Find research datasets worth reusing

opencc-by-4.0Oct 2019View details →

Dataset to the publication "A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking"

This repository accompanies the paper: "A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking". Organized into 14 folders it provides the data allowing the replication of all analyses and the manuscript's figures. For a more convenient download files were zipped. Upon publication of results using this dataset, please cite the following paper: Uetz-von Allmen E, Rippl AV, Farhan H, Legler DF. 2018. A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking. J Leukoc Biol 104(2):375-389.

opencc-by-4.0Aug 2021View details →

Source data for Synthetic dynamic hydrogels promote degradation-independent in vitro organogenesis

Source data and statistical analysis results for Synthetic dynamic hydrogels promote degradation-independent in vitro organogenesis

opencc-by-4.0Dec 2020View details →

Dataset for review on innovative contracts for the promotion of biodiversity and ecosystem services in agricultural management: contract design and governance characteristics

Dataset for H2020 project Contracts2.0 (GA No 818190), WP2, Task 2.1, Deliverable 2.1. This dataset contains the information needed to reproduce the results in: Bredemeier, Birte; Herrmann, Sylvia; Sattler, Claudia; Prager, Katrin; van Bussel, Lenny, Rex, Julia (submitted): Can the greater integration of biodiversity and ecosystem services into agricultural management be achieved through innovative contract design? Submitted to Ecosystem Services. The Contracts2.0 project aims to develop novel contract-based approaches to incentivise farmers for the increased provision of environmental public goods alongside private goods. Based on a literature review and integration of expert knowledge, we identified a comprehensive set of approaches to innovative contracts deviating from mainstream AECM contracts, and provide an overview of the variety of contracts currently being tested and experimented with. This includes different contract types like innovative Payments for Ecosystem Services (PES) approaches, value chain approaches and land tenure contracts, as well as their hybrids. We analysed 62 cases providing insights into characteristics of contract design and contract governance and the wider policy framework. The present dataset contains information on the criteria and specifications used to describe the cases studied, as well as the evaluation of each case. This information has been compiled to the best of our knowledge based on the sources available. For further information on the project Contracts2.0, please visit our website www.project-contracts20.eu.

opencc-by-4.0Oct 2021View details →

Dataset for "Fire disturbance promotes biodiversity of plants, lichens and birds in the Siberian subarctic tundra"

Data that support the findings of the study  "Fire disturbance promotes biodiversity of plants, lichens and birds in the Siberian subarctic tundra".

opencc-by-4.0Feb 2022View details →

Datasets generated by rurAllure project - promotion of rural museums and heritage sites in the vicinity of European pilgrimage routes

These datasets have been generated as part of rurAllure project (funded by the European Union’s Horizon 2020 Research and Innovation programme under grant agreement no 101004887). Main goal of rurAllure is the promotion of rural museums and heritage sites in the vicinity of European pilgrimage routes: https://rurallure.eu/project/about/

opencc-by-4.0Oct 2023View details →

Dataset for manuscript: Rock anisotropy promotes hydraulic fracture containment at depth

This is the experimental data used in manuscript: "Rock anisotropy promotes hydraulic fracture containment at depth". This data set has 5 folders:  K1, T2, M3 and M4 contain the raw data collected by active acoustic monitoring system and various pumps and transducers.  The readings of the Top Industrie syringe pump (for fluid injection), pressure transducers at downstream, and GDS pumps that provide confining stresses along all three directions via flatjacks are provided by two excel spreadsheets - Low_frequency_measurements.csv and Pump_reading.csv. For active acoustic data, there are four different files named by the starting time for each experiment. The .json file contains the basic information of each experiment. The .txt file contains the acquisition time for each active acoustic sequence. The .bin file contains the collected waveforms of all acoustic sequences. Processed_data includes the synchronized pressure data (Pressure_data.xlsx) and detailed acoustic emission results (AE_K1.csv, AE_T2.csv, AE_M3.csv, AE_M4.csv).

opencc-by-4.0Dec 2018View details →

The closure of a shallow tidal inlet promoted by infragravity waves

This file describes the original data that were used to generate figures 1, 2 and 3 in the manuscript by Bertin et al. to be published in Geophysical Research Letters: Bertin, X., Mendes, D., Martins, K., Fortunato, A.B. and Lavaud, L., 2019. The closure of a shallow tidal inlet promoted by infragravity waves. In revision to Geophysical Research Letters. *ADCP1_Bulkparameters_Albufeira_201810.dat This file includes the bulk parameters computed over 20’ samples at the ADCP1 that were used to generate figure 2. From left to right, each column corresponds to: date (yyyy mm dd)  time (HH MM SS) Free surface elevation [m/MSL] Hm0,G[m] Hm0,IG[m] Um[m/s] U10[m/s] U90[m/s] Qs,IGW[kg/s/m²] Qs,tide only[kg/s/m²] *ADCP1_2Hzdata_Albufeira_20181014.dat  This file includes the 20’ data sampled at 2Hz at the ADCP1 starting on the 14/10/2018 at 6h00. From left to right, each column corresponds to: date (yyyy mm dd) time (HH MM SS.S) water depth [m] alongstream currents [m/s] SSC [g/L]. *PT3_Albufeira_201810.dat This file includes the bulk parameters computed at PT3 based on 30’ samples and used to produce figure 2. From left to right, each column corresponds to: date (yyyy mm dd) time (HH MM SS.S) free surface elevation[m/MSL] Hm0,G[m] Hm0,IG[m]. *Topo_20181013_ ETRS89_MSL.dat This file corresponds the topography measured on the 13/10/2018 and includes 3 columns: X, Y and Z. X and Y are horizontal coordinates in the datum ETRS89-PTTM06 and Z is the topography with respect to mean sea level. *Topo_20181014_ ETRS89_MSL.dat This file corresponds the topography measured on the 14/10/2018 and includes 3 columns: X, Y and Z. X and Y are horizontal coordinates in the datum ETRS89-PTTM06 and Z is the topography with respect to mean sea level. *Coord_Sensores_ ETRS89_MSL.dat This file corresponds the position of the ADCP1 and PT3 sensors used in this study and includes 3 columns: X, Y and Z. X and Y are horizontal coordinates in the datum ETRS89-PTTM06 and Z is the position of the pressure sensor with respect to mean sea level.

opencc-by-4.0Nov 2019View details →

Teaser Promoting solar fuels at COP25!

Promotional video: We are happy to announce that SUNRISE will have a booth on December 5, 6 and 7 at COP25 in Madrid! The stand - number 2 - will be placed at the Green Zone of IFEMA, within the Science & Innovation area. Come & visit us!

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Data from: Populus euphratica WRKY1 binds the promoter of PeHA1 to enhance gene expression and salt tolerance

Plasma membrane proton pumps play a crucial role in maintaining ionic homeostasis in salt-resistant Populus euphratica under saline conditions. High levels of NaCl (200 mM) induced PeHA1 expression in P. euphratica roots and leaves. We isolated a 2022-bp promoter fragment upstream of the translational start of PeHA1 from P. euphratica. The promoter-reporter construct PeHA1-pro::GUS was transferred to tobacco plants, demonstrating that β-glucuronidase activities increased in root, leaf, and stem tissues under salt stress. DNA affinity purification sequencing revealed that PeWRKY1 protein targeted the PeHA1 gene. We assessed the salt-induced transcriptional response of PeWRKY1 and its interaction with PeHA1 in P. euphratica. PeWRKY1 binding to the PeHA1 W-box in promoter region was verified by a yeast one-hybrid assay, electrophoretic mobility shift assay, luciferase reporter assay, and virus-induced gene silencing. Transgenic tobacco plants overexpressing PeWRKY1 had improved expression of NtHA4, which has a cis-acting W-box in the regulatory region, and H+ pumping activity in both in vivo and in vitro assays. We conclude that salt stress upregulated PeHA1 transcription due to the binding of PeWRKY1 to the W-box in the promoter region of PeHA1. Thus, we conclude that enhanced H+ pumping activity enabled salt-stressed plants to retain Na+ homeostasis.

opencc-zeroNov 2020View details →

opencc-by-4.0Nov 2020View details →

Dataset for Freedom to Choose between Public Resources Promotes Cooperation

This dataset contains Matlab codes and Matlab data for "Freedom to choose between Public Resources promotes Cooperation". For a description of the dataset see the text file, "Description", in the dataset.

opencc-zeroJan 2016View details →

Supporting raw data for: The key role of the largest extant neotropical frugivore (Tapirus terrestris) in promoting admixture of plant genotypes across the landscape

These files contain the supporting raw data of the journal article The key role of the largest extant neotropical frugivore (Tapirus terrestris) in promoting admixture of plant genotypes across the landscape. They include the geographical coordinates and genotypes (microsatellites) of 259 palm (Syagrus romanzoffiana) individuals analyzed in the mentioned study, as well as an example of one input file for conducting data analysis with the software COLONY 2.0. A text file (´Readme') describing this archived supporting data in further detail is also provided.

opencc-by-4.0Jul 2024View details →

Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC (Spatial Transcriptomic 10X Visium portion)

Racial disparities in triple-negative breast cancer (TNBC) outcomes have been reported. However, the biological mechanisms underlying these disparities remain unclear. We integrated imaging mass cytometry and spatial transcriptomics, to characterize the tumor microenvironment (TME) of African American (AA) and European American (EA) patients with TNBC. The TME in AA patients was characterized by interactions between endothelial cells, macrophages, and mesenchymal-like cells, which were associated with poor patient survival. In contrast, the EA TNBC-associated niche is enriched in T-cells and neutrophils suggestive of an exhaustion and suppression of otherwise active T cell responses. Ligand-receptor and pathway analyses of race-associated niches found AA TNBC to be “immune cold” and hence immunotherapy resistant tumors, and EA TNBC as ‘inflamed’ tumors that evolved a distinctive immunosuppressive mechanism. Our study revealed the presence of racially distinct tumor-promoting and immunosuppressive microenvironments in AA and EA patients with TNBC, which may explain the poor clinical outcomes.   This dataset contains the 10X Visium Spatial Transcriptomic data of TNBC patients. There are two cohorts.   Baylor Scott and White (BSW) cohort: 10x.visium.tar.gz, containing 10 patients with TNBC from Baylor Scott and White affiliated Hospital.  Each sample is made of Space Ranger processed spot-separated gene expression data (processed to HDF5 AnnData file). There are also H&E images, and spot coordinate files available.    For Georgia validation cohort, 400 genes used for validation of ESG signatures (associated with BA-Community 1 and WA-Community-1) were obtained and provided by Ritu Aneja's lab. These 400 genes' spot-based expression data across Black and White TNBC patients are provided. See file georgia.validation.visium.tar.gz. Expression was normalized by total counts per spot, followed by log-normalization by Giotto.   As well in our paper, we integrated a published racial TNBC cohort for deriving some of initial results in the paper. This refers to the Bassiouni et al (Cancer Research) paper in Carpten's group. GSM_giotto_processed.tar.gz refers to this dataset, which we deposit here. The data were normalized by Giotto using standard procedure.

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Data and code for: Acute heat priming promotes short-term climate resilience of early life stages in a model sea anemone

Across diverse taxa, sublethal exposure to abiotic stressors early in life can lead to benefits such as increased stress tolerance upon repeat exposure. This phenomenon, known as hormetic priming, is largely unexplored in early life stages of marine invertebrates, which are increasingly threatened by anthropogenic climate change. To investigate this phenomenon, larvae of the sea anemone and model marine invertebrate Nematostella vectensis were exposed to control (18°C) or elevated (24°C, 30°C, 35°C, or 39°C) temperatures for 1 hour at 3 days post-fertilization (DPF), followed by return to control temperatures (18°C). The animals were then assessed for growth, development, metabolic rates, and heat tolerance at 4, 7, and 11 DPF. Priming at intermediately elevated temperatures (24°C, 30°C, or 35°C) augmented growth and development compared to controls or priming at 39°C. Indeed, priming at 39°C hampered developmental progression, with around 40% of larvae still in the planula stage at 11 DPF, in contrast to 0% for all other groups. Total protein content, a proxy for biomass, and respiration rates were not significantly affected by priming, suggesting metabolic resilience. Heat tolerance was quantified with acute heat stress exposures, and was significantly higher for animals primed at intermediate temperatures (24°C, 30°C, or 35°C) compared to controls or those primed at 39°C at all time points. To investigate a possible molecular mechanism for observed changes in heat tolerance, the expression of heat shock protein 70 (HSP70) was quantified at 11 DPF. Expression of HSP70 significantly increased with increasing priming temperature, with the presence of a doublet band for larvae primed at 39°C, suggesting persistent negative effects of priming on protein homeostasis. Interestingly, primed larvae in a second cohort cultured to 6 weeks post-fertilization continued to display hormetic growth responses, whereas benefits for heat tolerance were lost; in contrast, negative effects of short-term exposure to extreme heat stress (39°C) persisted. These results demonstrate that some dose-dependent effects of priming waned over time while others persisted, resulting in heterogeneity in organismal performance across ontogeny following priming. Overall, these findings suggest that heat priming may augment the climate resilience of marine invertebrate early life stages via the modulation of key developmental and physiological phenotypes, while also affirming the need to limit further anthropogenic ocean warming.

opencc-zeroNov 2023View details →

opengpl-3.0-or-laterNov 2023View details →

Data from: Species diversity promotes facilitation under stressful conditions.

All the data can be used to reproduce the analysis found at: https://github.com/alaindanet/plant-interactions-stress-strategiesAll the csv should be located in the `data-raw` folder to reproduce the analysis, expect `<a href="https://zenodo.org/api/records/10171339/draft/files/empty_file_for_traits-2.csv/content">empty_file_for_traits-2.csv</a>` that should be located under `data-raw/leaf/mars/` folder.

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Data from: The mechanism of promoting rhizosphere nutrient turnover for arbuscular mycorrhizal fungi attribute to recruited functional bacterial assembly

Symbiosis with arbuscular mycorrhizal (AM) fungi improves plant nutrient capture from the soil, yet there is limited knowledge about the diversity, structure, functioning, and assembly processes of AM fungi-related microbial communities. Here, 16S rRNA gene sequencing and metagenomic sequencing were used to detect bacteria in the rhizosphere of Lotus japonicus inoculated with and without AM fungi, and the L. japonicus mutant ljcbx (defective in symbiosis) inoculated with AM fungi in southern grassland soil. Our results show that AM symbiosis significantly increased bacterial diversity and promoted deterministic processes of bacterial community construction, suggesting that mycorrhizal symbiosis resulted in the directional enrichment of bacterial communities and established a stable rhizosphere bacterial community. AM fungi promoted the enrichment of nine bacteria, including Ohtaekwangia, Niastella, Gemmatimonas, Devosia, Sphingomonas, Novosphingobium, Opitutus, Lysobacter, Brevundimonas, which are positively correlated with NPK-related parameters. Through a functional identification experiment, we found that six of these genera, including Brevundimonas, Lysobacter, Ohtaekwangia, Sphingomonas, Devosia, and Gemmatimonas, demonstrated the ability to mineralize organophosphate and dissolve inorganic phosphorus, nitrogen, and potassium. Our study revealed that AM fungi can regulate rhizosphere bacterial community assembly and attract specific rhizosphere bacteria to promote soil nutrient turnover in southern grasslands.

opencc-zeroNov 2023View details →

opencc-by-4.0Dec 2023View details →

Dataset related to: Sirt3 deficiency promotes endothelial dysfunction and aggravates renal injury

The .xlsx file contains raw data related to the article "Sirt3 deficiency promotes endothelial dysfunction and aggravates renal injury. PLOS One. 2023 Oct 10;18(10):e0291909", available at the following <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0291909">link</a>. AbstractSirtuin 3 (SIRT3), the main deacetylase of mitochondria, modulates the acetylation levels of substrates governing metabolism and oxidative stress. In the kidney, we showed that SIRT3 affects the proper functioning of high energy-demanding cells, such as tubular cells and podocytes. Less is known about the role of SIRT3 in regulating endothelial cell function and its impact on the progression of kidney disease. Here, we found that whole body Sirt3-deficient mice exhibited reduced renal capillary density, reflecting endothelial dysfunction, and VEGFA expression compared to wild-type mice. This was paralleled by activation of hypoxia signaling, upregulation of HIF-1α and Angiopietin-2, and oxidative stress increase. These alterations did not result in kidney disease. However, when Sirt3-deficient mice were exposed to the nephrotoxic stimulus Adriamycin (ADR) they developed aggravated endothelial rarefaction, altered VEGFA signaling, and higher oxidative stress compared to wild-type mice receiving ADR. As a result, ADR-treated Sirt3-deficient mice experienced a more severe injury with exacerbated albuminuria, podocyte loss and fibrotic lesions. These data suggest that SIRT3 is a crucial regulator of renal vascular homeostasis and its dysregulation is a predisposing factor for kidney disease. By extension, our findings indicate SIRT3 as a pharmacologic target in progressive renal disease whose treatments are still imperfect.

FIGURE 1 in Does polyxenous symbiosis promote sympatric divergence? A morphometric and phylogeographic approach based on Oxydromus okupa (Annelida, Polychaeta, Hesionidae)

FIGURE 1 Sampled localities of the host bivalves harbouring Oxydromus okupa in the Gulf of Cadiz region: (CI) Cádiz Intertidal (Scrobicularia plana); (CS) Cádiz Subtidal (Macomopsis pellucida); (CH) Chipiona intertidal (M. pellucida). Images obtained from Google Earth v. 7.3, © Google 2018.

FIGURE 6 in Does polyxenous symbiosis promote sympatric divergence? A morphometric and phylogeographic approach based on Oxydromus okupa (Annelida, Polychaeta, Hesionidae)

FIGURE 6 Maximum-likelihood tree of 16S haplotype data. Bootstrap values for node support>75 are represent- ed on the corresponding branches.

FIGURE 3 Principal Component Analyses plots. A in Does polyxenous symbiosis promote sympatric divergence? A morphometric and phylogeographic approach based on Oxydromus okupa (Annelida, Polychaeta, Hesionidae)

FIGURE 3 Principal Component Analyses plots. A: Based on size independent data. B: Based on character proportions. CI: Cadiz Intertidal (Scrobicularia plana); CS: Cadiz Subtidal (Macomopsis pellucida); CH: Chipiona intertidal (M. pellucida). Character abbreviations as in fig. 2.

FIGURE 8 in Does polyxenous symbiosis promote sympatric divergence? A morphometric and phylogeographic approach based on Oxydromus okupa (Annelida, Polychaeta, Hesionidae)

FIGURE 8 Juvenile phases of Oxydromus okupa. A: The smallest exemplar collected in the study (0.96 mm long) at CH. B: A juvenile (1.10 mm long) found at CI. C: A juvenile (1.54 mm long) collected at CH.