cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25550/1-tqec
title: Manual: differential network analysis of gene expression data

description: This manual provides detailed steps on how to conduct a differential network analysis using the _dnapath_ R package. The manual walks through an application, where we download BAM files from FaceBase, pre-process the counts using TPM normalization and a log transformation, perform the differential network analysis, then summarize and visualize the results. The interpretation of the results is discussed at length, and one approach for validating initial results is shown.
DOI: 10.25550/1-s7gj
title: Runx2 regulates mouse tooth root development via activation of 1 WNT inhibitor Notum

description: Progenitor cells are crucial in controlling organ morphogenesis. Tooth development is a well established model for investigating the molecular and cellular mechanisms that regulate organogenesis. Despite advances in our understanding of how tooth crown formation is regulated, we have limited understanding of tooth root development. RUNX2 is a well-known transcription factor in osteogenic differentiation and early tooth development. However, the function of RUNX2 during tooth root formation remains unknown. We revealed in this study that RUNX2 is expressed in a subpopulation of GLI1+ root progenitor cells, and that loss of Runx2 in these GLI1+ progenitor cells and their progeny results in root developmental defects. Our results provide in vivo evidence that Runx2 plays a crucial role in tooth root development and in regulating the differentiation of root progenitor cells. Furthermore, we identified that Gli1, Pcp4, Notum, and Sfrp2 are downstream targets of Runx2 by integrating bulk and single-cell RNA sequencing analyses. Specifically, ablation of Runx2 results in downregulation of WNT inhibitor Notum and upregulation of canonical WNT signaling in the odontoblastic site, which disturbs normal odontoblastic differentiation. Significantly, exogenous NOTUM partially rescues the impaired root development in Runx2 mutant molars. Collectively, our studies elucidate how Runx2 achieves functional specificity in regulating the development of diverse organs and yields new insights into the network that regulates tooth root development.
DOI: 10.25550/1-tqft
title: Bioreactor study 1

description: Cells and scaffolds cultured in a bioreactor
DOI: 10.25550/1-dy3g
title: Tooth root development in Osr2-Cre;Ezh2fl/fl and control mice

description: Patterning is a critical step during organogenesis and is closely associated with the physiological function of organs. Tooth root shapes are finely tuned to provide precise occlusal support to facilitate the function of each tooth type. However, the mechanism regulating tooth root patterning and development is largely unknown. In this study, we provide the first in vivo evidence demonstrating that Ezh2 in the dental mesenchyme determines patterning and furcation formation during dental root development in mouse molars. Mechanistically, an antagonistic interaction between epigenetic regulators Ezh2 and Arid1a controls Cdkn2a expression in the dental mesenchyme to regulate dental root patterning and development. These findings indicate the importance of balanced epigenetic regulation in determining the tooth root pattern and the integration of roots with the jaw bones to achieve physiological function. Collectively, our study provides important clues about the regulation of organogenesis and has general implications for tooth regeneration in the future.
DOI: 10.25550/1-dtk2
title: Single Cell RNA-Sequencing of wild-type mouse mandible at E10.5, E12.5, and E14.5

description: Neural crest cells contribute to a diverse array of cell types during embryonic development. Dysregulation of neural crest cells leads to congenital malformations and diseases. It is unknown whether post-migratory cranial neural crest (CNC) cells undergo dynamic cellular movement and how the process of cell fate decision occurs within the first pharyngeal arch. Using single-cell RNA sequencing and RNAscope analyses, we uncovered striking heterogeneity within the CNC cell population and re-defined the patterning domains within the first pharyngeal arch.
DOI: 10.5281/zenodo.3980347
title: External and Internal Workload Demands in Youth Basketball Players

description: External and Internal Workload Demands in Youth Basketball Players
DOI: 10.5281/zenodo.3980315
title: External and Internal Workload Demands in Youth Basketball Players

description: External and Internal Workload Demands in Youth Basketball Players
DOI: 10.25550/1-x280
title: Runx2-Twist1 interaction coordinates cranial neural crest guidance of soft palate myogenesis

description: Cranial neural crest (CNC) cells give rise to bone, cartilage, tendons, and ligaments of the vertebrate craniofacial musculoskeletal complex, as well as regulate mesoderm-derived craniofacial muscle development through cell-cell interaction. Using the mouse soft palate as a model, we performed an unbiased single-cell RNA-seq analysis to investigate the heterogeneity and lineage commitment of CNC derivatives during craniofacial muscle development. We show that Runx2, a known osteogenic regulator, is expressed in the CNC-derived perimysial and progenitor populations. Loss of Runx2 in CNC-derivatives results in reduced expression of perimysial markers (Aldh1a2 and Hic1) as well as soft palate muscle defects in Osr2-KICre;Runx2fl/fl mice. We further reveal that Runx2 maintains perimysial marker expression through suppressing Twist1, and that myogenesis is restored in Osr2-KICre;Runx2fl/fl;Twist1fl/+ mice. Collectively, our findings highlight the roles of Runx2, Twist1, and their interaction in regulating the fate of CNC-derived cells as they guide craniofacial muscle development through cell-cell interactions.
DOI: 10.5281/zenodo.3980387
title: Regional tomography beneath Greenland and surrounding regions

description: Dear readers, These two files contain P-wave velocity model beneath Greenland and surrounding regions obtained by regional tomography (Toyokuni, Matsuno, & Zhao, 2020, JGR). model_equat: Model in the geographical coordinates (equatorial coordinates)<br> model_eclip: Model in the transformed coordinates (ecliptic coordinates) We note that the tomography was conducted in the transformed coordinates, and the results were brought back to the geographical coordinates using inverse coordinate transformation. The details of the coordinate transformation are described in Appendix A of the above paper. The format of these files is as follows:<br> Depth (km), Latitude(deg), Longitude(deg), Vp(km/s), dVp(%), Hit count We hope it is useful to you. Kind wishes, Genti Toyokuni & Dapeng Zhao<br> Tohoku University, Japan<br> E-mail: toyokuni@tohoku.ac.jp Reference:<br> Toyokuni, G., Matsuno, T., & Zhao, D. (2020).<br> P-wave tomography beneath Greenland and surrounding regions-I. Crust and upper mantle.<br> Journal of Geophysical Research: Solid Earth, under review.<br>
DOI: 10.5281/zenodo.3980386
title: Regional tomography beneath Greenland and surrounding regions

description: Dear readers, These two files contain P-wave velocity model beneath Greenland and surrounding regions obtained by regional tomography (Toyokuni, Matsuno, & Zhao, 2020, JGR). model_equat: Model in the geographical coordinates (equatorial coordinates)<br> model_eclip: Model in the transformed coordinates (ecliptic coordinates) We note that the tomography was conducted in the transformed coordinates, and the results were brought back to the geographical coordinates using inverse coordinate transformation. The details of the coordinate transformation are described in Appendix A of the above paper. The format of these files is as follows:<br> Depth (km), Latitude(deg), Longitude(deg), Vp(km/s), dVp(%), Hit count We hope it is useful to you. Kind wishes, Genti Toyokuni & Dapeng Zhao<br> Tohoku University, Japan<br> E-mail: toyokuni@tohoku.ac.jp Reference:<br> Toyokuni, G., Matsuno, T., & Zhao, D. (2020).<br> P-wave tomography beneath Greenland and surrounding regions-I. Crust and upper mantle.<br> Journal of Geophysical Research: Solid Earth, under review.<br>
DOI: 10.5281/zenodo.3763233
title: Maxims nudge equitable or efficient choices in a Trade-Off Game

description: The core problem in the distribution dilemma is how to trade-off between equity and efficiency. With the development of socio-economic conditions, the optimal decision will also change between equitable and efficient options. How to nudge decision-makers to make optimal allocation decisions without changing the event itself is extremely important. This study used a mixed design of 3 (division schemes: 12:15:23, 15:23:12, 23:12:15) x 2 (maxim: equity, efficiency) x 2 (stakes: low, medium, high), which explores the impact of additional maximal information on the trade-off between equity and efficiency, and explores whether the stakes and division scheme will affect the nudging effect of the maxim in a Trade-Off Game (TOG). We found that participants were affected by maxim information in decision-making scenarios, and participants showed different equal preference as the maxim information changed, no matter the stakes is small, medium or high. We also found that the nudging effect of the maxim only exists under the condition that the distributor's own interests are not affected.
DOI: 10.5281/zenodo.3763232
title: Maxims nudge equitable or efficient choices in a Trade-Off Game

description: The core problem in the distribution dilemma is how to trade-off between equity and efficiency. With the development of socio-economic conditions, the optimal decision will also change between equitable and efficient options. How to nudge decision-makers to make optimal allocation decisions without changing the event itself is extremely important. This study used a mixed design of 3 (division schemes: 12:15:23, 15:23:12, 23:12:15) x 2 (maxim: equity, efficiency) x 2 (stakes: low, medium, high), which explores the impact of additional maximal information on the trade-off between equity and efficiency, and explores whether the stakes and division scheme will affect the nudging effect of the maxim in a Trade-Off Game (TOG). We found that participants were affected by maxim information in decision-making scenarios, and participants showed different equal preference as the maxim information changed, no matter the stakes is small, medium or high. We also found that the nudging effect of the maxim only exists under the condition that the distributor's own interests are not affected.
DOI: 10.5281/zenodo.3974135
title: Human and mouse ALS histopathological tissue sections co-stained for FUS, SFPQ, CHAT and DAPI

description: Multichannel microscopy data from histopathological sections of 1/ SOD1- and VCP-mutant mouse models together with control co-stained for SFPQ, FUS, CHAT and DAPI The moues folder contains 2/ Healthy and sporadic ALS patients either co-stained for SFPQ or FUS together with CHAT and DAPI These two series of multichannel fluorescent microscopy data have been used in several manuscripts including: <strong>Luisier R, Tyzack GE, Hall CE, Mitchell JS, Devine H, Taha DM, et al. Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS. Nat Commun 2018; 9: 2010.</strong> <strong>Tyzack GE, Luisier R, Taha DM, Neeves J, Modic M, Mitchell JS, et al. Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis. Brain 2019; 142: 2572–80.</strong>
DOI: 10.5281/zenodo.3979750
title: PDB ID 6QVS raw images

description: Raw images of the PDB ID 6QVS (unliganded structure of the human wild type Beta-galactoside alpha-2,6-sialyltransferase 1 (ST6Gal1)).
DOI: 10.5281/zenodo.3979749
title: PDB ID 6QVS raw images

description: Raw images of the PDB ID 6QVS (unliganded structure of the human wild type Beta-galactoside alpha-2,6-sialyltransferase 1 (ST6Gal1)).
DOI: 10.5281/zenodo.3904304
title: Strong Scaling Tools 1 Al-Zn-Mg-Cu case study

description: All data, results, and scripts from Al-Zn-Mg-Cu high-throughput case study. <strong>*.zip</strong> are the specimen-specific PARAPROBE results and POS rawdata. <strong>*.pdf</strong> are the PDF reports that were created with the automation of paraprobe-autoreporter. <strong>src.zip</strong> contains the source code of the paraprobe-autoreporter Python classes with which the results were computed. This source code is meant as a documentation of the results only!<br> <strong>Instead, all users should always use the latest versions of the PARAPROBE tools from the GitLab repository https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe</strong><br> <strong>https://paraprobe-toolbox.readthedocs.org</strong>
DOI: 10.5281/zenodo.3904303
title: Strong Scaling Tools 1 Al-Zn-Mg-Cu case study

description: All data, results, and scripts from Al-Zn-Mg-Cu high-throughput case study. <strong>*.zip</strong> are the specimen-specific PARAPROBE results and POS rawdata. <strong>*.pdf</strong> are the PDF reports that were created with the automation of paraprobe-autoreporter. <strong>src.zip</strong> contains the source code of the paraprobe-autoreporter Python classes with which the results were computed. This source code is meant as a documentation of the results only!<br> <strong>Instead, all users should always use the latest versions of the PARAPROBE tools from the GitLab repository https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe</strong><br> <strong>https://paraprobe-toolbox.readthedocs.org</strong>
DOI: 10.5281/zenodo.3906906
title: Strong Scaling Tools 2 Additive manufacturing case study

description: All data, results, and scripts from the Al-Si-Sc additive manufacturing alloy design high-throughput case study. All data, results, and scripts from Al-Zn-Mg-Cu high-throughput case study. <strong>*.zip</strong> are the specimen-specific PARAPROBE results and POS rawdata. <strong>*.pdf</strong> are the PDF reports that were created with the automation of paraprobe-autoreporter. <strong>src.zip</strong> contains the source code of the paraprobe-autoreporter Python classes with which the results were computed. This source code is meant as a documentation of the results only!<br> <strong>Instead, all users should always use the latest versions of the PARAPROBE tools from the GitLab repository https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox</strong>/<strong>paraprobe</strong><br> <strong>https://paraprobe-toolbox.readthedocs.org</strong>
DOI: 10.5281/zenodo.3906905
title: Strong Scaling Tools 2 Additive manufacturing case study

description: All data, results, and scripts from the Al-Si-Sc additive manufacturing alloy design high-throughput case study. All data, results, and scripts from Al-Zn-Mg-Cu high-throughput case study. <strong>*.zip</strong> are the specimen-specific PARAPROBE results and POS rawdata. <strong>*.pdf</strong> are the PDF reports that were created with the automation of paraprobe-autoreporter. <strong>src.zip</strong> contains the source code of the paraprobe-autoreporter Python classes with which the results were computed. This source code is meant as a documentation of the results only!<br> <strong>Instead, all users should always use the latest versions of the PARAPROBE tools from the GitLab repository https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox</strong>/<strong>paraprobe</strong><br> <strong>https://paraprobe-toolbox.readthedocs.org</strong>
DOI: 10.5281/zenodo.3980539
title: dsmlr/40-Thai-Children-Stories

description: The dataset was collected from 40 Thai children stories. We manually split the text into sentences which leads to 1,964 sentences. Each sentence was manually tagged by experts into three classes which are positive, negative, and neutral according to the reader’s expressed emotion. The majority class given by the experts is neutral in this dataset. Sentences that were described by the same class chosen by all three experts are skimmed down to 1,114 sentences which comprise 298 negative sentences, 508 neutral sentences and 308 positive sentences. Descriptions: <strong>tale_name.csv</strong> id_sentence -- Sentence ID text -- Sentence id_tale -- Tale ID that corresponds to tale_data.csv Y_1 -- Label given by expert 1 Y_2 -- Label given by expert 2 Y_3 -- Label given by expert 3 Y_vote -- Voted Label consensus -- All experts gave the same label <strong>tale_data.csv</strong> id_tale -- Tale ID name_tale -- Tale name If you are interested in further investigating your own study throughout this dataset, please cite this article: Kitsuchart Pasupa, Ponruedee Netisopakul, Ratthawut Lertsuksakda, "Sentiment Analysis on Thai Children Stories", In Artificial Life and Robotics, vol. 21, no. 3, pp. 357-364, 2016. DOI: 10.1007/s10015-016-0283-8 We further compared a set of well-known deep learning techniques on this dataset. This can be found at: Kitsuchart Pasupa, Thititorn Seneewong Na Ayutthaya, "Thai Sentiment Analysis with Deep Learning Techniques: A Comparative Study based on Word Embedding, POS-Tag, and Sentic Features", Sustainable Cities and Society, vol. 50, pp. 101615, 2019. DOI: 10.1016/j.scs.2019.101615
DOI: 10.5281/zenodo.3980538
title: dsmlr/40-Thai-Children-Stories

description: The dataset was collected from 40 Thai children stories. We manually split the text into sentences which leads to 1,964 sentences. Each sentence was manually tagged by experts into three classes which are positive, negative, and neutral according to the reader’s expressed emotion. The majority class given by the experts is neutral in this dataset. Sentences that were described by the same class chosen by all three experts are skimmed down to 1,114 sentences which comprise 298 negative sentences, 508 neutral sentences and 308 positive sentences. Descriptions: <strong>tale_name.csv</strong> id_sentence -- Sentence ID text -- Sentence id_tale -- Tale ID that corresponds to tale_data.csv Y_1 -- Label given by expert 1 Y_2 -- Label given by expert 2 Y_3 -- Label given by expert 3 Y_vote -- Voted Label consensus -- All experts gave the same label <strong>tale_data.csv</strong> id_tale -- Tale ID name_tale -- Tale name If you are interested in further investigating your own study throughout this dataset, please cite this article: Kitsuchart Pasupa, Ponruedee Netisopakul, Ratthawut Lertsuksakda, "Sentiment Analysis on Thai Children Stories", In Artificial Life and Robotics, vol. 21, no. 3, pp. 357-364, 2016. DOI: 10.1007/s10015-016-0283-8 We further compared a set of well-known deep learning techniques on this dataset. This can be found at: Kitsuchart Pasupa, Thititorn Seneewong Na Ayutthaya, "Thai Sentiment Analysis with Deep Learning Techniques: A Comparative Study based on Word Embedding, POS-Tag, and Sentic Features", Sustainable Cities and Society, vol. 50, pp. 101615, 2019. DOI: 10.1016/j.scs.2019.101615
DOI: 10.5281/zenodo.3706423
title: Plasmid Design for Tunable Two‐Enzyme Co‐Expression Promotes Whole‐Cell Production of Cellobiose

description: We provide underlying data for the publication "Plasmid design for tunable two-enzyme co-expression promotes whole-cell production of cellobiose". Please find the abstract below. Catalyst development for biochemical cascade reactions often follows a “whole cell approach” in which a single microbial cell is made to express all of the required enzyme activities. Although attractive in principle, the approach can encounter limitations when efficient overall flux from substrate to product necessitates precise balancing between the individual activities. Here, we show effective integration of major design strategies from synthetic biology to a coherent development of plasmid vectors enabling tunable two‐enzyme co‐expression in <em>E. coli </em>, for the purpose of whole‐cell production of cellobiose. Flux efficiency in the transformation of sucrose and glucose into cellobiose by a parallel (countercurrent) cascade of disaccharide phosphorylases requires the enzyme co‐expression cope with large differences in the specific activity of cellobiose phosphorylase (14 U mg<sup>−1</sup>) and sucrose phosphorylase (122 U mg<sup>−1</sup>). Comparing mono‐ and bicistronic co‐expression strategies, we analyze genetic elements controlling transcription, transcription‐translation coupling or plasmid replication for effect on activity, and also stable producibility, of the whole cell catalyst. We discover a key role of the <em>bom </em>(basis of mobility) site for plasmid stability dependent on the origin of replication and demonstrate the importance of RBS (ribosome binding site) strength for balanced bicistronic co‐expression. Whole cell catalysts show high specific rates (460 μmol cellobiose min<sup>−1</sup> g<sup>−1</sup> dry cells) and performance metrics (30 g L<sup>−1</sup>; ∼82% yield; 3.8 g L<sup>−1</sup> h<sup>−1</sup> overall productivity) promising for cellobiose production.
DOI: 10.5281/zenodo.3706422
title: Plasmid Design for Tunable Two‐Enzyme Co‐Expression Promotes Whole‐Cell Production of Cellobiose

description: We provide underlying data for the publication "Plasmid design for tunable two-enzyme co-expression promotes whole-cell production of cellobiose". Please find the abstract below. Catalyst development for biochemical cascade reactions often follows a “whole cell approach” in which a single microbial cell is made to express all of the required enzyme activities. Although attractive in principle, the approach can encounter limitations when efficient overall flux from substrate to product necessitates precise balancing between the individual activities. Here, we show effective integration of major design strategies from synthetic biology to a coherent development of plasmid vectors enabling tunable two‐enzyme co‐expression in <em>E. coli </em>, for the purpose of whole‐cell production of cellobiose. Flux efficiency in the transformation of sucrose and glucose into cellobiose by a parallel (countercurrent) cascade of disaccharide phosphorylases requires the enzyme co‐expression cope with large differences in the specific activity of cellobiose phosphorylase (14 U mg<sup>−1</sup>) and sucrose phosphorylase (122 U mg<sup>−1</sup>). Comparing mono‐ and bicistronic co‐expression strategies, we analyze genetic elements controlling transcription, transcription‐translation coupling or plasmid replication for effect on activity, and also stable producibility, of the whole cell catalyst. We discover a key role of the <em>bom </em>(basis of mobility) site for plasmid stability dependent on the origin of replication and demonstrate the importance of RBS (ribosome binding site) strength for balanced bicistronic co‐expression. Whole cell catalysts show high specific rates (460 μmol cellobiose min<sup>−1</sup> g<sup>−1</sup> dry cells) and performance metrics (30 g L<sup>−1</sup>; ∼82% yield; 3.8 g L<sup>−1</sup> h<sup>−1</sup> overall productivity) promising for cellobiose production.
DOI: 10.5281/zenodo.3980545
title: Pictogramas ARASAAC Color, Part 1 of 16

description: Black and white pictograms created by Sergio Palao (http://www.palao.es) for ARASAAC (http://www.arasac.org).
DOI: 10.5281/zenodo.3980544
title: Pictogramas ARASAAC Color, Part 1 of 16

description: Black and white pictograms created by Sergio Palao (http://www.palao.es) for ARASAAC (http://www.arasac.org).
DOI: 10.5281/zenodo.3980599
title: Austrian Science Fund (FWF) funding statistics 2009-2019

description: Compilation of funding statistics from FWF's annual reports as longitudinal data from 2009-2019
DOI: 10.5281/zenodo.3980598
title: Austrian Science Fund (FWF) funding statistics 2009-2019

description: Compilation of funding statistics from FWF's annual reports as longitudinal data from 2009-2019