cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14805693.v1
title: Speedtest broadband performance by AUS Federal Electorate

description: This dataset analyses Speedtest Open Data by Australian Federal Electorate. Original dataset was Q1, 2020. Now updated (v.3) with Q1, 2021.<br>Analysis of GPS coordinates to Federal Electorate, thanks to E Helderop.<br>Jupyter analysis by Ferrers.<br>Changelog:v4. Added graph for 2021 analysis, overall uplift, plus analysis by Regional Type. (v1.2 ipynb)v3. Added data for Q1-2021. Source: Helderop.v2. Added pics by Electorate type; rural/provincial/inner-outerUrban (source: AEC link below), added four sample electorates comparison graph - like four cities comparison. Added updated Jupyter v1.1.v1 Initial load, data, pics and jupyter.<br>Speedtest data is CC-BY-NC-SA, so this derived dataset is too. (Link below)<br>
DOI: 10.6084/m9.figshare.14898419
title: Datasets from Late holocene spread of pastoralism coincides with endemic megafaunal extinction on Madagascar

description: include all new and reviewed data
DOI: 10.6084/m9.figshare.11425503
title: Interprofessional education and collaboration among healthcare students and professionals: a systematic review and call for action

description: Interprofessional education (IPE) is a prerequisite to building a collaborative practice environment and optimizing patient care. The purpose of this systematic review was to assess the impact of IPE on outcomes related to health-care pre-licensure learners and professionals, including: changes in attitudes/perceptions; acquisition of knowledge regarding other disciplines’ roles and development of collaborative skills; and change in collaborative behavior. We searched PubMed, CINAHL, Embase, and ERIC for studies published from 2007 to 2017 in English; 19 studies were eligible. The Joanna Briggs Institute appraisal tool was used to assess the quality of the studies. Thirteen studies used a quasi-experimental design. The studies varied in terms of setting, teaching methods, assessment measures, and quality. Seventeen of the 19 studies (89%) that assessed change in attitudes toward other disciplines and value placed on a team-based approach for improving patient care, found statistically significant improvements. All seven of the studies that assessed change in collaborative behavior found statistically significant improvements. Among the 12 studies that assessed the development of collaborative skills, there were mixed results. Future directions include: conducting more studies among health-care professionals, assessing the long-term impact of IPE, objectively assessing change in collaborative behavior, and assessing the impact of IPE on patient-centered outcomes.
DOI: 10.6084/m9.figshare.11425503.v1
title: Interprofessional education and collaboration among healthcare students and professionals: a systematic review and call for action

description: Interprofessional education (IPE) is a prerequisite to building a collaborative practice environment and optimizing patient care. The purpose of this systematic review was to assess the impact of IPE on outcomes related to health-care pre-licensure learners and professionals, including: changes in attitudes/perceptions; acquisition of knowledge regarding other disciplines’ roles and development of collaborative skills; and change in collaborative behavior. We searched PubMed, CINAHL, Embase, and ERIC for studies published from 2007 to 2017 in English; 19 studies were eligible. The Joanna Briggs Institute appraisal tool was used to assess the quality of the studies. Thirteen studies used a quasi-experimental design. The studies varied in terms of setting, teaching methods, assessment measures, and quality. Seventeen of the 19 studies (89%) that assessed change in attitudes toward other disciplines and value placed on a team-based approach for improving patient care, found statistically significant improvements. All seven of the studies that assessed change in collaborative behavior found statistically significant improvements. Among the 12 studies that assessed the development of collaborative skills, there were mixed results. Future directions include: conducting more studies among health-care professionals, assessing the long-term impact of IPE, objectively assessing change in collaborative behavior, and assessing the impact of IPE on patient-centered outcomes.
DOI: 10.6084/m9.figshare.14898327
title: Binchuan_Linear_Array.zip

description: Dataset for "Seismic Site Response Inferred from Records at a Dense Linear Array across the Chenghai Fault Zone, Binchuan, Yunnan" sumitted to Journal of Geophysical Research - Solid Earth. It contains both local and teleseismic waveforms recorded by a dense array. Computed HVSR results are also included.
DOI: 10.6084/m9.figshare.14898681
title: Supplementary Material for: Conservation of Epithelial-to-Mesenchymal Transition Process in Neural Crest Cells and Metastatic Cancer

description: Epithelial to mesenchymal transition (EMT) is a highly conserved cellular process in several species, from worms to humans. EMT plays a fundamental role in early embryogenesis, wound healing, and cancer metastasis. For neural crest cell (NCC) development, EMT typically results in forming a migratory and potent cell population that generates a wide variety of cell and tissue, including cartilage, bone, connective tissue, endocrine cells, neurons, and glia amongst many others. The degree of conservation between the signaling pathways that regulate EMT during development and metastatic cancer (MC) has not been fully established, despite ample studies. This systematic review and meta-analysis dissects the major signaling pathways involved in EMT of NCC development and MC to unravel the similarities and differences. While the FGF, TGFβ/BMP, SHH, and NOTCH pathways have been rigorously investigated in both systems, the EGF, IGF, HIPPO, Factor Receptor Superfamily, and their intracellular signaling cascades need to be the focus of future NCC studies. In general, meta-analyses of the associated signaling pathways show a significant number of overlapping genes (particularly ligands, transcription regulators, and targeted cadherins) involved in each signaling pathway of both systems without stratification by body segments and cancer type. Lack of stratification makes it difficult to meaningfully evaluate the intracellular downstream effectors of each signaling pathway. Finally, pediatric neuroblastoma and melanoma are NCC-derived malignancies, which emphasize the importance of uncovering the EMT events that convert NCC into treatment-resistant malignant cells.
DOI: 10.6084/m9.figshare.14898681.v1
title: Supplementary Material for: Conservation of Epithelial-to-Mesenchymal Transition Process in Neural Crest Cells and Metastatic Cancer

description: Epithelial to mesenchymal transition (EMT) is a highly conserved cellular process in several species, from worms to humans. EMT plays a fundamental role in early embryogenesis, wound healing, and cancer metastasis. For neural crest cell (NCC) development, EMT typically results in forming a migratory and potent cell population that generates a wide variety of cell and tissue, including cartilage, bone, connective tissue, endocrine cells, neurons, and glia amongst many others. The degree of conservation between the signaling pathways that regulate EMT during development and metastatic cancer (MC) has not been fully established, despite ample studies. This systematic review and meta-analysis dissects the major signaling pathways involved in EMT of NCC development and MC to unravel the similarities and differences. While the FGF, TGFβ/BMP, SHH, and NOTCH pathways have been rigorously investigated in both systems, the EGF, IGF, HIPPO, Factor Receptor Superfamily, and their intracellular signaling cascades need to be the focus of future NCC studies. In general, meta-analyses of the associated signaling pathways show a significant number of overlapping genes (particularly ligands, transcription regulators, and targeted cadherins) involved in each signaling pathway of both systems without stratification by body segments and cancer type. Lack of stratification makes it difficult to meaningfully evaluate the intracellular downstream effectors of each signaling pathway. Finally, pediatric neuroblastoma and melanoma are NCC-derived malignancies, which emphasize the importance of uncovering the EMT events that convert NCC into treatment-resistant malignant cells.
DOI: 10.6084/m9.figshare.14898408
title: Supplementary Material for: A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction

description: Fe(II) oxidation coupled to nitrate reduction (NRFO) has been described for many environments. Yet very few autotrophic microorganisms catalysing NRFO have been cultivated and their diversity, as well as their mechanisms for NRFO <i>in situ</i> remain unclear. A novel autotrophic NRFO enrichment culture, named culture BP, was obtained from freshwater sediment. After more than 20 transfers, culture BP oxidized 8.22 mM of Fe(II) and reduced 2.42 mM of nitrate within 6.5 days under autotrophic conditions. We applied metagenomic, metatranscriptomic, and metaproteomic analyses to culture BP to identify the microorganisms involved in autotrophic NRFO and to unravel their metabolism. Overall, twelve metagenome-assembled genomes (MAGs) were constructed, including a dominant <i>Gallionellaceae</i> sp. MAG (≥71% relative abundance). Genes and transcripts associated with potential Fe(II) oxidizers in culture BP, identified as a <i>Gallionellaceae</i> sp., <i>Noviherbaspirillum</i> sp., and <i>Thiobacillus</i> sp., were likely involved in metal oxidation (e.g., <i>cyc2</i>, <i>mtoA</i>), denitrification (e.g., <i>nirK</i>/<i>S</i>, <i>norBC</i>), carbon fixation (e.g., <i>rbcL</i>), and oxidative phosphorylation. The putative Fe(II)-oxidizing protein Cyc2 was detected for the <i>Gallionellaceae</i> sp. Overall, a complex network of microbial interactions among several Fe(II) oxidizers and denitrifiers was deciphered in culture BP that might resemble NRFO mechanisms <i>in situ</i>. Furthermore, 16S rRNA gene amplicon sequencing from environmental samples revealed 36 distinct <i>Gallionellaceae</i> taxa, including the key player of NRFO from culture BP (approx. 0.13% relative abundance <i>in situ</i>). Since several of these <i>in situ</i>-detected <i>Gallionellaceae</i> taxa were closely related to the key player in culture BP, this suggests that the diversity of organisms contributing to NRFO might be higher than currently known.
DOI: 10.6084/m9.figshare.14727903
title: NMR analysis of autophagy-related protein, Atg8 in the lipidated form.

description: NMR spectra for free Atg8, lipidated Atg8 and delipidated Atg8 described in the article.
DOI: 10.6084/m9.figshare.14727903.v1
title: NMR analysis of autophagy-related protein, Atg8 in the lipidated form.

description: NMR spectra for free Atg8, lipidated Atg8 and delipidated Atg8 described in the article.
DOI: 10.5281/zenodo.4749149
title: Dataset related to article "Volume-of-Interest Aware Deep Neural Networks for Rapid Chest CT-Based COVID-19 Patient Risk Assessment"

description: This record contains raw data related to article “Volume-of-Interest Aware Deep Neural Networks for Rapid Chest CT-Based COVID-19 Patient Risk Assessment" Since December 2019, the world has been devastated by the Coronavirus Disease 2019 (COVID-19) pandemic. Emergency Departments have been experiencing situations of urgency where clinical experts, without long experience and mature means in the fight against COVID-19, have to rapidly decide the most proper patient treatment. In this context, we introduce an artificially intelligent tool for effective and efficient Computed Tomography (CT)-based risk assessment to improve treatment and patient care. In this paper, we introduce a data-driven approach built on top of volume-of-interest aware deep neural networks for automatic COVID-19 patient risk assessment (discharged, hospitalized, intensive care unit) based on lung infection quantization through segmentation and, subsequently, CT classification. We tackle the high and varying dimensionality of the CT input by detecting and analyzing only a sub-volume of the CT, the Volume-of-Interest (VoI). Differently from recent strategies that consider infected CT slices without requiring any spatial coherency between them, or use the whole lung volume by applying abrupt and lossy volume down-sampling, we assess only the "most infected volume" composed of slices at its original spatial resolution. To achieve the above, we create, present and publish a new labeled and annotated CT dataset with 626 CT samples from COVID-19 patients. The comparison against such strategies proves the effectiveness of our VoI-based approach. We achieve remarkable performance on patient risk assessment evaluated on balanced data by reaching 88.88%, 89.77%, 94.73% and 88.88% accuracy, sensitivity, specificity and F1-score, respectively.
DOI: 10.5281/zenodo.5056541
title: DFTB study of silica glass under pressure (figures/samples trajectories)

description: This deposit contains: 1) Configurations (XYZ format) for selected densities/pressures (~100 configurations) extracted from the corresponding DFTB trajectories. (see configs-2-deposit.zip). The file readme-configs-2-deposit.txt gives details on configuration file and corresponding box size, pressure and density. 2) xmgrace source files of the manuscript's figures (file figures.zip). Each .agr file contains the XY data of the plotted quantities.
DOI: 10.5281/zenodo.5006799
title: DFTB study of silica glass under pressure (figures/samples trajectories)

description: This deposit contains: 1) Configurations (XYZ format) for selected densities/pressures (~100 configurations) extracted from the corresponding DFTB trajectories. (see configs-2-deposit.zip). The file readme-configs-2-deposit.txt gives details on configuration file and corresponding box size, pressure and density. 2) xmgrace source files of the manuscript's figures (file figures.zip). Each .agr file contains the XY data of the plotted quantities.
DOI: 10.5281/zenodo.5059711
title: Student activity data

description: This dataset includes anonymized records of student activities in a peer review activity performed through Synergy platform. This data comes from an educational technology course delivered in an European university. There were 30 participants from different departments (Computer science, Math, Physics, Preschool and Elementary Education) In this course, the main course assignment was a learning design project in which students worked in groups. The activity lasted 3 weeks and for each project 2-3 reviewers were assigned.
DOI: 10.5281/zenodo.4331704
title: Student activity data

description: This dataset includes anonymized records of student activities in a peer review activity performed through Synergy platform. This data comes from an educational technology course delivered in an European university. There were 30 participants from different departments (Computer science, Math, Physics, Preschool and Elementary Education) In this course, the main course assignment was a learning design project in which students worked in groups. The activity lasted 3 weeks and for each project 2-3 reviewers were assigned.
DOI: 10.5281/zenodo.5036677
title: Primary-level worker interventions for the care of mental disorders and distress in low- and middle-income countries - GRADE evidence profiles

description: This file includes all GRADE evidence profiles for the following Cochrane review: van Ginneken N, Chin WY, Lim YC, Ussif A, Singh R, Shahmalak U, Purgato M, Rojas-García A, Uphoff E, McMullen S, Foss HS, Thapa Pachya A, Rashidian L, Borghesani A, Henschke N, Chong L-Y, Lewin S. Primary-level worker interventions for the care of mental disorders and distress in low- and middle-income countries. Cochrane Database of Systematic Reviews. In press
DOI: 10.5281/zenodo.5031581
title: Primary-level worker interventions for the care of mental disorders and distress in low- and middle-income countries - GRADE evidence profiles

description: This file includes all GRADE evidence profiles for the following Cochrane review: van Ginneken N, Chin WY, Lim YC, Ussif A, Singh R, Shahmalak U, Purgato M, Rojas-García A, Uphoff E, McMullen S, Foss HS, Thapa Pachya A, Rashidian L, Borghesani A, Henschke N, Chong L-Y, Lewin S. Primary-level worker interventions for the care of mental disorders and distress in low- and middle-income countries. Cochrane Database of Systematic Reviews. In press
DOI: 10.5281/zenodo.5059735
title: Sample data for celltalker

description: Sample data for the tutorial of celltalker, downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139324
DOI: 10.5281/zenodo.5059734
title: Sample data for celltalker

description: Sample data for the tutorial of celltalker, downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139324
DOI: 10.6084/m9.figshare.14788857
title: Genome assemblies of 109 Mycobacterium avium subsp. hominissuis Osaka clinical strains

description: Genome assembly data used in "Genome-wide association study reveals putative bacterial risk factors for cavitary Mycobacterium avium complex lung disease" by Hirokazu Yano, Yukiko Nishiuchi, Kentaro Arikawa, Atsushi Ota, Mari Miki, Fumito Maruyama, Hiroshi Kida, Seigo Kitada, Tomotada Iwamoto
DOI: 10.15151/esrf-es-449124298
title: Hard X-ray Fluorescence mapping to decipher the deactivation processes of immobilised metallo-enzyme systems

description: Immobilisation of enzymatic cascades in porous materials is ideal to perform multi-enzymatic biotransformations in industrial settings. Yet, they suffer from exhaustion processes that hampers their use for long operational periods. The exact mechanism of inactivation is unknown until now, but spatial re-organisation of enzymes across the material or loss of metal ions from their active centers seems to be relevant. Unfortunately, optical microscopy is not ideal to study those events, as labelling enzymes with fluorescent tags can alter their catalytic properties. We intend to acquire X-Ray Fluorescence maps at ID16A on methacrylate beads carrying a cascade formed by Zn and Cu-dependent enzymes used to transform diols to relevant lactones, both before and after their operational run. This will provide valuable information on the importance of enzymatic re-organisation and metal leaching for the deactivation of immobilised multi-enzyme systems upon operation in chemical manufacturing.
DOI: 10.15151/esrf-es-449129200
title: Study of intracellular magnetosome degradation in 3D models of human lung carcinoma cells

description: Magnetosomes are magnetite (Fe3O4) nanoparticles synthesized by magnetotactic bacteria. Due to their stunning properties, they are recently been studied for several biomedical applications. However, little has been reported about the fate that these nanoparticles follow once they have performed their function in the human body and this aspect is essential if they are to be used for clinical applications. In this experiment, we aim to study the long-term intracellular degradation process that magnetosomes undergo in 3D models (spheroids) of human lung carcinoma cells (A549) by tracking the structural and electronic changes that Fe atoms undergo by means of Fe K-edge XANES spectroscopy. In parallel, the degradation of iron oxide commercial nanoparticles designed for biomedical applications will be studied to compare with that of magnetosomes.
DOI: 10.15151/esrf-es-470682597
title: Dinosaur eggs, embryos, and juveniles from the Upper Triassic and Lower Jurassic

description: Fossils with direct evidence on dinosaur reproduction behaviour and early ontogeny (development of embryos and hatchlings) are very rare, particularly those from deposits predating the Late Jurassic. We aim to reconstruct previously undescribed dinosaur embryos and juveniles from the Late Triassic-Early Jurassic of Poland and Sweden. The fossils to be scanned comprise: (1) eggshell fragments and infilled eggs from the newly discovered and oldest (latest Rhaetian) theropod nesting site (Skåne, Sweden), (2) eggs with probable theropod dinosaur embryos from an early Hettangian site (Holy Cross Mts., Poland), and (3) bones of a ?juvenile, basal theropod preserved in carbonate concretions from a mid-late Carnian site (Holy Cross Mts., Poland). By studying these specimens, we aim to cast new light on the ontogeny of some of the earliest large-sized theropod dinosaurs. Retrieving this information, however, will require the use of a powerful imaging technique.
DOI: 10.15151/esrf-es-470705446
title: Low-temperature crystal structure of the GaV4Se8 lacunar spinel
DOI: 10.5281/zenodo.5059693
title: Using GECKO-A to derive mechanistic understanding of SOA formation from the ubiquitous but understudied camphene

description: This data repository contains the simulation outputs of GECKO-A model used in the manuscript: <br> "Using GECKO-A to derive mechanistic understanding of secondary organic aerosol formation from the ubiquitous but understudied camphene"<br> by Afreh et al., 2021 in ACP The original ACP article should be properly cited when these data are used in a publication.
DOI: 10.5281/zenodo.5059692
title: Using GECKO-A to derive mechanistic understanding of SOA formation from the ubiquitous but understudied camphene

description: This data repository contains the simulation outputs of GECKO-A model used in the manuscript: <br> "Using GECKO-A to derive mechanistic understanding of secondary organic aerosol formation from the ubiquitous but understudied camphene"<br> by Afreh et al., 2021 in ACP The original ACP article should be properly cited when these data are used in a publication.
DOI: 10.6084/m9.figshare.14898419.v1
title: Datasets from Late holocene spread of pastoralism coincides with endemic megafaunal extinction on Madagascar

description: include all new and reviewed data
DOI: 10.5281/zenodo.5055284
title: In vitro protein and starch digestion kinetics of individual chickpea cells: from static to more complex in vitro digestion approaches

description: Attention has been given to more (semi-)dynamic <em>in vitro</em> digestion approaches ascertaining the consequences of dynamic <em>in vivo </em>aspects on <em>in vitro </em>digestion kinetics. As these often come with time and economical constraints, evaluating the consequence of stepwise increasing the complexity of static <em>in vitro </em>approaches using easy-to-handle digestion set-ups has been the center of our interest. Starting from the INFOGEST static <em>in vitro </em>protocol, we studied the influence of static gastric pH <em>versus </em>gradual gastric pH change (pH 6.3 to pH 2.5 in 2 h) on macronutrient digestion in individual cotyledon cells derived from chickpeas. Little effect on small intestinal proteolysis was observed comparing the applied digestion conditions. Contrary, the implementation of a gradual gastric pH change, with and without the addition of salivary α-amylase, altered starch digestion kinetics rates, and extents by 25%. The evaluation of starch and protein digestion, being co-embedded in cotyledon cells, did not only confirm but accounted for the interdependent digestion behavior. The insights generated in this study demonstrate the possibility of using a hypothesis-based approach to introduce dynamic factors to <em>in vitro</em> models while sticking to simple and cost-efficient set-ups. The data used for the graphs in the paper: K. Pälchen, D. Michels, D. Duijsens, S. T. Gwala, A. K. Pallares Pallares, M. Hendrickx, A. Van Loey and T. Grauwet, Food Funct., 2021, DOI: 10.1039/D1FO01123E