title: Test Dataset for Whole Slide Image Registration

description: Mouse duodenum fixed in 4% PFA overnight at 4°C, processed for paraffin infiltration using a standard histology procedure and cut at 4 microns were dewaxed, rehydrated, permeabilized with 0.5% Triton X-100 in PBS 1x and stained with Azide - Alexa Fluor 555 (Thermo Fisher) to detect EdU and DAPI for nuclei. The images were taken using a Leica DM5500 microscope with a 40X N.A.1 objective (black&white camera: DFC350FXR2, pixel dimension: 0.161 microns). Next, the slide was unmounted and stained using the fully automated Ventana Discovery xT autostainer (Roche Diagnostics, Rotkreuz, Switzerland). All steps were performed on automate with Ventana solutions. Sections were pretreated with heat using the CC1 solution under mild conditions. The primary rat anti BrDU (clone: BU1/75 (ICR1), Serotec, diluted 1:300) was incubated 1 hour at 37°C. After incubation with a donkey anti rat biotin diluted 1:200 (Jackson ImmunoResearch Laboratories), chromogenic revelation was performed with DabMap kit. The section was counterstained with Harris hematoxylin (J.T. Baker) before a second round of imaging on DM5500 PL Fluotar 40X N.A.1.0 oil (color camera: DFC 320 R2, pixel dimension: 0.1725 microns). Before acquisition, a white-balance as well as a shading correction is performed according to Leica LAS software wizard. The fluorescence and DAB images were converted in ome.tiff multiresolution file with the kheops Fiji Plugin. Sampled prepared in the EPFL histology core facility by Nathalie Müller and Gian-Filippo Mancini. Associated documents: https://c4science.ch/w/bioimaging_and_optics_platform_biop/teaching/dab-intensity/ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/wsi_registration_fjii_qupath/
DOI: 10.5281/zenodo.5675686
title: Test Dataset for Whole Slide Image Registration

description: Mouse duodenum fixed in 4% PFA overnight at 4°C, processed for paraffin infiltration using a standard histology procedure and cut at 4 microns were dewaxed, rehydrated, permeabilized with 0.5% Triton X-100 in PBS 1x and stained with Azide - Alexa Fluor 555 (Thermo Fisher) to detect EdU and DAPI for nuclei. The images were taken using a Leica DM5500 microscope with a 40X N.A.1 objective (black&white camera: DFC350FXR2, pixel dimension: 0.161 microns). Next, the slide was unmounted and stained using the fully automated Ventana Discovery xT autostainer (Roche Diagnostics, Rotkreuz, Switzerland). All steps were performed on automate with Ventana solutions. Sections were pretreated with heat using the CC1 solution under mild conditions. The primary rat anti BrDU (clone: BU1/75 (ICR1), Serotec, diluted 1:300) was incubated 1 hour at 37°C. After incubation with a donkey anti rat biotin diluted 1:200 (Jackson ImmunoResearch Laboratories), chromogenic revelation was performed with DabMap kit. The section was counterstained with Harris hematoxylin (J.T. Baker) before a second round of imaging on DM5500 PL Fluotar 40X N.A.1.0 oil (color camera: DFC 320 R2, pixel dimension: 0.1725 microns). Before acquisition, a white-balance as well as a shading correction is performed according to Leica LAS software wizard. The fluorescence and DAB images were converted in ome.tiff multiresolution file with the kheops Fiji Plugin. Sampled prepared in the EPFL histology core facility by Nathalie Müller and Gian-Filippo Mancini. Associated documents: https://c4science.ch/w/bioimaging_and_optics_platform_biop/teaching/dab-intensity/ https://imagej.net/plugins/bdv/warpy/warpy This document contains a full QuPath project with an example of registered image.
DOI: 10.5281/zenodo.8192833
title: Nutritional status of children affected by X-linked adrenoleukodystrophy

description: Children affected by X-linked adrenoleukodistrophy are not malnourished, but report a high body fat percentage.A low-fat diet could be adjuvant in the management of the disease.
DOI: 10.5281/zenodo.8192832
title: Nutritional status of children affected by X-linked adrenoleukodystrophy

description: Children affected by X-linked adrenoleukodistrophy are not malnourished, but report a high body fat percentage.A low-fat diet could be adjuvant in the management of the disease.
DOI: 10.5281/zenodo.8214400
title: PLANET/AI4COPERNICUS

description: This data set provides sample input and output data of the developed PLANET tool (hyPer Local climAte driven Tool) for the three use cases investigated (Kenya, Papua New Guinea, Puerto Rico.) funded by the AI4COPERNICUS project. The capabilities of the tool include A Generative Adversarial Network (GAN) that downscales the climate information and a feedforward neural network that classifies the land suitability for specific crops based on the refined input data. There are four steps, each with a dedicated folder: STEP1: Input data set (seasonal climate data, Reanalysis data, Digital elevation model data). STEP2: Downscaled seasonal climate data sets for each region with GANs. Each region is accompanied by the Generator Loss, the Peak signal to noise ratio (PSNR) in html formats, the output images during training by the generator (training.png) and a png with the downscaled meteorological fields. STEP3: Sample input data sets (FAO STAT) of yield data for maize and NDVI that are imported to a LSTM network for yield prediction. Output are yield prediction in CSV format, the lstm structure in png and the Mean Square Error of LSTM training over the epochs. Caution is needed as this step is not mandatory to Land Suitability in STEP4 but act as layer to investigate relationships of NDVI with yield prediction. FAO STAT data only provide crude yield data and user input to the model are more appropriate. STEP4: Land Suitability input and output data sets. Besides the meteorological data, SoilGrids data are utilised and a Feed forward network makes a classification ranging from not suitable at all to highly suitable. Output for each region include the confusion matrix in png and the suitability in CSV format for each region. The accuracy of the model is found in the file fnn_acc.html and the structure of the model in FNN_structure.png.
DOI: 10.5281/zenodo.8214399
title: PLANET/AI4COPERNICUS

description: This data set provides sample input and output data of the developed PLANET tool (hyPer Local climAte driven Tool) for the three use cases investigated (Kenya, Papua New Guinea, Puerto Rico.) funded by the AI4COPERNICUS project. The capabilities of the tool include A Generative Adversarial Network (GAN) that downscales the climate information and a feedforward neural network that classifies the land suitability for specific crops based on the refined input data. There are four steps, each with a dedicated folder: STEP1: Input data set (seasonal climate data, Reanalysis data, Digital elevation model data). STEP2: Downscaled seasonal climate data sets for each region with GANs. Each region is accompanied by the Generator Loss, the Peak signal to noise ratio (PSNR) in html formats, the output images during training by the generator (training.png) and a png with the downscaled meteorological fields. STEP3: Sample input data sets (FAO STAT) of yield data for maize and NDVI that are imported to a LSTM network for yield prediction. Output are yield prediction in CSV format, the lstm structure in png and the Mean Square Error of LSTM training over the epochs. Caution is needed as this step is not mandatory to Land Suitability in STEP4 but act as layer to investigate relationships of NDVI with yield prediction. FAO STAT data only provide crude yield data and user input to the model are more appropriate. STEP4: Land Suitability input and output data sets. Besides the meteorological data, SoilGrids data are utilised and a Feed forward network makes a classification ranging from not suitable at all to highly suitable. Output for each region include the confusion matrix in png and the suitability in CSV format for each region. The accuracy of the model is found in the file fnn_acc.html and the structure of the model in FNN_structure.png.
DOI: 10.34740/kaggle/dsv/6247673
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.5281/zenodo.8214723
title: Synthesis of Tris[2‐(dimethylamino)ethyl]amine with Regiospecific Deuterium Labels

description: Simple synthetic routes to regioselectively deuterated tris[2-(dimethylamino)ethyl]amine (Me6TREN) variants are described. Imine formation with formaldehyde-d2 from tris(2-aminoethyl)amine (TREN) and subsequent reductions with NaBD4 afforded N[CH2CH2N(CD3)2]3 or d18-Me6TREN in 79 % yield. A trisubstitution protocol from 2-bromo-N,N-dimethylacetamide and ammonium carbonate and subsequent reduction of the N(CH2CONMe2)3 intermediate by lithium aluminum deuteride has afforded N[CH2CD2N(CH3)2]3 or (d6-arm)-Me6TREN in three steps and 52 % overall yield. A similar protocol from 2-bromo-N,N-dimethyl-d2-acetamide, obtained in two steps from d4-acetic acid, with reduction of the N(CD2CONMe2)3 intermediate by lithium aluminum hydride has afforded N[CD2CH2N(CH3)2]3 or (d6-cap)-Me6TREN in four steps and 13 % overall yield from CD3COOD.
description: Financial support from NSF (CHE 2000391) is acknowledged. We also thank the CNRS (Centre National de la Recherche Scientifique) for support through the International Research Project (IRP) "Laboratory for Coordination Chemistry for Controlled Radical Polymerization" (LCC-CRP). J. S. gratefully acknowledges support by the Chateaubriand Fellowship of the Office for Science & Technology of the Embassy of France in the United States. A.G. acknowledges financial support in the form of the post-doctoral fellowship (Polish National Agency for Academic Exchange - Bekker Programme no. PPN/BEK/2018/1/00261; Polish-U.S. Fulbright Commission - Senior Award no. PL/2019/SR/41) and SONATA grant UMO-2020/39/D/ST4/01182 from National Science Centre, Poland.
DOI: 10.5281/zenodo.8214722
title: Synthesis of Tris[2‐(dimethylamino)ethyl]amine with Regiospecific Deuterium Labels

description: Simple synthetic routes to regioselectively deuterated tris[2-(dimethylamino)ethyl]amine (Me6TREN) variants are described. Imine formation with formaldehyde-d2 from tris(2-aminoethyl)amine (TREN) and subsequent reductions with NaBD4 afforded N[CH2CH2N(CD3)2]3 or d18-Me6TREN in 79 % yield. A trisubstitution protocol from 2-bromo-N,N-dimethylacetamide and ammonium carbonate and subsequent reduction of the N(CH2CONMe2)3 intermediate by lithium aluminum deuteride has afforded N[CH2CD2N(CH3)2]3 or (d6-arm)-Me6TREN in three steps and 52 % overall yield. A similar protocol from 2-bromo-N,N-dimethyl-d2-acetamide, obtained in two steps from d4-acetic acid, with reduction of the N(CD2CONMe2)3 intermediate by lithium aluminum hydride has afforded N[CD2CH2N(CH3)2]3 or (d6-cap)-Me6TREN in four steps and 13 % overall yield from CD3COOD.
description: Financial support from NSF (CHE 2000391) is acknowledged. We also thank the CNRS (Centre National de la Recherche Scientifique) for support through the International Research Project (IRP) "Laboratory for Coordination Chemistry for Controlled Radical Polymerization" (LCC-CRP). J. S. gratefully acknowledges support by the Chateaubriand Fellowship of the Office for Science & Technology of the Embassy of France in the United States. A.G. acknowledges financial support in the form of the post-doctoral fellowship (Polish National Agency for Academic Exchange - Bekker Programme no. PPN/BEK/2018/1/00261; Polish-U.S. Fulbright Commission - Senior Award no. PL/2019/SR/41) and SONATA grant UMO-2020/39/D/ST4/01182 from National Science Centre, Poland.
DOI: 10.6084/m9.figshare.23860017
title: Raw data Figure 1B

description: Raw data for figures
DOI: 10.6084/m9.figshare.23860017.v1
title: Raw data Figure 1B

description: Raw data for figures
DOI: 10.3886/e187441v1
title: Collins and Wanamaker Black Americans’ Landholdings and Economic Mobility after Emancipation

description: <b>Abstract:</b> Large and persistent racial disparities in land-based wealth were an important legacy of the Reconstruction era. To assess how these disparities were transmitted intergenerationally, we build a dataset to observe Black households’ landholdings in 1880 alongside a sample of White households. We then link sons from all households to the 1900 census records to observe their economic and human capital outcomes. We show that Black landowners (relative to laborers) transmitted substantial intergenerational advantages to their sons, including an 11 pp advantage in literacy. But such advantages were small relative to the racial gaps in metrics of economic status. <br><br><br><br><br>
DOI: 10.5281/zenodo.7042138
title: Research data supporting "Tin phosphide anodes for potassium-ion batteries: insights from crystal structure prediction"

description: This dataset contains the output files of crystal structure prediction calculations (density-functional theory relaxations, bandstructures, phonon calculations, GIPAW-NMR calculations) on the ternary K-Sn-P phase diagram. All calculations were performed with the CASTEP DFT package (https://www.castep.org/) and the "matador" Python library (https://github.com/ml-evs/matador). <strong>Contents:</strong> "convergence_tests.zip": contains the results of convergence tests on the K-P system at two levels of accuracy "polish" and "searches" on the corresponding edge of the K-Sn-P ternary system "phonons.zip": contains CASTEP output files for phonon calculations on the predicted low-lying phases on the corresponding edge of the K-Sn-P phase diagram "polish.zip": contains CASTEP output files of relaxations on the corresponding edge of the K-Sn-P system at the "polish" level of accuracy using various different xc-functionals or external pressures. "searches.zip": contains ".res" files that provide the relaxed structure from each different crystal structure prediction method on the corresponding edge of the K-Sn-P system. "bulk_modulus.zip" contains CASTEP output files for calculation of E(V) curves for low-lying KP phases with different xc-functionals. "nmr.zip" contains CASTEP output files for GIPAW-NMR calculations of chemical shifts for low-lying K-Sn-P phases. "spectral.zip" contains CASTEP and OptaDOS output files for projected bandstructure and DOS calculations of low-lying K-Sn-P phases. "digests.zip" contains JSON representations of all the structures from polish and searches, broken down into K-P and K-Sn-P specific digests.
DOI: 10.5281/zenodo.8214735
title: Metabolomics dataset relating to the pubblication: "Combining CRISPRi and metabolomics for functional annotation of compound libraries"

description: Metabolomics dataset relating to the pubblication: "Combining CRISPRi and metabolomics for functional annotation of compound libraries"
DOI: 10.5281/zenodo.8214736
title: Metabolomics dataset relating to the pubblication: "Combining CRISPRi and metabolomics for functional annotation of compound libraries"

description: Metabolomics dataset relating to the pubblication: "Combining CRISPRi and metabolomics for functional annotation of compound libraries"
DOI: 10.5281/zenodo.8214729
title: UVic-MOBI Last Glacial Maximum Marine Biogeochemistry Simulations

description: UVic-MOBI Earth System Model results used in the poster presentation at the International Conference on Paleoceanography, 2022: Somes et al., "Compensating effects of reduced sedimentary iron release and enhanced atmospheric deposition on the biological carbon pump and atmospheric CO2 drawdown during the Last Glacial Maximum. The core model version is based on Somes et al., (2017); Somes et al., (2021). Last Glacial Maximum scenarios include sensitivity simulations that test low and high estimates for atmospheric dust deposition (i.e. "AtmHigh", "AtmLow") and excluding the effect from reductive sedimentary iron release ("SedZero").
description: The study was supported by Deutsche Forschungsgemeinschaft (DFG) grant no. 445549720 and the EU COMOFRT project (see below).
DOI: 10.5281/zenodo.8214728
title: UVic-MOBI Last Glacial Maximum Marine Biogeochemistry Simulations

description: UVic-MOBI Earth System Model results used in the poster presentation at the International Conference on Paleoceanography, 2022: Somes et al., "Compensating effects of reduced sedimentary iron release and enhanced atmospheric deposition on the biological carbon pump and atmospheric CO2 drawdown during the Last Glacial Maximum. The core model version is based on Somes et al., (2017); Somes et al., (2021). Last Glacial Maximum scenarios include sensitivity simulations that test low and high estimates for atmospheric dust deposition (i.e. "AtmHigh", "AtmLow") and excluding the effect from reductive sedimentary iron release ("SedZero").
description: The study was supported by Deutsche Forschungsgemeinschaft (DFG) grant no. 445549720 and the EU COMOFRT project (see below).
DOI: 10.17632/7xsgxz98gj.1
title: Analysis of the coverage and discourse of the Sustainable Development Goals and the 2030 Agenda in the Spanish digital press (2015-2022)

description: Introduction: This research offers a longitudinal view of the coverage, as well as the main characteristics of the discourse on the SDGs and the United Nations 2030 Agenda, after analysing the ten digital newspapers with the highest readership in Spain. Methodology: A quantitative and descriptive approach of the news items that mention this topic was carried out, followed by an interpretative analysis of the content of the full texts and, finally, a semantic analysis and text mining. Results: It is observed that the number of news items mentioning this issue has increased by more than 1000%, setting 2020 as a turning point from which the coverage of this issue has become generalised in the media agenda. Despite this increase, news content featuring the SDGs and the 2030 Agenda has been decreasing to minimum levels. In terms of discourse, the results reveal that the terms most associated with 'SDG_2030Agenda' are 'UN', 'government', 'policies' and 'country'. The first three also appear in the associative analysis. In addition, four thematic groups are identified with terms that relate to: 'Global issues', 'UN', 'Institutional' and 'SDG Goals and Targets' Discussion: The data show that, despite the increase in the number of news items, the prominence of this initiative has been inversely proportional. Conclusions: Content about the UN plan gives greater prominence to compliance by governments and institutions than to the content of the goals themselves.
DOI: 10.17632/6hypzb9sn6.1
title: Pashaei Biohydrogenation

description: Final Ph.D. Thesis
DOI: 10.17632/4sx58vt8v9.1
title: Cross Fit Tsartsapakis et al. 2023

description: SPSS raw data of ultrasound thickness (relative to rest) of transversus abdominis (TrA) and Internal oblique (IO) and lumbar multifidus (LM) and EMG (% of maximum voluntary contraction) of rectus abdominis (RA), external oblique (EO) and iliocostalis lumborum (ES) during plank, side plank (S. Plank) and bridge using either bracing (BR) or hollowing (HOL), sex (1 - males, 2 - females)
DOI: 10.17632/mz3w5csbh7.1
title: Ferns_leaves_Sarawak

description: This dataset contain the information relative to the Manuscript entitled Fern species richness and leaves morphological traits change along a tropical riparian vegetation gradient, an example from Borneo.
DOI: 10.17632/grw74bp3p3.1
title: Data for the paper "App-based experiments"

description: The data presented in this study have been collected through a combination of laboratory experiments and app-based experiments in which university students participated.

In the paper, we elicit and compare behaviors in the laboratory and on a smartphone application that we developed for the study. Our participant pool consists of university students who are subjected to identical incentives and selection criteria. Behavior is similar across samples in measures of attitudes towards risk, effort, cognitive ability, strategic reasoning, trust, and lying aversion. Additionally, participants show comparable beliefs about the actions of the other players. We also identify certain quantitative differences between the two groups. Specifically, subjects using the app donate more in the dictator game, are faster, and show less consistency. These findings show the potential of using smartphone applications to organize experiments, and emphasize the importance of a clear and simple interface in this environment.
DOI: 10.17632/xrbcgz7wng.1
title: Emotional Maturity of Parents: A Prerequisite for Healthy Relations in Scheduled Tribe Families

description: The data supporting this research study assist in justifying the research question – Could relationships be reinforced in the family with the infusion of emotional maturity among parents? The data revolves around prominent themes such as emotion, emotional regulation, emotional responses, emotional maturity, family, and relationship. The data is gathered both at the primary and secondary levels. Preliminary data was gathered through Focus Group Discussion (FGD) among scheduled tribe parents hailing from the district of Ranchi (Jharkhand), and secondary data were assisted through various journal articles and book chapters. Then, the thematic analysis of the data was done to interpret the research findings. The findings state that parental emotional maturity reinforces healthy relations within the family. It highlights the importance of parental maturity in the daily course of family life. Parental emotional maturity enables emerging adults to build healthy relationships with their parents. The research study also states some recommendations which will assist greatly all parents in strengthening their emotional maturity. These suggestions will also motivate emerging adults to imbibe their personal emotional maturity for the total well-being of relationships in the family.
DOI: 10.17632/dzz98gctbc.1
title: FDI inflows

description: FDI inflows in China