cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19612677
title: Characterization of lactic acid bacteria isolated from budu, a West Sumatra fish fermentation product, and their ability to produce exopolysaccharides

description: Probiotics are instrumental in maintaining the equilibrium of the gut microbiota and improving the health of the human body. This study examined the presence and physiological features, including the ability to produce exopolysaccharides, of lactic acid bacteria from fermented Tenggiri (<em>Scomberomorus guttatus</em>) and Talang (<em>Chorinemus</em> spp.) fish, also known as budu fish.
DOI: 10.6084/m9.figshare.19612677.v3
title: Characterization of lactic acid bacteria isolated from budu, a West Sumatra fish fermentation product, and their ability to produce exopolysaccharides

description: Probiotics are instrumental in maintaining the equilibrium of the gut microbiota and improving the health of the human body. This study examined the presence and physiological features, including the ability to produce exopolysaccharides, of lactic acid bacteria from fermented Tenggiri (<em>Scomberomorus guttatus</em>) and Talang (<em>Chorinemus</em> spp.) fish, also known as budu fish.
DOI: 10.6084/m9.figshare.19612677.v2
title: Characterization of lactic acid bacteria isolated from budu, a West Sumatra fish fermentation product, and their ability to produce exopolysaccharides

description: Probiotics are instrumental in maintaining the equilibrium of the gut microbiota and improving the health of the human body. This study examined the presence and physiological features, including the ability to produce exopolysaccharides, of lactic acid bacteria from fermented Tenggiri (<em>Scomberomorus guttatus</em>) and Talang (<em>Chorinemus</em> spp.) fish, also known as budu fish.
DOI: 10.6084/m9.figshare.20939707
title: arius_gagora_ragtag_1.fasta.gz

description: .......
DOI: 10.6084/m9.figshare.20939707.v1
title: arius_gagora_ragtag_1.fasta.gz

description: .......
DOI: 10.34740/kaggle/dsv/4163738
title: COVID-19 Global Scientists Response Dataset
DOI: 10.6084/m9.figshare.20939743
title: barnardius_zonarius_zanfona_1.fasta.gz

description: .......
DOI: 10.6084/m9.figshare.20939743.v1
title: barnardius_zonarius_zanfona_1.fasta.gz

description: .......
DOI: 10.6084/m9.figshare.20468916
title: Skeletal muscle phenotype of the DE50-MD dog: GLIMMPSE data

description: This dataset contains all GLIMMPSE power calculation/sample size data used in the manuscript <br> <strong>The skeletal muscle phenotype of the DE50-MD dog model of Duchenne muscular dystrophy</strong> <br> Included are: 1) Longintudinal vastus data used for GLIMMPSE analysis, in .json format, and exported results files 2) Post-mortem muscle data used for GLIMMPSE analysis, in .json format, and exported results files 3) A summary excel spreadsheet containing collated power calculation data from both datasets -this file contains a sheet (Data Key) with all acronyms/variable names explained in full <br> GLIMMPSE is accessible at the following location https://glimmpse.samplesizeshop.org/
DOI: 10.6084/m9.figshare.20468916.v2
title: Skeletal muscle phenotype of the DE50-MD dog: GLIMMPSE data

description: This dataset contains all GLIMMPSE power calculation/sample size data used in the manuscript <br> <strong>The skeletal muscle phenotype of the DE50-MD dog model of Duchenne muscular dystrophy</strong> <br> Included are: 1) Longintudinal vastus data used for GLIMMPSE analysis, in .json format, and exported results files 2) Post-mortem muscle data used for GLIMMPSE analysis, in .json format, and exported results files 3) A summary excel spreadsheet containing collated power calculation data from both datasets -this file contains a sheet (Data Key) with all acronyms/variable names explained in full <br> GLIMMPSE is accessible at the following location https://glimmpse.samplesizeshop.org/
DOI: 10.6084/m9.figshare.20468916.v1
title: Skeletal muscle phenotype of the DE50-MD dog: GLIMMPSE data

description: This dataset contains all GLIMMPSE power calculation/sample size data used in the manuscript <br> <strong>The skeletal muscle phenotype of the DE50-MD dog model of Duchenne muscular dystrophy</strong> <br> Included are: 1) Longintudinal vastus data used for GLIMMPSE analysis, in .json format, and exported results files 2) Post-mortem muscle data used for GLIMMPSE analysis, in .json format, and exported results files 3) A summary excel spreadsheet containing collated power calculation data from both datasets <br> GLIMMPSE is accessible at the following location https://glimmpse.samplesizeshop.org/
DOI: 10.34740/kaggle/dsv/4163806
title: COVID Vaccination in World (updated daily)
DOI: 10.6084/m9.figshare.19337123
title: EDGAR-FOOD_AP_v6.0

description: The EDGAR-FOOD_AP dataset provides air pollutant emissions from the food system at the global level over the time period 1970-2018. This dataset is created from the Emissions Database for Global Atmospheric Research (EDGARv6.0) and is described in detail in the following publications: Crippa, M., Solazzo, E., Guizzardi, D., Van Dingenen, R. and Leip, A.: Global environmental impacts from food system emissions, submitted, Nature Food, 2022. Crippa, M., Solazzo, E., Guizzardi, D., Monforti-Ferrario, F., Tubiello, F.N. and Leip, A.: Food systems are responsible for a third of global anthropogenic GHG emissions, Nature Food, 2021.<br>The EDGAR-FOOD data are also available on the EDGAR website: https://edgar.jrc.ec.europa.eu/edgar_food<br> <br>
DOI: 10.6084/m9.figshare.19337123.v2
title: EDGAR-FOOD_AP_v6.0

description: The EDGAR-FOOD_AP dataset provides air pollutant emissions from the food system at the global level over the time period 1970-2018. This dataset is created from the Emissions Database for Global Atmospheric Research (EDGARv6.0) and is described in detail in the following publications: Crippa, M., Solazzo, E., Guizzardi, D., Van Dingenen, R. and Leip, A.: Global environmental impacts from food system emissions, submitted, Nature Food, 2022. Crippa, M., Solazzo, E., Guizzardi, D., Monforti-Ferrario, F., Tubiello, F.N. and Leip, A.: Food systems are responsible for a third of global anthropogenic GHG emissions, Nature Food, 2021.<br>The EDGAR-FOOD data are also available on the EDGAR website: https://edgar.jrc.ec.europa.eu/edgar_food<br> <br>
DOI: 10.25592/uhhfdm.10172
title: FESST@HH meteorological network measurements

description: This data set contains meteorological measurement data collected during the Field Experiment on Sub-mesoscale Spatio-Temporal variability at Hamburg (FESST@HH) between June and August 2020. The observational set up of FESST@HH consisted of a ground-based network of 103 autonomous measurement stations (see photos), that covered the greater area (50 km x 35 km) of Hamburg (Germany; 53.5 °N 10.0 °E) with the primary goal to observe the spatial dimension of convective cold pools. During the experiment 82 low-cost and self-designed APOLLO (Autonomous cold POoL LOgger) stations sampled air temperature and pressure at 1-s resolution, while 21 WXT weather stations with commercial sensors provided additional information on relative humidity, wind speed and precipitation at 10-s resolution. All variables are sampled at a height of 3 m above ground, if not indicated otherwise.
description: Project: FESSTVaL (Field Experiment on submesoscale spatio-temporal variability in Lindenberg), a measurement campaign initiated by the Hans-Ertel-Center for Weather Research. This research was carried out in the Hans Ertel Center for Weather Research (HErZ). This German research network of universities, research institutions, and the German Weather Service (DWD) is funded by the BMVI (Federal Ministry of Transport and Digital Infrastructure).
description: {"references": ["Kirsch, B., Hohenegger, C., Klocke, D., Senke, R., Offermann, M., and Ament, F.: Sub-mesoscale observations of convective cold pools with a dense station network in Hamburg, Germany, Earth Syst. Sci. Data, 14, 3531\u20133548, https://doi.org/10.5194/essd-14-3531-2022, 2022."]}
DOI: 10.25592/uhhfdm.8966
title: FESST@HH meteorological network measurements

description: This data set contains meteorological measurement data collected during the Field Experiment on Sub-mesoscale Spatio-Temporal variability at Hamburg (FESST@HH) between June and August 2020. The observational set up of FESST@HH consisted of a ground-based network of 103 autonomous measurement stations (see photos), that covered the greater area (50 km x 35 km) of Hamburg (Germany; 53.5 °N 10.0 °E) with the primary goal to observe the spatial dimension of convective cold pools. During the experiment 82 low-cost and self-designed APOLLO (Autonomous cold POoL LOgger) stations sampled air temperature and pressure at 1-s resolution, while 21 WXT weather stations with commercial sensors provided additional information on relative humidity, wind speed and precipitation at 10-s resolution. All variables are sampled at a height of 3 m above ground, if not indicated otherwise.
description: Project: FESSTVaL (Field Experiment on submesoscale spatio-temporal variability in Lindenberg), a measurement campaign initiated by the Hans-Ertel-Center for Weather Research. This research was carried out in the Hans Ertel Center for Weather Research (HErZ). This German research network of universities, research institutions, and the German Weather Service (DWD) is funded by the BMVI (Federal Ministry of Transport and Digital Infrastructure).
description: {"references": ["Kirsch, B., Hohenegger, C., Klocke, D., Senke, R., Offermann, M., and Ament, F.: Sub-mesoscale observations of convective cold pools with a dense station network in Hamburg, Germany, Earth Syst. Sci. Data, 14, 3531\u20133548, https://doi.org/10.5194/essd-14-3531-2022, 2022."]}
DOI: 10.5281/zenodo.7015015
title: Functional precision profiling reveals non-mutational rewiring of kinase signaling networks in colorectal cancer

description: Multi-omics profiling of colorectal cancer (CRC) patients and associated patient-derived organoids. Tumor organoids were characterized in steady-state and perturbed using kinase inhibitors.
DOI: 10.5281/zenodo.7015014
title: Functional precision profiling reveals non-mutational rewiring of kinase signaling networks in colorectal cancer

description: Multi-omics profiling of colorectal cancer (CRC) patients and associated patient-derived organoids. Tumor organoids were characterized in steady-state and perturbed using kinase inhibitors.
DOI: 10.5281/zenodo.7050721
title: Amplicon structure creates collateral therapeutic vulnerability in cancer

description: Raw RNA sequencing data expressed in KELLY cells with vs. without ectopic DDX1 expression AH_YB_021 DDX1, AH_YB_023 DDX1, AH_YB_025 DDX1, : DDX1 - AH_YB_022 DDX1, AH_YB_024 DDX1, AH_YB_026 DDX1, : DDX1 +
DOI: 10.5281/zenodo.7050720
title: Amplicon structure creates collateral therapeutic vulnerability in cancer

description: Raw RNA sequencing data expressed in KELLY cells with vs. without ectopic DDX1 expression AH_YB_021 DDX1, AH_YB_023 DDX1, AH_YB_025 DDX1, : DDX1 - AH_YB_022 DDX1, AH_YB_024 DDX1, AH_YB_026 DDX1, : DDX1 +
DOI: 10.6084/m9.figshare.19953740
title: LBANet_D0_300522_basic_dataset

description: LBANet dataset D0 issued on 30/05/22. A dataset of 13383 .jpg files across 11 classes. Each .jpg contains the chromatic signature encoding a linear bifurcation buckling (LBA) eigenmode of a cylindrical shell under one of 11 classes of buckling eigenmode. Used to initially train the LBANet convolutional neural network classifier. See corresponding publication: https://doi.org/10.1016/j.advengsoft.2022.103257.
DOI: 10.6084/m9.figshare.19953740.v1
title: LBANet_D0_300522_basic_dataset

description: LBANet dataset D0 issued on 30/05/22. A dataset of 13392 .jpg files across 11 classes. Each .jpg contains the chromatic signature encoding a linear bifurcation buckling (LBA) eigenmode of a cylindrical shell under one of 11 classes of buckling eigenmode. Used to initially train the LBANet convolutional neural network classifier. See corresponding publication: https://doi.org/10.1016/j.advengsoft.2022.103257.
DOI: 10.6084/m9.figshare.19953740.v2
title: LBANet_D0_300522_basic_dataset

description: LBANet dataset D0 issued on 30/05/22. A dataset of 13383 .jpg files across 11 classes. Each .jpg contains the chromatic signature encoding a linear bifurcation buckling (LBA) eigenmode of a cylindrical shell under one of 11 classes of buckling eigenmode. Used to initially train the LBANet convolutional neural network classifier. See corresponding publication: https://doi.org/10.1016/j.advengsoft.2022.103257.
DOI: 10.6084/m9.figshare.18591347
title: lpxC diversity in published E. coli datasets

description: Data and scripts for analysing the diversity of the gene lpxC in public <i>Escherichia coli </i>datasets on NCBI. Analysis provided linked to paper [1].<br>Scripts provided 'as is'. Please get in touch if you have any questions about using them (see contact details in README.md).<br><br>Analysis.zip - zipped archive containing data and scripts for the analysis of lpxC sequences. See README.md for more details.<br>Assemblies.zip - combined assemblies from three datasets for n=X isolates (combination of new assemblies from short-reads on NCBI and existing NCBI assemblies). Also contains short script for identifying lpxC in the assembly and extracting sequence with blast.assembly-pipeline.sh - example assembly script used to trim and assemble short reads from NCBI SRA.<br>[1] Pre-existing chromosomal polymorphisms in pathogenic <i>E. coli</i> potentiate the evolution of antibiotic resistance by MCR-1 plasmid acquisition. Pramod K. Jangir*, Qiue Yang*, Liam P. Shaw, Julio Diaz Caballero, Lois Ogunlana, Rachel M. Wheatley, Timothy R. Walsh, and Craig MacLean. <br>* = equal contribution
DOI: 10.6084/m9.figshare.18591347.v1
title: lpxC diversity in published E. coli datasets

description: Data and scripts for analysing the diversity of the gene lpxC in public <i>Escherichia coli </i>datasets on NCBI. Analysis provided linked to paper [1].<br>Scripts provided 'as is'. Please get in touch if you have any questions about using them (see contact details in README.md).<br><br>Analysis.zip - zipped archive containing data and scripts for the analysis of lpxC sequences. See README.md for more details.<br>Assemblies.zip - combined assemblies from three datasets for n=X isolates (combination of new assemblies from short-reads on NCBI and existing NCBI assemblies). Also contains short script for identifying lpxC in the assembly and extracting sequence with blast.assembly-pipeline.sh - example assembly script used to trim and assemble short reads from NCBI SRA.<br>[1] Pre-existing chromosomal polymorphisms in pathogenic <i>E. coli</i> potentiate the evolution of antibiotic resistance by MCR-1 plasmid acquisition. Pramod K. Jangir*, Qiue Yang*, Liam P. Shaw, Julio Diaz Caballero, Lois Ogunlana, Rachel M. Wheatley, Timothy R. Walsh, and Craig MacLean. <br>* = equal contribution
DOI: 10.5281/zenodo.7050809
title: Molecular dynamics trajectories for "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessiblity"

description: Dataset of molecular dynamics trajectories obtained for "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessiblity" Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is causing a devastating social and economic impact all over the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, and increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes, via its receptor binding domain (RBD) that binds to angiotensin-converting enzyme 2 (ACE2). In an attempt to understand the effect of RBD mutations in the VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some VOCs mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (alpha, beta, delta, and omicron). Our results show that, in solution, wt RBD presents two distinct conformations: an “open” conformation where it is free to bind ACE2; and a “closed” conformation, where the RBM ridge blocks the binding surface. The alpha and beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the delta and omicron variants showed extreme results, with the closed conformation either barely observed or not observed at all. The delta variant also differed from the other variants substantially, alternating between the open conformation and an alternative “reversed” one, with a significantly changed orientation of the RBM ridge. This alternate conformation could potentially provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the omicron and delta variant, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of delta, antibody escape.
DOI: 10.5281/zenodo.7050808
title: Molecular dynamics trajectories for "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessiblity"

description: Dataset of molecular dynamics trajectories obtained for "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessiblity" Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is causing a devastating social and economic impact all over the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, and increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes, via its receptor binding domain (RBD) that binds to angiotensin-converting enzyme 2 (ACE2). In an attempt to understand the effect of RBD mutations in the VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some VOCs mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (alpha, beta, delta, and omicron). Our results show that, in solution, wt RBD presents two distinct conformations: an “open” conformation where it is free to bind ACE2; and a “closed” conformation, where the RBM ridge blocks the binding surface. The alpha and beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the delta and omicron variants showed extreme results, with the closed conformation either barely observed or not observed at all. The delta variant also differed from the other variants substantially, alternating between the open conformation and an alternative “reversed” one, with a significantly changed orientation of the RBM ridge. This alternate conformation could potentially provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the omicron and delta variant, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of delta, antibody escape.
DOI: 10.6084/m9.figshare.20941144.v1
title: Source Data.xlsx

description: Source data are provided with the article: <strong>Hybrid Chalcogen Bonds in Prodrug Nanoassemblies Provides Dual Redox-Responsivity in the Tumour Microenvironment</strong>.
DOI: 10.6084/m9.figshare.20940949
title: aspistor_quadriscutis_ragtag_1.fasta.gz

description: ......
DOI: 10.6084/m9.figshare.20940949.v1
title: aspistor_quadriscutis_ragtag_1.fasta.gz

description: ......
DOI: 10.6084/m9.figshare.20941435
title: Data for qPCR

description: Tolerance to dietary linalool involves co-expression of cytochrome P450s and cuticular proteins in Pagiophloeus tsushimanus (Coleoptera: Curculionidae) larvae using SMRT sequencing and RNA-seq
DOI: 10.6084/m9.figshare.20941435.v1
title: Data for qPCR

description: Tolerance to dietary linalool involves co-expression of cytochrome P450s and cuticular proteins in Pagiophloeus tsushimanus (Coleoptera: Curculionidae) larvae using SMRT sequencing and RNA-seq
DOI: 10.6084/m9.figshare.20941657.v1
title: RADAR data

description: RADAR data for analysis without baseline
DOI: 10.5517/ccdc.csd.cc28f6b8
title: CCDC 2098059: Experimental Crystal Structure Determination

description: Related Article: Hai-Wei Yan, Ya-Nan Yang, Xu Zhang, Jian-Shuang Jiang, Xiang Yuan, Zi-Ming Feng, Pei-Cheng Zhang|2022|Bioorg.Chem.|128|106091|doi:10.1016/j.bioorg.2022.106091
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29yxy4
title: CCDC 2143927: Experimental Crystal Structure Determination

description: Related Article: Narayanasamy Nivetha, Reshma Mary Martiz, Shashank M. Patil, Ramith Ramu, Swamy Sreenivasa, Sivan Velmathi|2022|RSC Advances|12|24192|doi:10.1039/D2RA04452H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.20941657
title: RADAR data

description: RADAR data for analysis without baseline
DOI: 10.25424/cmcc-0cb5-gz74
title: Dynamical Downscaling with COSMO-CLM of historical (1979/2005) and future climate (2006/2100) data under scenario RCP4.5 and RCP8.5 at 8 km over Italy

description: The present dataset was developed by dynamically downscaling of historical and climate scenario RCP4.5 and RCP8.5 to 8 km resolution (0.0715?). Dynamical downscaling has been conducted through the COSMO Regional Climate Model (RCM). The temporal resolution of outputs is daily. Runs cover the whole Italian territory (and neighbouring areas according to the necessary computation boundary) so to provide comprehensive (in terms of meteorological fields) dataset of climatological data for the period 1979/2005 (historical run) and 2006/2100 (scenario rcp4.5 and rcp8.5 run).
DOI: 10.6084/m9.figshare.20941735
title: RADAR Baseline

description: Baseline RADAR data for drone deterrence experiment
DOI: 10.6084/m9.figshare.20941879
title: RADAR data 100-400

description: Additional data for RADAR analysis processing <br>
DOI: 10.6084/m9.figshare.20941879.v1
title: RADAR data 100-400

description: Additional data for RADAR analysis processing <br>