cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4537506
title: Dataset related to article: "A novel insight into the anticancer mechanism of metformin in pancreatic neuroendocrine tumor cells"

description: This record contains data related to article: "A novel insight into the anticancer mechanism of metformin in pancreatic neuroendocrine tumor cells." The antidiabetic drug metformin displays anticancer properties in several neoplasms. In pituitary NETs, aryl hydrocarbon receptor-interacting protein (AIP) is up-regulated by the somatostatin analog octreotide. Metformin inhibited QGP-1 cell proliferation in a dose- and time-dependent manner, at concentrations similar to those achievable in treated patients (−31 ± 12%, p &lt; 0.05 vs basal at 100 μM). Moreover, metformin decreased pancreatic neuroendocrine tumors (PAN-NETs) cell proliferation (−62 ± 15%, p &lt; 0.0001 vs basal at 10 mM), without any additive effect when combined with octreotide. Both octreotide and metformin induced AIP up-regulation. AIP silencing abolished the reduction of mTOR phosphorylation induced by metformin and octreotide. Moreover, metformin decreased HSP70, increased Zac1 and AhR expression; these effects were abolished in AIP silenced QGP-1 cells. In conclusion, metformin acts as an anticancer agent in PAN-NET cells, its activity is mediated by AIP and its interacting proteins. These findings provide a novel insight into the antitumorigenic mechanism of metformin.
DOI: 10.5281/zenodo.4537505
title: Dataset related to article: "A novel insight into the anticancer mechanism of metformin in pancreatic neuroendocrine tumor cells"

description: This record contains data related to article: "A novel insight into the anticancer mechanism of metformin in pancreatic neuroendocrine tumor cells." The antidiabetic drug metformin displays anticancer properties in several neoplasms. In pituitary NETs, aryl hydrocarbon receptor-interacting protein (AIP) is up-regulated by the somatostatin analog octreotide. Metformin inhibited QGP-1 cell proliferation in a dose- and time-dependent manner, at concentrations similar to those achievable in treated patients (−31 ± 12%, p &lt; 0.05 vs basal at 100 μM). Moreover, metformin decreased pancreatic neuroendocrine tumors (PAN-NETs) cell proliferation (−62 ± 15%, p &lt; 0.0001 vs basal at 10 mM), without any additive effect when combined with octreotide. Both octreotide and metformin induced AIP up-regulation. AIP silencing abolished the reduction of mTOR phosphorylation induced by metformin and octreotide. Moreover, metformin decreased HSP70, increased Zac1 and AhR expression; these effects were abolished in AIP silenced QGP-1 cells. In conclusion, metformin acts as an anticancer agent in PAN-NET cells, its activity is mediated by AIP and its interacting proteins. These findings provide a novel insight into the antitumorigenic mechanism of metformin.
DOI: 10.5281/zenodo.4537805
title: BENCHMARK SYNTHETIC SINUSOIDAL BED FORMS

description: Archetypical or synthetic bed forms are needed for testing bed form geometrical descriptors and methods of bed form characterization. Such synthetic bed forms must be an idealized representation of their natural counterparts. They must describe their most important geometrical features, so that the variation of these features can be parametrized to test how the studied metric reacts to such variations. This data set includes a group of synthetic bed forms generated from sinusoidal functions. The data set was used for testing a three-dimensionality metric, but the included synthetic bed forms can also serve as benchmark for future studies of bed form three-dimensionality or to test other geometrical bed form descriptors. The dataset is related to the paper: "Development and validation of a novel metric for bed form three-dimensionality description" by F. Núñez-González, D. Hesse, B. Ettmer<sup> </sup>, R. R. Gutiérrez & O. Link, submitted to Geomorphology
DOI: 10.5281/zenodo.4537804
title: BENCHMARK SYNTHETIC SINUSOIDAL BED FORMS

description: Archetypical or synthetic bed forms are needed for testing bed form geometrical descriptors and methods of bed form characterization. Such synthetic bed forms must be an idealized representation of their natural counterparts. They must describe their most important geometrical features, so that the variation of these features can be parametrized to test how the studied metric reacts to such variations. This data set includes a group of synthetic bed forms generated from sinusoidal functions. The data set was used for testing a three-dimensionality metric, but the included synthetic bed forms can also serve as benchmark for future studies of bed form three-dimensionality or to test other geometrical bed form descriptors. The dataset is related to the paper: "Development and validation of a novel metric for bed form three-dimensionality description" by F. Núñez-González, D. Hesse, B. Ettmer<sup> </sup>, R. R. Gutiérrez & O. Link, submitted to Geomorphology
DOI: 10.5281/zenodo.4537718
title: Dataset related to article "Control of Complement Activation by the Long Pentraxin PTX3: Implications in Age-Related Macular Degeneration"

description: This record contains data related to article "Control of Complement Activation by the Long Pentraxin PTX3: Implications in Age-Related Macular Degeneration" <strong>Abstract. </strong>Dysregulation of the complement system is central to age-related macular degeneration (AMD), the leading cause of blindness in the developed world. Most of the genetic variation associated with AMD resides in complement genes, with the greatest risk associated with polymorphisms in the <em>complement factor H</em> (<em>CFH</em>) gene; factor H (FH) is the major inhibitor of the alternative pathway (AP) of complement that specifically targets C3b and the AP C3 convertase. Long pentraxin 3 (PTX3) is a soluble pattern recognition molecule that has been proposed to inhibit AP activation via recruitment of FH. Although present in the human retina, if and how PTX3 plays a role in AMD is still unclear. In this work we demonstrated the presence of PTX3 in the human vitreous and studied the PTX3-FH-C3b crosstalk and its effects on complement activation in a model of retinal pigment epithelium (RPE). RPE cells cultured in inflammatory AMD-like conditions overexpressed the PTX3 protein, and up-regulated AP activating genes. PTX3 bound RPE cells in a physiological setting, however this interaction was reduced in inflammatory conditions, whereby PTX3 had no complement-inhibiting activity on inflamed RPE. However, on non-cellular surfaces, PTX3 formed a stable ternary complex with FH and C3b that acted as a "hot spot" for complement inhibition. Our findings suggest a protective role for PTX3 in response to complement dysregulation in AMD and point to a novel mechanism of complement regulation by this pentraxin with potential implications in pathology and pharmacology of AMD.
DOI: 10.5281/zenodo.4537717
title: Dataset related to article "Control of Complement Activation by the Long Pentraxin PTX3: Implications in Age-Related Macular Degeneration"

description: This record contains data related to article "Control of Complement Activation by the Long Pentraxin PTX3: Implications in Age-Related Macular Degeneration" <strong>Abstract. </strong>Dysregulation of the complement system is central to age-related macular degeneration (AMD), the leading cause of blindness in the developed world. Most of the genetic variation associated with AMD resides in complement genes, with the greatest risk associated with polymorphisms in the <em>complement factor H</em> (<em>CFH</em>) gene; factor H (FH) is the major inhibitor of the alternative pathway (AP) of complement that specifically targets C3b and the AP C3 convertase. Long pentraxin 3 (PTX3) is a soluble pattern recognition molecule that has been proposed to inhibit AP activation via recruitment of FH. Although present in the human retina, if and how PTX3 plays a role in AMD is still unclear. In this work we demonstrated the presence of PTX3 in the human vitreous and studied the PTX3-FH-C3b crosstalk and its effects on complement activation in a model of retinal pigment epithelium (RPE). RPE cells cultured in inflammatory AMD-like conditions overexpressed the PTX3 protein, and up-regulated AP activating genes. PTX3 bound RPE cells in a physiological setting, however this interaction was reduced in inflammatory conditions, whereby PTX3 had no complement-inhibiting activity on inflamed RPE. However, on non-cellular surfaces, PTX3 formed a stable ternary complex with FH and C3b that acted as a "hot spot" for complement inhibition. Our findings suggest a protective role for PTX3 in response to complement dysregulation in AMD and point to a novel mechanism of complement regulation by this pentraxin with potential implications in pathology and pharmacology of AMD.
DOI: 10.25345/c5gn59
title: MassIVE MSV000086857 - Skeletal Muscle Metabolism of the Astyanax mexicanus
title: The muscle composition of cave dwelling and surface fish was analyzed by proteomics. Specifically, the composition of the myosin heavy chain was determined by in-gel digestion followed by reversed phase LC-MS/MS. The proteome of the different muscle types was analyzed by tandem mass tags and phosphorylation differences were determined by enriching for the modification.
DOI: 10.25380/iastate.12245846
title: High-throughput sequencing (HTS) data of plasmid library subjected to natural and high-fidelity Cas9 cleavage

description: SpCas9 is an RNA-guided endonuclease in the CRISPR-Cas immune system that is used for genome editing as it can be easily programmed to generate double-stranded breaks at desired target sites. Many natural Cas9 orthologs and engineered SpCas9 variants have been used to enable high-fidelity genome editing. To understand the native cleavage specificity and cleavage activity of Cas9 variants, we employed high-throughput <i>in vitro</i> cleavage assays using a plasmid library (pLibrary). We tested the cleavage activity of two natural Cas9 orthologs – SpCas9 and SaCas9, and three engineered variants – SpCas9 HF1, HypaCas9 and HiFi Cas9. We used two different crRNA sequences and corresponding target libraries (pLibrary), referred to as pLibrary PS4 and EMX1. The data set is the high-throughput sequencing (HTS) reads of pLibrary subjected to cleavage by different Cas9 variants. The README file contains details about the content of the HTS data set, and the key to the file names and corresponding samples. This HTS data set supports the research article: "High-throughput <i>in vitro</i> specificity profiling of natural and high-fidelity CRISPR-Cas9 variants".<br><br>Version 2: Raw data files used to plot all heatmap figures in the research paper are uploaded with information about the data within each file.<br><br>Version 3: Raw data files (V1) used to plot all heatmap figures in the research paper are updated with new corrected data and information about the data within each file.
DOI: 10.25380/iastate.12245846.v3
title: High-throughput sequencing (HTS) data of plasmid library subjected to natural and high-fidelity Cas9 cleavage

description: SpCas9 is an RNA-guided endonuclease in the CRISPR-Cas immune system that is used for genome editing as it can be easily programmed to generate double-stranded breaks at desired target sites. Many natural Cas9 orthologs and engineered SpCas9 variants have been used to enable high-fidelity genome editing. To understand the native cleavage specificity and cleavage activity of Cas9 variants, we employed high-throughput <i>in vitro</i> cleavage assays using a plasmid library (pLibrary). We tested the cleavage activity of two natural Cas9 orthologs – SpCas9 and SaCas9, and three engineered variants – SpCas9 HF1, HypaCas9 and HiFi Cas9. We used two different crRNA sequences and corresponding target libraries (pLibrary), referred to as pLibrary PS4 and EMX1. The data set is the high-throughput sequencing (HTS) reads of pLibrary subjected to cleavage by different Cas9 variants. The README file contains details about the content of the HTS data set, and the key to the file names and corresponding samples. This HTS data set supports the research article: "High-throughput <i>in vitro</i> specificity profiling of natural and high-fidelity CRISPR-Cas9 variants".<br><br>Version 2: Raw data files used to plot all heatmap figures in the research paper are uploaded with information about the data within each file.<br><br>Version 3: Raw data files (V1) used to plot all heatmap figures in the research paper are updated with new corrected data and information about the data within each file.
DOI: 10.25380/iastate.12245846.v2
title: High-throughput sequencing (HTS) data of plasmid library subjected to natural and high-fidelity Cas9 cleavage

description: SpCas9 is an RNA-guided endonuclease in the CRISPR-Cas immune system that is used for genome editing as it can be easily programmed to generate double-stranded breaks at desired target sites. Many natural Cas9 orthologs and engineered SpCas9 variants have been used to enable high-fidelity genome editing. To understand the native cleavage specificity and cleavage activity of Cas9 variants, we employed high-throughput <i>in vitro</i> cleavage assays using a plasmid library (pLibrary). We tested the cleavage activity of two natural Cas9 orthologs – SpCas9 and SaCas9, and three engineered variants – SpCas9 HF1, HypaCas9 and HiFi Cas9. We used two different crRNA sequences and corresponding target libraries (pLibrary), referred to as pLibrary PS4 and EMX1. The data set is the high-throughput sequencing (HTS) reads of pLibrary subjected to cleavage by different Cas9 variants. The README file contains details about the content of the HTS data set, and the key to the file names and corresponding samples. This HTS data set supports the research article: "High-throughput <i>in vitro</i> specificity profiling of natural and high-fidelity CRISPR-Cas9 variants".<br><br>Version 2: Raw data files fused to plot all heatmap figures in the research paper are uploaded with information about the data within each file.<br>
DOI: 10.25380/iastate.8178938
title: High-throughput sequencing (HTS) data of plasmid library subjected to Cas12a cleavage

description: Cas12a (formerly Cpf1) is an RNA-guided endonuclease in the CRISPR-Cas immune system that can be easily programmed for genome editing. To understand the native cleavage specificity and cleavage activity of Cas12a, we employed high-throughput <i>in vitro</i> cleavage assays using a plasmid library (pLibrary). We tested the cleavage activity of three Cas12a orthologs – FnCas12a, LbCas12a and AsCas12a. For each Cas12a ortholog, we used three different crRNA sequences and corresponding target libraries (pLibrary), referred to as pLibrary PS4, EMX1 and CCR5. The data set is the high-throughput sequencing (HTS) reads of pLibrary subjected to cleavage by different Cas12a orthologs. The README file contains details about the content of the HTS data set, and the key to the file names and corresponding samples.<br> This HTS data set supports the research article: "CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects". <br>Previous title: "Pervasive off-target and double-stranded DNA nicking by CRISPR-Cas12a". <br>Version 2: New data set for pLibrary CCR5 uploaded with updated "README" file (v2).<br>Version 3: Data set corrected for pLibrary PS4 with updated "README" file (v3).<br><br>Version 4: "README" file (v4) and reference updated with new title and link to publication.
DOI: 10.5281/zenodo.4536626
title: 2D symmetrically unstable rotating gravity current

description: The tar file contains 6 directories corresponding to experiments used in motivating/developing a parameterization for symmetric instability in: "Parameterization of submesoscale symmetric instability in dense flows along topography" by Elizabeth Yankovsky, Sonya Legg, and Robert Hallberg (submitted to JAMES, 2021). The included test cases are: -2D Z* coordinates at nominal resolution with the SI parameterization on/off -2D Z* coordinates at degraded resolution (4x coarser than nominal in x and z) with the SI parameterization on/off -2D layered isopycnal coordinates at nominal resolution with the SI parameterization on/off We include the data output for all time steps, a Jupyter notebook for analysis, and the MOM_input parameter file used to specify inputs in the model. For documentation and initial condition setup for the rotating gravity current experiment (upon which these simulations are based) please see: https://github.com/NOAA-GFDL/MOM6-examples/tree/dev/gfdl/ocean_only/rotating_gravity_current Contact eyankovsky@gmail.com for questions.
DOI: 10.5281/zenodo.4536625
title: 2D symmetrically unstable rotating gravity current

description: The tar file contains 6 directories corresponding to experiments used in motivating/developing a parameterization for symmetric instability in: "Parameterization of submesoscale symmetric instability in dense flows along topography" by Elizabeth Yankovsky, Sonya Legg, and Robert Hallberg (submitted to JAMES, 2021). The included test cases are: -2D Z* coordinates at nominal resolution with the SI parameterization on/off -2D Z* coordinates at degraded resolution (4x coarser than nominal in x and z) with the SI parameterization on/off -2D layered isopycnal coordinates at nominal resolution with the SI parameterization on/off We include the data output for all time steps, a Jupyter notebook for analysis, and the MOM_input parameter file used to specify inputs in the model. For documentation and initial condition setup for the rotating gravity current experiment (upon which these simulations are based) please see: https://github.com/NOAA-GFDL/MOM6-examples/tree/dev/gfdl/ocean_only/rotating_gravity_current Contact eyankovsky@gmail.com for questions.
DOI: 10.5281/zenodo.4537747
title: Data and code for analysis in preprint "Fighting over defence chemicals disrupts mating behaviour"

description: Data and code for analysis in bioRxiv preprint "Fighting over defence chemicals disrupts mating behaviour". The point at which each data sheet is used in the analysis is specified in the code and code for each respective figure in paper is also given (with the exception of Figure 1, which is a figure of the experimental design). A renv lockfile is also included for version control.
DOI: 10.5281/zenodo.4275738
title: EXAMON data from Marconi HPC system - Massimo Schembri internship

description: Partial snapshot of the data collected by EXAMON on the Marconi supercomputer (hosted at CINECA, Bologna, Italy) in the following periods: January 2020 May 2020 This data has been gathered and analyzed by Massimo Schembri during his internship at University of Bologna, with the supervision of Andrea Borghesi (assistant professor at the same university).
description: This work was partially supported by EU H2020 IoTwins Innovation Action project (g.a. 857191). We also want to thank CINECA and E4 for granting us the access to their systems.
DOI: 10.5281/zenodo.4275723
title: EXAMON data from Marconi HPC system - Massimo Schembri internship

description: Partial snapshot of the data collected by EXAMON on the Marconi supercomputer (hosted at CINECA, Bologna, Italy) in the following periods: January 2020 May 2020 This data has been gathered and analyzed by Massimo Schembri during his internship at University of Bologna, with the supervision of Andrea Borghesi (assistant professor at the same university).
description: This work was partially supported by EU H2020 IoTwins Innovation Action project (g.a. 857191). We also want to thank CINECA and E4 for granting us the access to their systems.
DOI: 10.5281/zenodo.4537279
title: Observing the evolution of fatigue damage and associated strain fields in a correlative, multiscale 3D time-lapse study of quasi-unidirectional glass fibre composites

description: X-ray tomography and DIC/Strain mapping datasets behind the publication: Observing the evolution of fatigue damage and associated strain fields in a correlative, multiscale 3D time-lapse study of quasi-unidirectional glass fibre composites Anuj Prajapati <em>et al</em> 2020 <em>IOP Conf. Ser.: Mater. Sci. Eng.</em> <strong>942</strong> 012039 Three ZIP files include the formats: XCT data in 3D .tiff. DIC Raw data in .vc7 and associated metadata .exp, .ims, .attr, .xml, .scales, and .set. DIC strain maps in .mp4 movies.
DOI: 10.6084/m9.figshare.12915368
title: Southern Sierra RHESSys-Fire Simultation Data

description: This is a R Workspace that contains all simulation results associated with Kennedy et al. (2021) and referenced therein. <br>Big Creek simulation results <br>AllMCFireResults_Mar24_2020.RData contains results from 208-210 MC replicate simulation results with wildfire. The first 200 of these were used for the publication. These are contained in a results.list with the following components (referencing scenarios): "Base" "Drought" "Plus2" "DroughtPlus2" "Plus4" "DroughtPlus4".<br>Each component, e.g., results.list$Base contains two data frames: rhessys.results, fire.results. <br>The rhessys.results data frame (e.g., results.list$Base$rhessys.results) has the following: "Rep" "day" "month" "year" "lai" "litrc" "streamflow" "understory_leafc" "understory_stemc" "understory_biomassc" "understory_height" "overstory_leafc" "overstory_stemc" "overstory_biomassc" "overstory_height" <br>Note that *_biomassc results are inconsistent and shouldn't be used. <br>The fire.results data frame (e.g., results.list$Base$rhessys.results) has the following: "FirePix" "Year" "Month" "wind1" "wind2" "nign" "Rep" "AreaBurned.ha"<br>AllMCNoFireResults.RData contains results from single runs of RHESSys without fire. It contains the list resultsNoFire.list, which contains data frames called "Base" "Drought" "Plus2" "DroughtPlus2" "Plus4" "DroughtPlus4". These dataframes follow the same structure as the rhessys.results data frames above.
DOI: 10.6084/m9.figshare.12915368.v1
title: Southern Sierra RHESSys-Fire Simultation Data

description: This is a R Workspace that contains all simulation results associated with Kennedy et al. (2021) and referenced therein. <br>Big Creek simulation results <br>AllMCFireResults_Mar24_2020.RData contains results from 208-210 MC replicate simulation results with wildfire. The first 200 of these were used for the publication. These are contained in a results.list with the following components (referencing scenarios): "Base" "Drought" "Plus2" "DroughtPlus2" "Plus4" "DroughtPlus4".<br>Each component, e.g., results.list$Base contains two data frames: rhessys.results, fire.results. <br>The rhessys.results data frame (e.g., results.list$Base$rhessys.results) has the following: "Rep" "day" "month" "year" "lai" "litrc" "streamflow" "understory_leafc" "understory_stemc" "understory_biomassc" "understory_height" "overstory_leafc" "overstory_stemc" "overstory_biomassc" "overstory_height" <br>Note that *_biomassc results are inconsistent and shouldn't be used. <br>The fire.results data frame (e.g., results.list$Base$rhessys.results) has the following: "FirePix" "Year" "Month" "wind1" "wind2" "nign" "Rep" "AreaBurned.ha"<br>AllMCNoFireResults.RData contains results from single runs of RHESSys without fire. It contains the list resultsNoFire.list, which contains data frames called "Base" "Drought" "Plus2" "DroughtPlus2" "Plus4" "DroughtPlus4". These dataframes follow the same structure as the rhessys.results data frames above.
DOI: 10.18112/openneuro.ds003516.v1.0.0
title: Attended speaker paradigm (own name in ignored)