cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19432523
title: Supplementary Material for: Static magnetic field promotes proliferation, migration, differentiation, and AKT activation of periodontal ligament stem cells

description: Periodontal ligament stem cells (PDLSCs) possess self-renewal and multilineage differentiation potential and exhibit great potential for the treatment of bone tissue defects caused by inflammation. Previous studies have indicated that static magnetic field (SMF) can enhance the proliferation and differentiation of mesenchymal stem cells (MSCs). SMF has been widely used to repair bone defects and for orthodontic and implantation treatment. In this study, we revealed that a 320 mT SMF upregulates the protein expression levels of cytokines such as MCM7 and PCNA in proliferating PDLSCs. Cell counting kit-8 (CCK-8) results revealed that the SMF group had higher optical density (OD) values than the control group. The ratio of cells in the S phase to those in the G2/M phase was significantly increased after exposure to a 320 mT SMF. In scratch assays, the SMF-treated PDLSCs exhibited a higher migration rate than the sham-exposed group after 24 h of culture, indicating that the SMF promoted the migratory ability of PDLSCs. The activity level of the early differentiation marker alkaline phosphatase (ALP) and the late marker matrix mineralization, as well as osteoblast-specific gene and protein expression, were enhanced in PDLSCs exposed to the SMF. Furthermore, AKT signalling pathway were activated by SMF. Our data demonstrated that the potential mechanism of action of SMF may enhance PDLSCs proliferation and osteogenic differentiation by activating the phosphorylated AKT pathways. The elucidation of this molecular mechanism may lead to a better understanding of bone repair responses and aid in improved stem cell-mediated regeneration.
DOI: 10.5281/zenodo.5347802
title: FDup deduplication software data benchmark: 10Mi OpenAIRE Publications Dump

description: This dataset is a random subset of publications extracted from the OpenAIRE Research Graph (http://doi.org/10.5281/zenodo.4707307). The dataset contains ~10Mi JSON publications records. The file is a zip archive containing gz files, each with one JSON per line. Each JSON is compliant to the schema available at http://doi.org/10.5281/zenodo.4723403.<br> <br> Learn more about the OpenAIRE Research Graph at https://graph.openaire.eu.
description: {"references": ["FDup: a framework for general-purpose and efficient entity deduplication of record collections: https://peerj.com/articles/cs-1058/"]}
DOI: 10.6084/m9.figshare.16850419.v1
title: #GlobalCollembola: site-level database and analyses

description: Site-level database of the #GlobalCollembola initiative and programming code for path analysis and geospatial modelling in the synthesis publication: "Globally invariant metabolism but density-diversity mismatch in springtails". Four files are attached:1) GCdatabase_sites.csv - site-level database structured for path analysis2) Rcode_PathAnalysis - markdown pdf with the R code for path analysis3) 20210527_collembola_sampled.csv - site-level database structured for geospatial modelling4) 20210630_collembola_pipeline.py - the Python code for geospatial modelling
DOI: 10.5281/zenodo.7053395
title: Dataset for paper submission: "Revisiting the Long-Run Relationship Between Inward/Outward FDI and Income Inequality: New Evidence from the OECD"

description: The relatively small panel cointegration literature on the dynamics between FDI and income inequality predominantly finds that FDI will reduce income inequality in the long-run in developed countries. However, we point out an important technical oversight in the literature. Not accounting for cross-section dependence in panel data methodologies may yield unreliable results. Expanding on the work of @herzer/nunnenkamp:13, who pioneered the use of panel cointegration in the European context, we obtain different results when we account for cross-section dependence and employ economic procedures robust to it. Using a panel containing 16 OECD countries (1979-2017), 2 income inequality measures, and 4 FDI measures, we begin by showing strong evidence for the existence of cross-section dependence. Then, using second-generation econometric procedures, we do not find any evidence for a cointegrating relationship between inward FDI and income inequality. We do find evidence that outward FDI is cointegrated with income inequality; however, contrary to the main results of the literature, we find that it widens the income gap in the long-run. Additionally, our results support the view that fiscal policy is an important tool to reduce income inequality.
DOI: 10.5281/zenodo.7053394
title: Dataset for paper submission: "Revisiting the Long-Run Relationship Between Inward/Outward FDI and Income Inequality: New Evidence from the OECD"

description: The relatively small panel cointegration literature on the dynamics between FDI and income inequality predominantly finds that FDI will reduce income inequality in the long-run in developed countries. However, we point out an important technical oversight in the literature. Not accounting for cross-section dependence in panel data methodologies may yield unreliable results. Expanding on the work of @herzer/nunnenkamp:13, who pioneered the use of panel cointegration in the European context, we obtain different results when we account for cross-section dependence and employ economic procedures robust to it. Using a panel containing 16 OECD countries (1979-2017), 2 income inequality measures, and 4 FDI measures, we begin by showing strong evidence for the existence of cross-section dependence. Then, using second-generation econometric procedures, we do not find any evidence for a cointegrating relationship between inward FDI and income inequality. We do find evidence that outward FDI is cointegrated with income inequality; however, contrary to the main results of the literature, we find that it widens the income gap in the long-run. Additionally, our results support the view that fiscal policy is an important tool to reduce income inequality.
DOI: 10.5281/zenodo.7053299
title: Dataset for Patcherizer

description: Java patches and their paired descriptions
DOI: 10.5281/zenodo.7053298
title: Dataset for Patcherizer

description: Java patches and their paired descriptions
DOI: 10.6084/m9.figshare.19213929
title: Sequence alignments and phylogenetic trees for Cyphellophora endoradicis - Fungal Planet 1408 - 12 July 2022

description: Sequence alignments and phylogenetic trees for the description of Cyphellophora endoradicis - Fungal Planet 1408 - 12 July 2022
DOI: 10.6084/m9.figshare.19213929.v1
title: Sequence alignments and phylogenetic trees for Cyphellophora endoradicis - Fungal Planet 1408 - 12 July 2022

description: Sequence alignments and phylogenetic trees for the description of Cyphellophora endoradicis - Fungal Planet 1408 - 12 July 2022
DOI: 10.6084/m9.figshare.20973550
title: Datasets for dissertation

description: The file contains all the data collected from the reviews and video content for analysis in the dissertation.
DOI: 10.5281/zenodo.6778020
title: Combined proton radiography and irradiation for high-precision preclinical studies in small animals

description: Data used for the publication "Combined proton radiography and irradiation for high-precision preclinical studies in small animals". The repository contains all data that was used to generate the quantitative results and figures in the submitted manuscript. Further documentation for the provided code can be found here: https://github.com/jo-mueller/radiographic_workflow_evaluation
DOI: 10.5281/zenodo.6778021
title: ExponatONE: a high-precision small animal irradiation setup using proton radiography

description: Data used for the publication "ExponatONE: a high-precision small animal irradiation setup using proton radiography". The repository contains all data that was used to generate the quantitative results and figures in the submitted manuscript.
DOI: 10.5281/zenodo.6998723
title: Combined proton radiography and irradiation for high-precision preclinical studies in small animals

description: Data used for the publication "Combined proton radiography and irradiation for high-precision preclinical studies in small animals". The repository contains all data that was used to generate the quantitative results and figures in the submitted manuscript. Further documentation for the provided code can be found here: https://github.com/jo-mueller/radiographic_workflow_evaluation
DOI: 10.6084/m9.figshare.19310963
title: Sequence alignments and phylogenetic trees for Endoradiciella communis - Fungal Planet 1409 - 12 July 2022

description: Sequence alignments and phylogenetic trees for Endoradiciella communis - Fungal Planet 1409 - 12 July 2022
DOI: 10.6084/m9.figshare.19310963.v1
title: Sequence alignments and phylogenetic trees for Endoradiciella communis - Fungal Planet 1409 - 12 July 2022

description: Sequence alignments and phylogenetic trees for Endoradiciella communis - Fungal Planet 1409 - 12 July 2022
DOI: 10.5281/zenodo.7038714
title: Training data for ship track detection machine learning algorithms

description: The training data and labels used to train the linked machine learning algorithm
DOI: 10.6084/m9.figshare.20972488
title: Genomic data of FC-RILs and LA-RILAs

description: Genomic data of FC-RILs and LA-RILAs for QTL analysis.
DOI: 10.6084/m9.figshare.20972488.v1
title: Genomic data of FC-RILs and LA-RILAs

description: Genomic data of FC-RILs and LA-RILAs for QTL analysis.
DOI: 10.34740/kaggle/dsv/4167586
title: YouTube Daily
DOI: 10.34740/kaggle/dsv/4167594
title: US Board on Geographic Names
DOI: 10.6084/m9.figshare.16964875
title: Retrospective evaluation of routine whole genome sequencing of <i>Mycobacterium tuberculosis</i> at the Belgian National Reference Center, 2019

description: Objectives: Since January 2019, the Belgian National Reference Center for Mycobacteria (NRC) has switched from conventional typing to prospective whole-genome sequencing (WGS) of all submitted <i>Mycobacterium tuberculosis</i> complex (MTB) isolates. The ISO17025 validated procedure starts with semi-automated extraction and purification of gDNA directly from the submitted MGIT tubes, without preceding subculturing. All samples are then sequenced on an Illumina MiSeq sequencer and analyzed using an in-house developed and validated bioinformatics workflow to determine the species and antimicrobial resistance. In this study, we retrospectively compare results obtained via WGS to conventional phenotypic and genotypic testing, for all Belgian MTB strains analyzed in 2019 (n = 306). Results: In all cases, the WGS-based procedure was able to identify correctly the MTB species. Compared to MGIT drug susceptibility testing (DST), the sensitivity and specificity of genetic prediction of resistance to first-line antibiotics were respectively 100 and 99% (rifampicin, RIF), 90.5 and 100% (isoniazid, INH), 100 and 98% (ethambutol, EMB) and 61.1 and 100% (pyrazinamide, PZA). The negative predictive value was above 95% for these four first-line drugs. A positive predictive value of 100% was calculated for INH and PZA, 80% for RIF and 45% for EMB. Conclusions: Our study confirms the effectiveness of WGS for the rapid detection of <i>M. tuberculosis</i> complex and its drug resistance profiles for first-line drugs even when working directly on MGIT tubes, and supports the introduction of this test into the routine workflow of laboratories performing tuberculosis diagnosis.
DOI: 10.6084/m9.figshare.16964875.v1
title: Retrospective evaluation of routine whole genome sequencing of <i>Mycobacterium tuberculosis</i> at the Belgian National Reference Center, 2019

description: Objectives: Since January 2019, the Belgian National Reference Center for Mycobacteria (NRC) has switched from conventional typing to prospective whole-genome sequencing (WGS) of all submitted <i>Mycobacterium tuberculosis</i> complex (MTB) isolates. The ISO17025 validated procedure starts with semi-automated extraction and purification of gDNA directly from the submitted MGIT tubes, without preceding subculturing. All samples are then sequenced on an Illumina MiSeq sequencer and analyzed using an in-house developed and validated bioinformatics workflow to determine the species and antimicrobial resistance. In this study, we retrospectively compare results obtained via WGS to conventional phenotypic and genotypic testing, for all Belgian MTB strains analyzed in 2019 (n = 306). Results: In all cases, the WGS-based procedure was able to identify correctly the MTB species. Compared to MGIT drug susceptibility testing (DST), the sensitivity and specificity of genetic prediction of resistance to first-line antibiotics were respectively 100 and 99% (rifampicin, RIF), 90.5 and 100% (isoniazid, INH), 100 and 98% (ethambutol, EMB) and 61.1 and 100% (pyrazinamide, PZA). The negative predictive value was above 95% for these four first-line drugs. A positive predictive value of 100% was calculated for INH and PZA, 80% for RIF and 45% for EMB. Conclusions: Our study confirms the effectiveness of WGS for the rapid detection of <i>M. tuberculosis</i> complex and its drug resistance profiles for first-line drugs even when working directly on MGIT tubes, and supports the introduction of this test into the routine workflow of laboratories performing tuberculosis diagnosis.
DOI: 10.6084/m9.figshare.20424148
title: What difference might retractions make? An estimate of the potential epistemic cost of retractions on meta-analyses

description: The extent to which a retraction might require revising previous scientific estimates and beliefs – which we define as the epistemic cost – is unknown. We collected a sample of 229 meta-analyses published between 2013 and 2016 that had cited a retracted study, assessed whether this study was included in the meta-analytic estimate and, if so, re-calculated the summary effect size without it. The majority (68% of N = 229) of retractions had occurred at least one year prior to the publication of the citing meta-analysis. In 53% of these avoidable citations, the retracted study was cited as a candidate for inclusion, and only in 34% of these meta-analyses (13% of total) the study was explicitly excluded because it had been retracted. Meta-analyses that included retracted studies were published in journals with significantly lower impact factor. Summary estimates without the retracted study were lower than the original if the retraction was due to issues with data or results and higher otherwise, but the effect was small. We conclude that meta-analyses have a problematically high probability of citing retracted articles and of including them in their pooled summaries, but the overall epistemic cost is contained.
DOI: 10.6084/m9.figshare.20972560
title: siBRD1_E2.bigwig

description: KAS pipe siBRD1 E2 trial 1
DOI: 10.6084/m9.figshare.20972560.v1
title: siBRD1_E2.bigwig

description: KAS pipe siBRD1 E2 trial 1
DOI: 10.5281/zenodo.7053509
title: Municipal Innovation Partnerships project documentation analysis

description: The purpose of the study is to provide empirical evidence about the under researched area of university-government relation in building a culture of entrepreneurial initiative inside triple helix model in a rural region. The study deploys a qualitative case study research method based on the content analysis of project documentation and further internal documents both from university and municipality.
description: Project was financed by German Federal Ministry for Science and Research German Federal Ministry for Science and Research (BMBF) and the Common Science Conference (GWK)
DOI: 10.5281/zenodo.7053508
title: Municipal Innovation Partnerships project documentation analysis

description: The purpose of the study is to provide empirical evidence about the under researched area of university-government relation in building a culture of entrepreneurial initiative inside triple helix model in a rural region. The study deploys a qualitative case study research method based on the content analysis of project documentation and further internal documents both from university and municipality.
description: Project was financed by German Federal Ministry for Science and Research German Federal Ministry for Science and Research (BMBF) and the Common Science Conference (GWK)
DOI: 10.6084/m9.figshare.12425249
title: Platonic Solids and High Genus Covers of Lattice Surfaces

description: We study the translation surfaces obtained by considering the unfoldings of the surfaces of Platonic solids. We show that they are all lattice surfaces and we compute the topology of the associated Teichmüller curves. Using an algorithm that can be used generally to compute Teichmüller curves of translation covers of primitive lattice surfaces, we show that the Teichmüller curve of the unfolded dodecahedron has genus 131 with 19 cone singularities and 362 cusps. We provide both theoretical and rigorous computer-assisted proofs that there are no closed saddle connections on the surfaces associated to the tetrahedron, octahedron, cube, and icosahedron. We show that there are exactly 31 equivalence classes of closed saddle connections on the dodecahedron, where equivalence is defined up to affine automorphisms of the translation cover. Techniques established here apply more generally to Platonic surfaces and even more generally to translation covers of primitive lattice surfaces and their Euclidean cone surface and billiard table quotients.
DOI: 10.6084/m9.figshare.12425249.v1
title: Platonic Solids and High Genus Covers of Lattice Surfaces

description: We study the translation surfaces obtained by considering the unfoldings of the surfaces of Platonic solids. We show that they are all lattice surfaces and we compute the topology of the associated Teichmüller curves. Using an algorithm that can be used generally to compute Teichmüller curves of translation covers of primitive lattice surfaces, we show that the Teichmüller curve of the unfolded dodecahedron has genus 131 with 19 cone singularities and 362 cusps. We provide both theoretical and rigorous computer-assisted proofs that there are no closed saddle connections on the surfaces associated to the tetrahedron, octahedron, cube, and icosahedron. We show that there are exactly 31 equivalence classes of closed saddle connections on the dodecahedron, where equivalence is defined up to affine automorphisms of the translation cover. Techniques established here apply more generally to Platonic surfaces and even more generally to translation covers of primitive lattice surfaces and their Euclidean cone surface and billiard table quotients.
DOI: 10.6084/m9.figshare.16850419.v2
title: #GlobalCollembola: site-level database and analyses

description: Site-level database of the #GlobalCollembola initiative and programming code for path analysis and geospatial modelling in the synthesis publication: "Globally invariant metabolism but density-diversity mismatch in springtails". Four files are attached: 1) GCdatabase_sites.csv - site-level database structured for path analysis 2) Rcode_PathAnalysis - markdown pdf with the R code for path analysis 3) 20210527_collembola_sampled.csv - site-level database structured for geospatial modelling 4) 20210630_collembola_pipeline.py - the Python code for geospatial modelling 4) #GCdatabase Events - sampling even database used for additional analysis (accounting for the sampling year and months)
DOI: 10.6084/m9.figshare.20973610
title: Probiotic Bifidobacterium animalis ssp. lactis Probio-M8 improves the properties and organic acid metabolism of fermented goats’ milk

description: The addition of <em>Bifidobacterium</em> to goats’ milk has a dual effect on health. The effect of <em>Bifidobacterium animalis</em> ssp. <em>lactis </em>Probio-M8 (Probio-M8) on fermentation characteristics, formation of organic acid, sensory properties, and storage characteristics of fermented goats’ milk (added 4.0% sucrose) was explored. The results showed that the addition of Probio-M8 decreased the fermentation time (<em>P</em> &lt; 0.05) and significantly increased the content of functional organic acids such as acetic acid (<em>P</em>-value &lt; 0.001), and functional long-chain unsaturated fatty acids (LCUFAs) including linoleic acid (<em>P</em>-value &lt; 0.001), α-linolenic acid (<em>P</em>-value &lt; 0.01), and DHA (<em>P</em>-value &lt; 0.001). Furthermore, the content of medium-chain and short-chain fatty acids (MCFAs and SCFAs) related to the ‘goaty’ flavour was significantly lower in the Probio-M8 treatment compared with the control. The number of livings Probio-M8 decreased from 8.27 log 10 CFU·mL-1 (1.80× 108 CFU·mL-1) to 7.94 Log CFU·mL-1 (0.79×108CFU·mL-1) after 28d of storage. In addition, pH-value and titratable acidity were not significantly different between the two group. The result of sensory evaluation also indicated a lower ‘goaty’ flavour and odour. Results suggest that the addition of probiotic Probio-M8 could improve the sensory, physicochemical, and functional properties of fermented goats’ milk.
DOI: 10.6084/m9.figshare.20973610.v1
title: Probiotic Bifidobacterium animalis ssp. lactis Probio-M8 improves the properties and organic acid metabolism of fermented goats’ milk

description: The addition of <em>Bifidobacterium</em> to goats’ milk has a dual effect on health. The effect of <em>Bifidobacterium animalis</em> ssp. <em>lactis </em>Probio-M8 (Probio-M8) on fermentation characteristics, formation of organic acid, sensory properties, and storage characteristics of fermented goats’ milk (added 4.0% sucrose) was explored. The results showed that the addition of Probio-M8 decreased the fermentation time (<em>P</em> &lt; 0.05) and significantly increased the content of functional organic acids such as acetic acid (<em>P</em>-value &lt; 0.001), and functional long-chain unsaturated fatty acids (LCUFAs) including linoleic acid (<em>P</em>-value &lt; 0.001), α-linolenic acid (<em>P</em>-value &lt; 0.01), and DHA (<em>P</em>-value &lt; 0.001). Furthermore, the content of medium-chain and short-chain fatty acids (MCFAs and SCFAs) related to the ‘goaty’ flavour was significantly lower in the Probio-M8 treatment compared with the control. The number of livings Probio-M8 decreased from 8.27 log 10 CFU·mL-1 (1.80× 108 CFU·mL-1) to 7.94 Log CFU·mL-1 (0.79×108CFU·mL-1) after 28d of storage. In addition, pH-value and titratable acidity were not significantly different between the two group. The result of sensory evaluation also indicated a lower ‘goaty’ flavour and odour. Results suggest that the addition of probiotic Probio-M8 could improve the sensory, physicochemical, and functional properties of fermented goats’ milk.
DOI: 10.5281/zenodo.7053579
title: Waveforms and RFs for Luoyang Basin

description: The teleseismic waveforms and calculated RFs from dense nodal array in Luoyang Basin.
DOI: 10.5281/zenodo.7053578
title: Waveforms and RFs for Luoyang Basin

description: The teleseismic waveforms and calculated RFs from dense nodal array in Luoyang Basin.