cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6540453
title: Tesseract OCR of IIT-CDIP Dataset

description: This is Tesseract generated <strong>transcriptions (no images)</strong> of (most of) the IIT-CDIP dataset. To download the images of the IIT-CDIP dataset go to https://data.nist.gov/od/id/mds2-2531 The directory struture of this dataset is the same as the IIT-CDIP dataset (although has everything in one tar, with "a.a", "a.b", ... directories) and can thus be combine with the image IIT-CDIP dataset using rsync or similar tool. This dataset contains a "X.layout.json" for each "X.png" in the IIT-CDIP dataset (doesn't have sections 'a', 'w', 'x', 'y', and 'z'). The jsons contain block/paragraph, line and word bounding boxes, with transcriptions for the words following the Tesseract format. The line and word annotations are directly taken from Tesseract. The block and paragraph output of Tesseract was discarded. The images were then run through both the Publaynet and PrimaNet models available on LayoutParser (https://layout-parser.github.io/). The combine output of these models became the block/paragraph annotations (we kept the Tesseract output format, but each block has 1 paragraph of exactly the same shape). <strong>Important:</strong> There is also a "rotation" value in the json (0, 90, 180, or 270) indicating the json may be for a rotated version of the IIT-CDIP image by the given amount (attempted to rotated documents to upright position to get better OCR results). These are the annotations used to pre-train <strong>Dessurt</strong> (https://arxiv.org/abs/2203.16618). These annotations will be worse than those that would be obtained using a commercial OCR system (like those used to pre-train LayoutLMv2/v3). The code used to produce these annotations is available here: https://github.com/herobd/ocr
DOI: 10.5281/zenodo.5838093
title: Patients' stem cells differentiation in a 3D environment as a promising experimental tool for the study of Amyotrophic Lateral Sclerosis

description: The database includes the raw data of the article “Patients’ stem cells differentiation in a 3D environment as a promising experimental tool for the study of Amyotrophic Lateral Sclerosis”. Aim of this work was to demonstrate the validity of 3D cultures for the differentiation of stem cells for the study of Amyotrophic Lateral Sclerosis in a more realistic model. The database contains the data obtained by the following evaluations: a) immunofluorescence analysis for the study of cells’ proliferation during differentiation b) confocal microscopy for the evaluation of differentiation markers c) RT-qPCR for the confirmation of stem cells’ differentiation d) immunofluorescence analysis for the evaluation of the electrophysiological characteristics of differentiated NSC34 cells. We first reprogrammed healthy and sALS PBMCs in iPSCs and differentiated them in NSCs in 2D. NSCs were then included in Cellink Bioink and printed. We differentiated NSCs first in MNPs and finally in MNs and evaluated every step of 3D differentiation in comparison with 2D. We found that NSCs maintain a good viability and proliferation rate during the differentiation in 3D. Moreover, we confirmed the good differentiation by confocal microscopy and RT-qPCR by the use of specific markers for every specific differentiation step. We concluded that cell’s inclusion in the hydrogel does not interfere with the correct differentiation process. Moreover, Bioprinting allows the study of cells in a 3D environment which better mimics tissue organization. Furthermore, RT-qPCR results suggest that the 3D environment increases the differentiation of CTRL MNPs in mature MNs when compared to 2D. Finally, we evidenced that the electrophysiological characteristics of cells are maintained after the inclusion and the printing. Such evidence confirmed that 3D Bioprinting can be considered a good model for the study of ALS pathogenesis.
description: Funding: Ricerca Corrente 2020-2021 Ministry of Health (Italy)
DOI: 10.5281/zenodo.5838092
title: Patients' stem cells differentiation in a 3D environment as a promising experimental tool for the study of Amyotrophic Lateral Sclerosis

description: The database includes the raw data of the article “Patients’ stem cells differentiation in a 3D environment as a promising experimental tool for the study of Amyotrophic Lateral Sclerosis”. Aim of this work was to demonstrate the validity of 3D cultures for the differentiation of stem cells for the study of Amyotrophic Lateral Sclerosis in a more realistic model. The database contains the data obtained by the following evaluations: a) immunofluorescence analysis for the study of cells’ proliferation during differentiation b) confocal microscopy for the evaluation of differentiation markers c) RT-qPCR for the confirmation of stem cells’ differentiation d) immunofluorescence analysis for the evaluation of the electrophysiological characteristics of differentiated NSC34 cells. We first reprogrammed healthy and sALS PBMCs in iPSCs and differentiated them in NSCs in 2D. NSCs were then included in Cellink Bioink and printed. We differentiated NSCs first in MNPs and finally in MNs and evaluated every step of 3D differentiation in comparison with 2D. We found that NSCs maintain a good viability and proliferation rate during the differentiation in 3D. Moreover, we confirmed the good differentiation by confocal microscopy and RT-qPCR by the use of specific markers for every specific differentiation step. We concluded that cell’s inclusion in the hydrogel does not interfere with the correct differentiation process. Moreover, Bioprinting allows the study of cells in a 3D environment which better mimics tissue organization. Furthermore, RT-qPCR results suggest that the 3D environment increases the differentiation of CTRL MNPs in mature MNs when compared to 2D. Finally, we evidenced that the electrophysiological characteristics of cells are maintained after the inclusion and the printing. Such evidence confirmed that 3D Bioprinting can be considered a good model for the study of ALS pathogenesis.
description: Funding: Ricerca Corrente 2020-2021 Ministry of Health (Italy)
DOI: 10.6084/m9.figshare.19758661
title: Data from SHOT study in Norway with biological data

description: Psychological and biological data collected from 2016-2018 on trauma patients attending an outpatient clinic. Also, 40 healty control subjects.
DOI: 10.6084/m9.figshare.19758661.v1
title: Data from SHOT study in Norway with biological data

description: Psychological and biological data collected from 2016-2018 on trauma patients attending an outpatient clinic. Also, 40 healty control subjects.
DOI: 10.6084/m9.figshare.18154715
title: An enhanced battery materials database auto-generated using ChemDataExtractor and further classified using the BatteryBERT language model.

description: An enhanced battery materials database auto-generated using ChemDataExtractor and further classified using the BatteryBERT language model. <br> Two battery material databases are included: <br> (1) a new battery property database v2.0 that contains 210,416 data about battery materials and five of its key properties: capacity, voltage, conductivity, Coulombic efficiency and energy. This database supersedes v1.0 (Huang, S. & Cole, J. M. A database of battery materials autogenerated using ChemDataExtractor. <em>figshare</em> https://doi.org/10.6084/m9.figshare.11888115.v2 (2020)) owing to its: (i) enhancement of data from the last two years (2020 and 2021) as well as from papers belonging to Springer journals; (ii) filtering off of non-relevant data from non-battery papers that has been made possible via our implementation of a binary classification model. <br> (2) A device-classified database that contains 300,622 anode, cathode or electrolyte materials that have been classified using our BatteryBERT language model. <br> Both databases have been provided in JSON, SQL, and CSV format.<br>
DOI: 10.5281/zenodo.1219620
title: A Canadian French Emotional Speech Dataset

description: The Canadian French Emotional (CaFE) speech dataset contains six different sentences, pronounced by six male and six female actors, in six basic emotions plus one neutral emotion. The six basic emotions are acted in two different intensities: mild ("Faible") and strong ("Fort"). This dataset is freely available under a Creative Commons license (CC BY-NC-SA 4.0). The dataset was digitally recorded at a high-resolution (192 kHz sampling rate, 24 bits per sample). A filtered and downsampled version at a lower resolution (48 kHz sampling rate, 16 bits per sample) is also available. This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit Creative Commons
DOI: 10.5281/zenodo.6544368
title: Towards Just-In-Time Feature Request Approval Prediction

description: This is the dataset of our publication "Towards Just-In-Time Feature Request Approval Prediction", which consists of feature requests collected from Sourceforge.net.
DOI: 10.5281/zenodo.6544367
title: Towards Just-In-Time Feature Request Approval Prediction

description: This is the dataset of our publication "Towards Just-In-Time Feature Request Approval Prediction", which consists of feature requests collected from Sourceforge.net.
DOI: 10.6084/m9.figshare.19758670
title: Weddell_Data

description: Weddell Sea data
DOI: 10.6084/m9.figshare.19758670.v1
title: Weddell_Data

description: Weddell Sea data
DOI: 10.5066/p9palkqz
title: Stream temperature predictions for the Willamette River Basin, northwestern Oregon estimated from regression equations (1954 - 2018)

description: This data release contains estimated stream temperature metrics at three locations in the Willamette River Basin, northwestern Oregon for various periods between 1954 and 2018. These locations were the Willamette River at Albany, the Willamette River at Harrisburg, and the Willamette River at Keizer. A regression program (written in the R programming language) was used to relate the values for two stream temperature metrics (the seven-day average of the daily mean and the seven-day average of the daily maximum) to the seven-day average of the daily mean or the seven-day average of the daily maximum air temperature, and to the mean daily streamflow for five seasonal time periods at each of the locations. The regression equations were used to predict the seven-day average of the daily mean stream temperature and the seven-day average of the daily maximum stream temperature for each day during the modeled time period at each location. The regression equations were based on data collected at these three locations and at nine additional locations. These additional locations included the Willamette River at Willamette Falls, the Willamette River at Newberg, the Willamette River at Owosso Bridge, the Santiam River at Jefferson, the North Santiam River near Mehama, the McKenzie River at Hayden Bridge, the McKenzie River at Vida, the Middle Fork Willamette River at Jasper, and the Coast Fork Willamette River at Goshen.
DOI: 10.5281/zenodo.6544490
title: Buteo oreophilus SPAdes preassembly

description: .
DOI: 10.5281/zenodo.6544489
title: Buteo oreophilus SPAdes preassembly

description: .
DOI: 10.6084/m9.figshare.3761562.v2216
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.26024/tp2m-af86
title: CESM2 Forced Ocean Sea-Ice (FOSI) Experiment

description: These high-resolution Forced-Ocean-Sea-Ice (FOSI) experiments uses version 2 of the Community Earth System Model (CESM). The ocean component is the Parallel Ocean Program version 2 (POP2) run at nominal 0.1° horizontal resolution with 62 vertical levels. The sea ice model is the Community Ice Code version 5 (CICE5) and is run on the same horizontal grid as the ocean. FOSI is forced at the surface with historical atmospheric state and flux fields from the JRA55-do dataset. JRA55-do cover the 1958–2018 period.
DOI: 10.5281/zenodo.6544552
title: SciKGTeX Scientific Contribution Metadata LaTeX Package User Evaluation Results & Analysis

description: The responses and measured variables from 26 participants of the first user test of the SciKGTeX package. https://github.com/Christof93/SciKGTeX Also the raw text source for the evaluation tasks and the result analysis notebook with the results saved as tsv file.
DOI: 10.5281/zenodo.6518994
title: SciKGTeX Scientific Contribution Metadata LaTeX Package User Evaluation Results & Analysis

description: The responses and measured variables from 26 participants of the first user test of the SciKGTeX package. https://github.com/Christof93/SciKGTeX Also the raw text source for the evaluation tasks and the result analysis notebook with the results saved as tsv file.
DOI: 10.21227/tbm7-w030
title: Code of Paper: Smart Economic and Mobility Aware Cooperation for Resource Sharing in Multi-Tier Edge Slicing

description: In this paper, we propose a novel cooperative resource sharing in a multi-tier edge slicing networks which isrobust to imperfect channel state information (CSI) caused by user equipments’ (UEs) mobility. Due to the mobilityof UEs, the dynamic requirements of their tasks, and the limited resources of the network, we propose a smart jointdynamic pricing and resources sharing (SJDPRS) scenario that can incentivize the infrastructure provider (InP) andmobile network operators (MNOs). Aiming to maximize the profits of UEs, MNOs and the InP under the taskfulfillment constraints, we formulate an optimization problem by deploying the multi-objective optimization methodwhere in addition to the resource allocation variables, the price values are also the optimization variables. To solvethe problem, we adopt a new deep reinforcement learning (DRL) method based on a carefully designed rewardfunction. The simulation results indicate that the proposed resource sharing scenario can increase total profits forthe UEs, MNOs, and InP in comparison to non-cooperative case, while also providing almost complete fairnessamong the players. In specific, the obtained results show that the average fulfilled tasks, minimum profit of MNOs,and average profit for the InP enhanced by 78%, 75%, and 79%, respectively.
DOI: 10.5281/zenodo.6544562
title: Supporting data for "Modeling the albedo neutron decay source of radiation belt electrons and protons"

description: Data sets are provided in support of the publication to appear in JGR-Space Physics. They include tabulated values of computed albedo neutron flux above the atmosphere, and of resulting radiation belt electron and proton source functions. Data format is described in the README files.
DOI: 10.5281/zenodo.6544540
title: Supporting data for "Modeling the albedo neutron decay source of radiation belt electrons and protons"

description: Data sets are provided in support of the publication to appear in JGR-Space Physics. They include tabulated values of computed albedo neutron flux above the atmosphere, and of resulting radiation belt electron and proton source functions. Data format is described in the README files.
DOI: 10.6084/m9.figshare.19380230
title: Additional files_Monocyte biomarkers define sargramostim treatment outcomes for Parkinson’s disease

description: Clinical and pathobiological diversity of Parkinson's disease (PD) presents a major challenge in the development of relevant biomarkers to monitor disease progression and disease-modifying therapies. Based on the involvement of innate immunity in the onset and tempo of PD, transcriptomic and proteomic monocyte cell signatures were evaluated in five PD patients during the course of granulocyte-macrophage colony-stimulating factor (GM-CSF, Sargramostim, Leukine<sup>R</sup>) Therapy. Sargramostim, a well-known immune modulator, may provide a monocyte signature capable of scoring clinical motor functions during disease-linked immune transformation therapy.<br>
DOI: 10.6084/m9.figshare.19380230.v1
title: Additional files_Monocyte biomarkers define sargramostim treatment outcomes for Parkinson’s disease

description: Clinical and pathobiological diversity of Parkinson's disease (PD) presents a major challenge in the development of relevant biomarkers to monitor disease progression and disease-modifying therapies. Based on the involvement of innate immunity in the onset and tempo of PD, transcriptomic and proteomic monocyte cell signatures were evaluated in five PD patients during the course of granulocyte-macrophage colony-stimulating factor (GM-CSF, Sargramostim, Leukine<sup>R</sup>) Therapy. Sargramostim, a well-known immune modulator, may provide a monocyte signature capable of scoring clinical motor functions during disease-linked immune transformation therapy.<br>
DOI: 10.5281/zenodo.6544541
title: Supporting data for "Modeling the albedo neutron decay source of radiation belt electrons and protons"

description: Data sets are provided in support of the publication to appear in JGR-Space Physics. They include tabulated values of computed albedo neutron flux above the atmosphere, and of resulting radiation belt electron and proton source functions. Data format is described in the README files (left out of version 1.0, added to version 1.1).
DOI: 10.48661/fk2/n0bvvj/hv69b7
title: output(2).pdf

description: :unav
DOI: 10.48661/fk2/n0bvvj
title: Dataset ejemplo

description: Prueba de afiliaciones
DOI: 10.5281/zenodo.6473977
title: Dataset: 1,000 QM/MM minimum energy pathway conformations for the deacylation reactions of GES-5/imipenem

description: This dataset consists of 1,000 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the deacylation reactions between a Class A beta-lactamases (GES-5) and the imipenem antibiotic molecules. All pathway conformations were optimized at DFTB3/3OB-f/CHARMM36 level with 36 replicas. All single point calculations and charge population analysis were done at B3LYP-D3/6-31+G(d,p)/CHARMM36 level. 0.paths_ges_imi_d1.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions. 0.paths_ges_imi_d2.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions. 1.eners.zip: The single point replica energies along all GES-5/IPM pathways. 1.chrgs.zip: The NBO charges of the QM region of all replica conformations along all GES-5/IPM pathways. 2.datasets.zip: The Python codes to postprocess the molecular data and the featurized the NumPy arrays. 3.gnn.zip: The Python codes that implements the edge-conditioned graph convolutional NN to predict the deacylation barriers. 5.representative_conf.zip: The pathway conformations of all cluster centroids and an energetic representative (pathway id 22) pathway. Note: This file also serves as a peephole of how the pathway conformations from Reaction Path with Holonomic Constrains calculations looks like. 6.benchmark.zip: The benchmark calculations that validates the DFTB3/3OB-f/CHARMM36 against DFTB3/3OB/CHARMM36 and B3LYP/6-31G(d,p)/CHARMM36 level of theory on the energetic representative (pathway id 22) pathway conformations.
DOI: 10.6084/m9.figshare.16585895
title: FS3-Shukla etal-Intestinal GR in Alcohol effects

description: Corticosterone, the stress hormone, exacerbates alcohol-associated tissue injury, but the mechanism involved is unknown. We examined the role of the glucocorticoid receptor (GR) in corticosterone-mediated potentiation of alcohol-induced gut barrier dysfunction and systemic response. Hepatocyte-specific GR deficient (<em>GR</em><sup><em>HC</em></sup>) and intestinal epithelial-specific GR deficient (<em>GR</em><sup><em>IEC</em></sup>) mice were fed ethanol, combined with corticosterone treatment. Intestinal epithelial tight junction integrity, mucosal barrier function, microbiota dysbiosis, endotoxemia, systemic inflammation, liver damage, and neuroinflammation were assessed. Corticosterone potentiated ethanol-induced epithelial tight junction disruption, mucosal permeability, and inflammatory response in <em>GR</em><sup><em>HC</em></sup> mouse colon; these effects of ethanol and corticosterone were absent in <em>GR</em><sup><em>IEC</em></sup> mice. Gut microbiota compositions in ethanol-fed <em>GR</em><sup><em>IEC</em></sup> and <em>GR</em><sup><em>IEC</em></sup> mice were similar to each other. However, corticosterone treatment in ethanol-fed mice shifted the microbiota composition to distinctly different directions in <em>GR</em><sup><em>HC</em></sup> and <em>GR</em><sup><em>IEC</em></sup> mice. Ethanol and corticosterone synergistically elevated the abundance of <em>Enterobacteriaceae</em>and <em>E. coli</em> and reduced the abundance of <em>Lactobacillus</em> in <em>GR</em><sup><em>HC</em></sup>mice but not in <em>GR</em><sup><em>IEC</em></sup> mice. In <em>GR</em><sup><em>HC</em></sup> mice, corticosterone potentiated ethanol-induced endotoxemia and systemic inflammation, but these effects were absent in <em>GR</em><sup><em>IEC</em></sup> mice. Interestingly, ethanol-induced liver damage and its potentiation by corticosterone were observed in <em>GR</em><sup><em>HC</em></sup> mice but not in <em>GR</em><sup><em>IEC</em></sup> mice. <em>GR</em><sup><em>IEC</em></sup>mice were also resistant to ethanol and corticosterone-induced inflammatory response in the hypothalamus. These data indicate that the intestinal epithelial GR plays a central role in alcohol and corticosterone-induced gut barrier dysfunction, microbiota dysbiosis, endotoxemia, systemic inflammation, liver damage, and neuroinflammation. This study identifies a novel target for potential therapeutic for alcohol-associated tissue injury.
DOI: 10.6084/m9.figshare.16585895.v1
title: FS3-Shukla etal-Intestinal GR in Alcohol effects

description: Corticosterone, the stress hormone, exacerbates alcohol-associated tissue injury, but the mechanism involved is unknown. We examined the role of the glucocorticoid receptor (GR) in corticosterone-mediated potentiation of alcohol-induced gut barrier dysfunction and systemic response. Hepatocyte-specific GR deficient (<em>GR</em><sup><em>HC</em></sup>) and intestinal epithelial-specific GR deficient (<em>GR</em><sup><em>IEC</em></sup>) mice were fed ethanol, combined with corticosterone treatment. Intestinal epithelial tight junction integrity, mucosal barrier function, microbiota dysbiosis, endotoxemia, systemic inflammation, liver damage, and neuroinflammation were assessed. Corticosterone potentiated ethanol-induced epithelial tight junction disruption, mucosal permeability, and inflammatory response in <em>GR</em><sup><em>HC</em></sup> mouse colon; these effects of ethanol and corticosterone were absent in <em>GR</em><sup><em>IEC</em></sup> mice. Gut microbiota compositions in ethanol-fed <em>GR</em><sup><em>IEC</em></sup> and <em>GR</em><sup><em>IEC</em></sup> mice were similar to each other. However, corticosterone treatment in ethanol-fed mice shifted the microbiota composition to distinctly different directions in <em>GR</em><sup><em>HC</em></sup> and <em>GR</em><sup><em>IEC</em></sup> mice. Ethanol and corticosterone synergistically elevated the abundance of <em>Enterobacteriaceae</em>and <em>E. coli</em> and reduced the abundance of <em>Lactobacillus</em> in <em>GR</em><sup><em>HC</em></sup>mice but not in <em>GR</em><sup><em>IEC</em></sup> mice. In <em>GR</em><sup><em>HC</em></sup> mice, corticosterone potentiated ethanol-induced endotoxemia and systemic inflammation, but these effects were absent in <em>GR</em><sup><em>IEC</em></sup> mice. Interestingly, ethanol-induced liver damage and its potentiation by corticosterone were observed in <em>GR</em><sup><em>HC</em></sup> mice but not in <em>GR</em><sup><em>IEC</em></sup> mice. <em>GR</em><sup><em>IEC</em></sup>mice were also resistant to ethanol and corticosterone-induced inflammatory response in the hypothalamus. These data indicate that the intestinal epithelial GR plays a central role in alcohol and corticosterone-induced gut barrier dysfunction, microbiota dysbiosis, endotoxemia, systemic inflammation, liver damage, and neuroinflammation. This study identifies a novel target for potential therapeutic for alcohol-associated tissue injury.