cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24711120.v1
title: Datsets for manuscript <b>Antagonistic interactions safeguard mitotic propagation of genetic and epigenetic information</b>Divine-Fondzenyuy Lawir<sup>1</sup>, Cristian Soza-Ried<sup>1</sup>, Norimasa Iwanami<sup>1</sup>, Iliana Siamishi<sup>1</sup>, Göran O. Bylund<sup>4</sup>, Connor O´Meara<sup>1</sup>, Katarzyna Sikora<sup>1,2</sup>, Benoît Kanzler<sup>3</sup>, Erik Johansson<sup>4</sup>, Michael Schorpp<sup>1</sup>, Pierre Cauchy<sup>1</sup> & Thomas Boehm<sup>1,5</sup>

description: <br><b>Abstract</b>The stability of cellular phenotypes in developing organisms depends on error-free transmission of epigenetic and genetic information during mitosis. Methylation of cytosine residues in genomic DNA is a key epigenetic mark that modulates gene expression and prevents genome instability. Here, we report on a genetic test of the relationship between DNA replication and methylation in the context of the developing vertebrate organism instead of cell lines. Our analysis is based on the identification of hypomorphic alleles of <i>dnmt1</i>, encoding the DNA maintenance methylase Dnmt1, and <i>pole1</i>, encoding the catalytic subunit of leading-strand DNA polymerase epsilon holoenzyme (Pole). Homozygous <i>dnmt1</i> mutants exhibit genome-wide DNA hypomethylation, whereas the <i>pole1</i> mutation is associated with increased DNA methylation levels. In <i>dnmt1</i>/<i>pole1</i> double-mutant zebrafish larvae, DNA methylation levels are restored to near normal values, associated with partial rescue of mutant-associated transcriptional changes and phenotypes. Hence, a balancing antagonism between DNA replication and maintenance methylation buffers against replicative errors contributing to the robustness of vertebrate development.<br>
DOI: 10.6084/m9.figshare.24711162.v1
title: <b>Oleanolic acid </b><b>alleviate intestinal inflammation</b><b> by inhibiting </b><b>Takeda G-coupled protein receptor (TGR) 5 mediated Cell</b><b> </b><b>A</b><b>poptosis</b>

description: Oleanolic acid (OA) is a bioactive compound present in plant-based foods known for its benificial impact on gastrointestinal health, specifically in alleviating diarrhea. Nonetheless, the underlying mechanisms by which OA mitigates gut epithelial damage have yet to be elucidated. In this study, OA significantly markedly amerliorated adverse effects induced by Dextran Sulfate Sodium (DSS), including weight loss, splenic hypertrophy, reductions in the size and mass of the small intestine and colon, along with impaired diminished intestinal weight, epithelial morphological damage, and intestinal organoid formation (P&lt;0.05) in a murine model. Remarkably, compared to normal mice, standalone administration of OA had no discernible impact on the animals. Concurrently, we identified a significant up-regulation in the expression levels of TGR5, TNF-α, and BAX in the intestines of DSS-exposed mice, coupled with a decline in Bcl2 expression. Oral administration of OA efficaciously counteracted these alterations (P&lt;0.05).Correlation analyses revealed a robust association between TGR5 and BAX expression (R=0.60). Minimal changes were observed in bile acid composition and gut microbiota. To probe the role of TGR5 in cellular apoptosis, further, a lentivirus transfection approach was utilized to induce TGR5 overexpression in intestinal epithelial cells (IPEC-J2). RNA sequencing indicated that TGR5 overexpression significantly influenced biological processes, particularly in modulating cellular activation and intercellular adhesion, in contrast to the control group cells. Functional assays, namely CCK-8, EdU, and IP staining, substantiated that TGR5 overexpression compromised cell viability and accelerated apoptosis. Additionally, TGR5 overexpression led to a pronounced downregulation of PCNA, Claudin-1, and Bcl2. Notably, OA treatment in TGR5-overexpressed cells restored cell viability, suppressed TGR5 and BAX expression, and augmented Bcl2 expression. In sum, our data suggest that OA mitigates intestinal epithelial apoptosis and bolsters cellular proliferation by downregulating TGR5. This research provides valuable insights into the prospective utility of OA as a functional food supplement or adjunctive therapeutic agent for enhancing gastrointestinal health.
DOI: 10.6084/m9.figshare.24711162
title: <b>Oleanolic acid </b><b>alleviate intestinal inflammation</b><b> by inhibiting </b><b>Takeda G-coupled protein receptor (TGR) 5 mediated Cell</b><b> </b><b>A</b><b>poptosis</b>

description: Oleanolic acid (OA) is a bioactive compound present in plant-based foods known for its benificial impact on gastrointestinal health, specifically in alleviating diarrhea. Nonetheless, the underlying mechanisms by which OA mitigates gut epithelial damage have yet to be elucidated. In this study, OA significantly markedly amerliorated adverse effects induced by Dextran Sulfate Sodium (DSS), including weight loss, splenic hypertrophy, reductions in the size and mass of the small intestine and colon, along with impaired diminished intestinal weight, epithelial morphological damage, and intestinal organoid formation (P&lt;0.05) in a murine model. Remarkably, compared to normal mice, standalone administration of OA had no discernible impact on the animals. Concurrently, we identified a significant up-regulation in the expression levels of TGR5, TNF-α, and BAX in the intestines of DSS-exposed mice, coupled with a decline in Bcl2 expression. Oral administration of OA efficaciously counteracted these alterations (P&lt;0.05).Correlation analyses revealed a robust association between TGR5 and BAX expression (R=0.60). Minimal changes were observed in bile acid composition and gut microbiota. To probe the role of TGR5 in cellular apoptosis, further, a lentivirus transfection approach was utilized to induce TGR5 overexpression in intestinal epithelial cells (IPEC-J2). RNA sequencing indicated that TGR5 overexpression significantly influenced biological processes, particularly in modulating cellular activation and intercellular adhesion, in contrast to the control group cells. Functional assays, namely CCK-8, EdU, and IP staining, substantiated that TGR5 overexpression compromised cell viability and accelerated apoptosis. Additionally, TGR5 overexpression led to a pronounced downregulation of PCNA, Claudin-1, and Bcl2. Notably, OA treatment in TGR5-overexpressed cells restored cell viability, suppressed TGR5 and BAX expression, and augmented Bcl2 expression. In sum, our data suggest that OA mitigates intestinal epithelial apoptosis and bolsters cellular proliferation by downregulating TGR5. This research provides valuable insights into the prospective utility of OA as a functional food supplement or adjunctive therapeutic agent for enhancing gastrointestinal health.
DOI: 10.5281/zenodo.10007823
title: neo4jsbml dataset

description: neo4jsbml dataset with:

arrows: JSON, SVG files were created with https://arrows.app
gems: E. coli GEMs: 

iML1515, iAF1260, e_coli_core were downloaded from http://bigg.ucsd.edu
bigg_iML1515.sbml3, bigg_iAF1260.sbml3 were downloaded from https://www.metanetx.org
other XML files were extracted from the SBML specifications L3V2, L2V5, Qualitative Models L3V1R1, Layout L3V1, Groups L3V1R1, Flux Balance Constraints L3V2
DOI: 10.5281/zenodo.8059651
title: neo4jsbml dataset

description: neo4jsbml dataset with: - a database schema. JSON format to load data into Neo4j using neo4jsbml, created with https://arrows.app (PNG format for viewing purposes) - <em>E. coli</em> GEMs: iML1515, iAF1260, e_coli_core. Downloading from http://bigg.ucsd.edu/
DOI: 10.5281/zenodo.10245426
title: neo4jsbml dataset

description: neo4jsbml dataset with:

arrows: JSON, SVG files were created with https://arrows.app
gems: E. coli GEMs: 

iML1515, iAF1260, e_coli_core were downloaded from http://bigg.ucsd.edu
bigg_iML1515.sbml3, bigg_iAF1260.sbml3 were downloaded from https://www.metanetx.org
other XML files were extracted from the SBML specifications L3V2, L2V5, Qualitative Models L3V1R1, Layout L3V1, Groups L3V1R1, Flux Balance Constraints L3V2
DOI: 10.5281/zenodo.8059650
title: neo4jsbml dataset

description: neo4jsbml dataset with:

arrows: JSON, SVG files were created with https://arrows.app
gems: E. coli GEMs: 

iML1515, iAF1260, e_coli_core were downloaded from http://bigg.ucsd.edu
bigg_iML1515.sbml3, bigg_iAF1260.sbml3 were downloaded from https://www.metanetx.org
other XML files were extracted from the SBML specifications L3V2, L2V5, Qualitative Models L3V1R1, Layout L3V1, Groups L3V1R1, Flux Balance Constraints L3V2
DOI: 10.6084/m9.figshare.24711210
title: Dataset: Academics’ continuance intention to use learning technologies during COVID-19 and beyond

description: Data set for the article "Academics’ continuance intention to use learning technologies during COVID-19 and beyond".
DOI: 10.5281/zenodo.10231378
title: Zurich Natural Image Database

description: Zip-File containing a set of 128 natural images that have been used in various eye-tracking studies. Thumbnails.jpg provides an overview. Images were captured with a 3.3 Mega pixel colour mosaic CCD camera (Nikon Coolpix 995, Tokyo, Japan) in RGB and have a resolution (WxH) of 2048 x 1536 pixels.
You are free to use these images for scientific purposes, provided at least one of the following papers is appropriately cited:
Einhäuser, W., & König, P. (2003). Does luminance‐contrast contribute to a saliency map for overt visual attention?. European Journal of Neuroscience, 17(5), 1089-1097. https://doi.org/10.1046/j.1460-9568.2003.02508.x [used the first 8 images in grayscale]
Einhäuser, W., Kruse, W., Hoffmann, K. P., & König, P. (2006). Differences of monkey and human overt attention under natural conditions. Vision Research, 46(8-9), 1194-1209. https://doi.org/10.1016/j.visres.2005.08.032 [used the first 108 images in grayscale]
Frey, HP., König, P. & Einhäuser, W. The role of first- and second-order stimulus features for human overt attention. Perception & Psychophysics, 69, 153–161 (2007). https://doi.org/10.3758/BF03193738 [used the images in color]
DOI: 10.5281/zenodo.10231379
title: Zurich Natural Image Database

description: Zip-File containing a set of 128 natural images that have been used in various eye-tracking studies. Thumbnails.jpg provides an overview. Images were captured with a 3.3 Mega pixel colour mosaic CCD camera (Nikon Coolpix 995, Tokyo, Japan) in RGB and have a resolution (WxH) of 2048 x 1536 pixels.
You are free to use these images for scientific purposes, provided at least one of the following papers is appropriately cited:
Einhäuser, W., & König, P. (2003). Does luminance‐contrast contribute to a saliency map for overt visual attention?. European Journal of Neuroscience, 17(5), 1089-1097. https://doi.org/10.1046/j.1460-9568.2003.02508.x [used the first 8 images in grayscale]
Einhäuser, W., Kruse, W., Hoffmann, K. P., & König, P. (2006). Differences of monkey and human overt attention under natural conditions. Vision Research, 46(8-9), 1194-1209. https://doi.org/10.1016/j.visres.2005.08.032 [used the first 108 images in grayscale]
Frey, HP., König, P. & Einhäuser, W. The role of first- and second-order stimulus features for human overt attention. Perception & Psychophysics, 69, 153–161 (2007). https://doi.org/10.3758/BF03193738 [used the images in color]
DOI: 10.5281/zenodo.10245442
title: Bailie_et_al_2023_RSET_DATASET

description: This dataset contains the underlying data for the following publication: Bailie, A., Pied, M., Vaillancourt, K., Bahn, O., Koasidis, K., Gambhir, A., ... & Nikas, A. (2023). Co-creating Canada's path to net-zero: a stakeholder-driven modelling analysis. Renewable and Sustainable Energy Transition, 4, 100061., https://doi.org/10.1016/j.rset.2023.100061
DOI: 10.5281/zenodo.10245443
title: Bailie_et_al_2023_RSET_DATASET

description: This dataset contains the underlying data for the following publication: Bailie, A., Pied, M., Vaillancourt, K., Bahn, O., Koasidis, K., Gambhir, A., ... & Nikas, A. (2023). Co-creating Canada's path to net-zero: a stakeholder-driven modelling analysis. Renewable and Sustainable Energy Transition, 4, 100061., https://doi.org/10.1016/j.rset.2023.100061
DOI: 10.6084/m9.figshare.24711213
title: Untitled project

description: Albinism is a unique problem encountered in tissue culture experiments, but the underlying mechanism remains unclear in most bamboo species. In this study, we identified the putative regulatory genes in an albino mutant of Bambusa oldhamii using comparative physiology and transcriptome analysis. The degeneration of chloroplasts, low chlorophyll (Chl) content and re-duced photosynthetic capacity were observed in albinotic B. oldhamii compared to normal lines. A total of 6191 unigenes were identified that were clearly differentially expressed between albino and normal lines by transcriptome sequencing. Most genes related to chloroplast development (such as Psa, Psb) and pigment biosynthesis (such as LHC, GUN4, ZEP) were downregulated significantly in albinotic lines, which might be responsible for the albino phenotype. Moreover, some transcription factors (TFs) such as PIF and GLK1 were identified to be involved in chloroplast development and Chl synthesis, indicating the involvement of putative regulatory pathways PIF-LHC and GLK1-LHC/Psa/Psb in albinotic B. oldhamii. Finally, the downregulation of some stress responsive TFs (like ICE1 and EREB1) suggested a reduction in stress resistance of albinotic B. oldhamii. The above findings provided new insights into the molecular mechanism of albinism in bamboo.
DOI: 10.5281/zenodo.10245452
title: Dataset related to article "Prospective Validation of the ROL System in Substaging pT1 High-Grade Urothelial Carcinoma: Results from a Mono-Institutional Confirmatory Analysis in BCG Treated Patients"

description: This record contains raw data related to article "Prospective Validation of the ROL System in Substaging pT1 High-Grade Urothelial Carcinoma: Results from a Mono-Institutional Confirmatory Analysis in BCG Treated Patients"
Abstract
Patients with pT1 high-grade (HG) urothelial carcinoma (UC) and a very high risk of progression might benefit from immediate radical cystectomy (RC), but this option remains controversial. Validation of a standardized method to evaluate the extent of lamina propria (LP) invasion (with recognized prognostic value) in transurethral resection (TURBT) specimens is still needed. The Rete Oncologica Lombarda (ROL) system showed a high predictive value for progression after TURBT in recent retrospective studies. The ROL system was supposed to be validated on a large prospective series of primary urothelial carcinomas from a single institution. From 2016 to 2020, we adopted ROL for all patients with pT1 HG UC on TURBT. We employed a 1.0-mm threshold to stratify tumors in ROL1 and ROL2. A total of 222 pT1 HG UC were analyzed. The median age was 74 years, with a predominance of men (73.8%). ROL was feasible in all cases: 91 cases were ROL1 (41%), and 131 were ROL2 (59%). At a median follow-up of 26.9 months (IQR 13.8-40.6), we registered 81 recurrences and 40 progressions. ROL was a significant predictor of tumor progression in both univariable (HR 3.53; CI 95% 1.56-7.99; p < 0.01) and multivariable (HR 2.88; CI 95% 1.24-6.66; p = 0.01) Cox regression analyses. At Kaplan-Meier estimates, ROL showed a correlation with both PFS (p = 0.0012) and RFS (p = 0.0167). Our results confirmed the strong predictive value of ROL for progression in a large prospective series. We encourage the application of ROL for reporting the extent of LP invasion, substaging T1 HG UC, and improving risk tables for urological decision-making.
DOI: 10.5281/zenodo.10245451
title: Dataset related to article "Prospective Validation of the ROL System in Substaging pT1 High-Grade Urothelial Carcinoma: Results from a Mono-Institutional Confirmatory Analysis in BCG Treated Patients"

description: This record contains raw data related to article "Prospective Validation of the ROL System in Substaging pT1 High-Grade Urothelial Carcinoma: Results from a Mono-Institutional Confirmatory Analysis in BCG Treated Patients"
Abstract
Patients with pT1 high-grade (HG) urothelial carcinoma (UC) and a very high risk of progression might benefit from immediate radical cystectomy (RC), but this option remains controversial. Validation of a standardized method to evaluate the extent of lamina propria (LP) invasion (with recognized prognostic value) in transurethral resection (TURBT) specimens is still needed. The Rete Oncologica Lombarda (ROL) system showed a high predictive value for progression after TURBT in recent retrospective studies. The ROL system was supposed to be validated on a large prospective series of primary urothelial carcinomas from a single institution. From 2016 to 2020, we adopted ROL for all patients with pT1 HG UC on TURBT. We employed a 1.0-mm threshold to stratify tumors in ROL1 and ROL2. A total of 222 pT1 HG UC were analyzed. The median age was 74 years, with a predominance of men (73.8%). ROL was feasible in all cases: 91 cases were ROL1 (41%), and 131 were ROL2 (59%). At a median follow-up of 26.9 months (IQR 13.8-40.6), we registered 81 recurrences and 40 progressions. ROL was a significant predictor of tumor progression in both univariable (HR 3.53; CI 95% 1.56-7.99; p < 0.01) and multivariable (HR 2.88; CI 95% 1.24-6.66; p = 0.01) Cox regression analyses. At Kaplan-Meier estimates, ROL showed a correlation with both PFS (p = 0.0012) and RFS (p = 0.0167). Our results confirmed the strong predictive value of ROL for progression in a large prospective series. We encourage the application of ROL for reporting the extent of LP invasion, substaging T1 HG UC, and improving risk tables for urological decision-making.
DOI: 10.5281/zenodo.10245499
title: Chirped Bloch-harmonic oscillations in a parametrically forced optical lattice

description: Dataset and codes of the publication "Chirped Bloch-harmonic oscillations in a parametrically forced optical lattice" by Usman Ali, Martin Holthaus, and Torsten Meier,published in PHYSICAL REVIEW RESEARCH 5, 043152 (2023)( https://doi.org/10.1103/PhysRevResearch.5.043152 )
DOI: 10.5281/zenodo.10245500
title: Chirped Bloch-harmonic oscillations in a parametrically forced optical lattice

description: Dataset and codes of the publication "Chirped Bloch-harmonic oscillations in a parametrically forced optical lattice" by Usman Ali, Martin Holthaus, and Torsten Meier,published in PHYSICAL REVIEW RESEARCH 5, 043152 (2023)( https://doi.org/10.1103/PhysRevResearch.5.043152 )
DOI: 10.6084/m9.figshare.24711278
title: Flo output

description: This is the final output of the flo algorithm in transporting the differentmv gene models over to the GCF_932526225.1_jaNemVect1.1 assembly.
DOI: 10.6084/m9.figshare.24711278.v1
title: Flo output

description: This is the final output of the flo algorithm in transporting the differentmv gene models over to the GCF_932526225.1_jaNemVect1.1 assembly.
DOI: 10.6084/m9.figshare.24204309
title: A multi-component forager-to-herder sequence at Kapsoo Rockshelter (Chebinyiny) on the Uasin Gishu Plateau, Kenya

description: Early archaeological investigations of the Uasin Gishu Plateau of west-central Kenya highlighted its potential importance as a geographic link between the Central Rift, the Lake Victoria Basin and the western Kenyan highlands from the Middle Stone Age to the Pastoral Neolithic and Iron Age periods. Despite this, the region has seen little focused research in recent decades. Here, we report on archaeological research at the site of Kapsoo Rockshelter, Chebinyiny Hill (GmJf1), near Moiben on the northern end of the Uasin Gishu Plateau. We combine data from original fieldwork in 1982 with renewed test excavations at Kapsoo carried out in 2022. Results of lithic, faunal and material analyses combined with radiocarbon dating reflect occupation of the northern plateau from the late Pleistocene to the late Holocene and provide the first radiometric dates for the presence of mobile herders in this region. Quantitative assessment of the rich lithic record at the site identifies significant technological change over time, providing a description of the regional Later Stone Age sequence. Finally, we present hypotheses for the relationship between Kapsoo and the nearby undated sequence at Muringa, as well as how these records fit into broader patterns of economic change across southwestern Kenya.
DOI: 10.6084/m9.figshare.24204309.v1
title: A multi-component forager-to-herder sequence at Kapsoo Rockshelter (Chebinyiny) on the Uasin Gishu Plateau, Kenya

description: Early archaeological investigations of the Uasin Gishu Plateau of west-central Kenya highlighted its potential importance as a geographic link between the Central Rift, the Lake Victoria Basin and the western Kenyan highlands from the Middle Stone Age to the Pastoral Neolithic and Iron Age periods. Despite this, the region has seen little focused research in recent decades. Here, we report on archaeological research at the site of Kapsoo Rockshelter, Chebinyiny Hill (GmJf1), near Moiben on the northern end of the Uasin Gishu Plateau. We combine data from original fieldwork in 1982 with renewed test excavations at Kapsoo carried out in 2022. Results of lithic, faunal and material analyses combined with radiocarbon dating reflect occupation of the northern plateau from the late Pleistocene to the late Holocene and provide the first radiometric dates for the presence of mobile herders in this region. Quantitative assessment of the rich lithic record at the site identifies significant technological change over time, providing a description of the regional Later Stone Age sequence. Finally, we present hypotheses for the relationship between Kapsoo and the nearby undated sequence at Muringa, as well as how these records fit into broader patterns of economic change across southwestern Kenya.