Find research datasets worth reusing

opencc-by-4.0Dec 2019View details →

Carbon-Phosphorous Lyase Enzyme Activity Profiles in the North Pacific Subtropical Gyre

These datasets contain oceanic enzyme activity measurements of Carbon-Phosphorus (C-P) lyase, a catalytic enzyme pathway, which cleaves C-P bonds, allowing microbial utilization of phosphonates as a phosphorous source. These activity measurements were made in the North Pacific Subtropical Gyre. Samples were collected in the top 1000 m of the water column on KM1717, KM1821, and KM2001 cruises and in the top 225 m of the water column on FK180310-2.

opencc-zeroJun 2020View details →

Data from: Dynamic reorganization of neuronal activity patterns in parietal cortex dataset

Neuronal representations change as associations are learned between sensory stimuli and behavioral actions. However, it is poorly understood whether representations for learned associations stabilize in cortical association areas or continue to change following learning. We tracked the activity of posterior parietal cortex neurons for a month as mice stably performed a virtual-navigation task. The relationship between cells' activity and task features was mostly stable on single days but underwent major reorganization over weeks. The neurons informative about task features (trial type and maze locations) changed across days. Despite changes in individual cells, the population activity had statistically similar properties each day and stable information for over a week. As mice learned additional associations, new activity patterns emerged in the neurons used for existing representations without greatly affecting the rate of change of these representations. We propose that dynamic neuronal activity patterns could balance plasticity for learning and stability for memory.

opencc-by-4.0Jun 2020View details →

Dataset The Lactate Receptor HCAR1 Modulates Neuronal Network Activity through the Activation of G(α) and G(βγ) Subunits

This dataset is related to the study:  "The Lactate Receptor HCAR1 Modulates Neuronal Network Activity through the Activation of G(α) and G(βγ) Subunits" by de Castro Abrantes H, Briquet M, Schmuziger C, Restivo L, Puyal J, Rosenberg N, Rocher AB, Offermanns S, Chatton JY. J Neurosci. 2019 Jun 5;39(23):4422-4433. doi: 10.1523/JNEUROSCI.2092-18.2019. Epub 2019 Mar 29. PubMed PMID: 30926749; PubMed Central PMCID: PMC6554634.

opencc-by-4.0Jun 2020View details →

Supplementary videos for "Active flow network generates molecular transport by packets: case of the endoplasmic reticulum"

Videos showing simulated motion on the active flow network for different switching timescales. In particular, compare \(\tau_{\text{switch}} = 3 \text{ s}\) to \(\tau_{\text{switch}} = 30 \text{ ms}\). The red bubbles are proportional to the number of particles present in a node. Initially, all particles are placed in a central source node.

CO2 emissions changes due to COVID-19: modified SSP2-4.5 to account for sector activity level

Monthly CO2 emission projections, modified by the country-specific impacts of COVID-19 lockdown.  This repository holds the netcdf files for CO2 emissions projected by the scenario SSP2-4.5, from the Scenario4MIPs database ( <a href="https://esgf-node.llnl.gov/search/input4mips/">https://esgf-node.llnl.gov/search/input4mips/</a>), modified by the country and sector activity levels associated with lockdown, projected out for 3 years after 2020 before returning to baseline. The details of these activity estimates can be found in <a href="https://github.com/Priestley-Centre/COVID19_emissions">https://github.com/Priestley-Centre/COVID19_emissions</a>. The methodology behind these calculations is based on <a href="https://github.com/Rlamboll/modify_COVID19_netCDF_Emissions/">https://github.com/Rlamboll/modify_COVID19_netCDF_Emissions/</a>, a slight modification of the approach used in <a href="https://zenodo.org/record/3947917#.XxR_qyhKhPZ">https://zenodo.org/record/3947917#.XxR_qyhKhPZ</a> for aerosols emissions, and version numbers used here are consistent with the data seen in that database. We present only a single scenario (called 2-year blip, featuring a one year recovery after the end of the 2 years) compared to the baseline.  Funding was provided by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement nos. 820829 (CONSTRAIN) <a href="http://constrain-eu.org/">http://constrain-eu.org/</a>

S72 | NTUPHTW | Pharmaceutically Active Substances Suspect List from National Taiwan University

This is the collection associated with list S72 NTUPHTW Pharmaceutically Active Substances Suspect List from National Taiwan University on the NORMAN Suspect List Exchange. <a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a> A suspect list based on Agilent PCDLs containing pharmaceutically active substances from the College of Public Health, National Taiwan University, kindly provided by Wen-Ling Chen. Dataset DOI: <a href="https://doi.org/10.5281/zenodo.3955664">10.5281/zenodo.3955664</a>.

Weekly NOx aviation emissions changes due to COVID-19: modified SSP2-4.5 to account for sector activity level

Weekly NOx aviation emissions estimates for 2020 until 21/07/2020, modified by the country-specific impacts of COVID-19 lockdown.  This repository holds the netcdf files for NOx emissions projected by the scenario SSP2-4.5, from the Scenario4MIPs database (<a href="https://esgf-node.llnl.gov/search/input4mips/">https://esgf-node.llnl.gov/search/input4mips/</a>), modified by the country and sector activity levels associated with lockdown for 2020, with observation-based data up until the 5th of July and a fixed estimate thereafter. This is the weekly equivalent of the aviation file in <a href="https://zenodo.org/record/3951601#.XxYBsihKhPY">https://zenodo.org/record/3951601#.XxYBsihKhPY</a> for a shorter time period, although the version number is different since we have more information available and the normalisation process has been improved.  Funding was provided by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement nos. 820829 (CONSTRAIN) <a href="http://constrain-eu.org/">http://constrain-eu.org/</a>  see <a href="https://github.com/Priestley-Centre/COVID19_emissions">https://github.com/Priestley-Centre/COVID19_emissions</a> for more details on the methodology.

Data set for "Projection-specific activity of layer 2/3 neurons imaged in mouse primary somatosensory barrel cortex during a whisker detection task"

Data set for: Vavladeli A, Daigle T, Zeng H, Crochet S, Petersen CCH (2020) Projection-specific activity of layer 2/3 neurons imaged in mouse primary somatosensory barrel cortex during a whisker detection task. FUNCTION 1: zqaa008. doi: 10.1093/function/zqaa008 There are 2 files in this upload: 1. The file named "2020_Vavladeli_FUNCTION.pdf" is the Open Access pdf file of the manuscript published in FUNCTION. 2. The file named "Vavladeli_data_code.zip" (~2 GB) is a zipped version of a folder named "Vavladeli_data_code" (~2 GB), which contains the data analysed in the study along with the Matlab code used to generate the published figures. When unzipped, the folder contains 8 Matlab '.m' files with analysis code and two '.mat' data files. In order to run the analysis of the data set, you need to execute the '.m' file with the corresponding figure name.

opencc-zeroJul 2020View details →

Data from: Antibacterial activity of graphene oxide nanosheet against multi drug resistant superbugs isolated from infected patients

Graphene oxide (GO) is a derivative of graphene nanosheet which is the most promising material of the decade in biomedical research. In particular, it has been known as an antimicrobial nanomaterial with good biocompatibility. In this study, we have synthesized and characterize GO and checked its antimicrobial property against different Gram-negative and Gram-positive multi drug resistant (MDR) hospital superbugs grown in solid agar-based nutrient plates with and without human serum through the utilization of agar well diffusion method, live/dead fluorescent staining and genotoxicity analysis. The main focus of the antimicrobial activity analysis is to distinguish the killing performance of GO in artificial and blood containing media because after injection into the bloodstream the activity of GO may be modified by adsorption of blood proteins or other biomolecules. No significant changes in antibacterial activity were found in these two different conditions. We also compare the bactericidal capability of GO with some commonly administrated antibiotics and in all cases the degree of inhibition is found to be higher. The data presented here are novel and show that GO is an effective bactericidal agents against different superbugs and can be used as a future antibacterial agent.

opencc-zeroJul 2020View details →

Life history data for longer-lived tropical songbirds reduce breeding activity as they buffer impacts of drought

Droughts are expected to increase in frequency and severity with climate change. Population impacts of such harsh environmental events are theorized to vary with life history strategies among species. However, existing demographic models generally do not consider behavioral plasticity that may modify the impact of harsh events. Here we show that tropical songbirds in the New and Old World reduced reproduction during drought, with greater reductions in species with higher average long-term survival. Large reductions in reproduction by longer-lived species were associated with higher survival during drought than pre-drought years in Malaysia, whereas shorter-lived species maintained reproduction and survival decreased. Behavioral strategies of longer-lived, but not shorter-lived, species mitigated the effect of increasing drought frequency on long-term population growth. Behavioral plasticity can buffer the impact of climate change on populations of some species, and differences in plasticity among species related to their life histories are critical for predicting population trajectories.

opencc-by-4.0Aug 2020View details →

Facebook activity of Romanian libraries during the COVID-19 crisis

This dataset shows the activity on Facebook (no of posts, shares, and reactions) of the Romanian county libraries during the COVID-19 crisis.

opencc-by-4.0Aug 2020View details →

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

We prepared these datasets associated with the paper “Genome-scale imaging of the 3D organization and transcriptional activity of chromatin” published in Cell: <a href="https://doi.org/10.1016/j.cell.2020.07.032">https://doi.org/10.1016/j.cell.2020.07.032</a>. Please find detailed descriptions of individual data files in the README_August 2020.txt. We provide example codes to load and analyze these datasets in: <a href="https://github.com/ZhuangLab/Chromatin_Analysis_2020_cell">https://github.com/ZhuangLab/Chromatin_Analysis_2020_cell</a>. If you use these datasets, please cite our Cell paper.

opencc-by-4.0Aug 2020View details →

NUclear Receptor Activity (NURA) dataset

Dataset information NURA (NUclear Receptor Activity) dataset collects curated information on small molecules that modulate nuclear receptors (NRs), to be intended for both pharmacological and toxicological applications. NURA contains bioactivity annotations for 15,247 molecules and 11 selected NRs, and it was obtained by integrating and curating data from toxicological and pharmacological databases (i.e., Tox21, ChEMBL, NR-DBIND and BindingDB). NURA dataset is a useful tool to bridge the gap between toxicology- and medicinal-chemistry-related databases, as it is enriched in terms of number of molecules, structural diversity and covered atomic scaffolds compared to the single sources.  To the best of our knowledge, NURA dataset is the most exhaustive collection of small molecules annotated for their modulation of the chosen nuclear receptors. NURA dataset is intended to support decision-making in pharmacology and toxicology, as well as to contribute to data-driven applications, such as machine learning.  Content Three files are provided: <ol> <li>"Nura_v1.0.0.csv" [datafile] dataset containing activity labels for each molecule (rows, identified by a unique ID and the canonical SMILES string) and each nuclear receptor endpoint (columns).</li> <li>"Nura_v1.0.0_details" [datafile], containing information on the individual records used to generate the dataset.</li> <li>"curation_pipeline.zip" [software], containing the data curation pipeline in KNIME ("NURA_Dataset.knwf") as well as a help file ('help.pdf').</li> </ol> Additional details on the content and curation pipeline can be found in the uploaded, non peer-reviewed, preprint ("NURApreprint.pdf"). Version information <ul> <li>v1.0.1: data curation pipeline uploaded.</li> <li>v.1.0.0: initial upload.</li> </ul> Contact If you have any question, contact us! (Francesca Grisoni, francesca.grisoni@pharma.ethz.ch; Davide Ballabio, davide.ballabio@unimib.it)

opencc-by-4.0Sep 2020View details →

Logger data for article "Effects of blood parasite infections on spatiotemporal migration patterns and activity budgets in a long-distance migratory passerine"

The supplement loggerDATA.zip is a ZIP Archive (to be unzipped e.g. with <a href="https://www.izarc.org/downloads">https://www.izarc.org/downloads</a>) containing 40 folders and one .txt file. In the readME.txt file one can find a detailed description of the folder content and the data specifications of the files used for the analyses in the article "Effects of blood parasite infections on spatiotemporal migration patterns and activity budgets in a long-distance migratory passerine". For more information of how the data can be analysed and visualised please see: <a href="https://kiranlda.github.io/PAMLrManual/">https://kiranlda.github.io/PAMLrManual/</a>.

opencc-zeroSep 2020View details →

Data from: Nonlinearities between inhibition and T-type calcium channel activity bidirectionally regulate thalamic oscillations

Absence seizures result from 3-5 Hz generalized thalamocortical oscillations that depend on highly regulated inhibitory neurotransmission in the thalamus. Efficient reuptake of the inhibitory neurotransmitter GABA is essential, and reuptake failure worsens seizures. Here, we show that blocking GABA transporters (GATs) in acute brain slices containing key parts of the thalamocortical seizure network modulates epileptiform activity. As expected, we found that blocking either GAT1 or GAT3 prolonged oscillations. However, blocking both GATs unexpectedly suppressed oscillations. Integrating experimental observations into single-neuron and network-level computational models shows how a non-linear dependence of T-type calcium channel opening on GABAB receptor activity regulates network oscillations. Receptor activity that is either too brief or too protracted fails to sufficiently open T-type channels necessary for sustaining oscillations. Only within a narrow range does prolonging GABAB receptor activity promote channel opening and intensify oscillations. These results have implications for therapeutics that modulate GABA transporters.

Supplementary information to the article by van Beijnum et al. "Integrating phenotypic search and phosphoproteomic profiling of active kinases for optimization of drug mixtures for RCC treatment"

Supplementary information to the article "Integrating phenotypic search and phosphoproteomic profiling of active kinases for optimization of drug mixtures for RCC treatment". Judy R. van Beijnum1, Andrea Weiss2, 3, Robert H. Berndsen1,2 , Tse J. Wong1, Louise C. Reckman1, Sander R. Piersma4,5, Marloes Zoetemelk2,3, Richard de Haas1,4,5, Olivier Dormond6, Axel Bex7,8, Alexander A. Henneman4,5, Connie R. Jimenez4,5, Arjan W. Griffioen1, Patrycja Nowak-Sliwinska2,3,9*   1    Angiogenesis Laboratory, Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands; 2    Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland*; 3   Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland 4   Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands 5    OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands 6    Department of Visceral surgery, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland               7   Royal Free London NHS Foundation Trust, Renal Cancer Centre, UCL Division of Surgical and Interventional Science, London, UK 8   Netherlands Cancer Institute, Amsterdam, The Netherlands 9  Translational Research Centre in Oncohaematology, Geneva, Switzerland  Correspondence: <a href="mailto:Patrycja.Nowak-Sliwinska@unige.ch">Patrycja.Nowak-Sliwinska@unige.ch</a>

opencc-by-4.0Sep 2020View details →

Displacement accumulation and sampling of paleoearthquakes on active normal faults of Crete in the eastern Mediterranean

The Table S1 (uploaded separately) presents fault data and calculated values of earthquake parameters that underpin the interpretations and conclusions presented in Nicol et al. (G3, submitted June 20, 2020). The Locations of each fault are shown in Figure 2 of the main manuscript. In detail: The Table S1 summarises the attributes on all active faults studied on Crete. Single Event Displacement (SED), Recurrence Interval (RI), Moment Magnitude (Mw) and number of paeoearthquakes have been estimated for each fault using topographic fault lengths and Quaternary displacement rates in conjunction with the Wesnousky (2008) equations (see table footnote for equations used to calculate SED and Mw). Mw calculated using Wesnously (2008) equations are unconstrained at lengths < 15.5 km. Note that the short-term (e.g. the post-glacial period) displacement rates for the Lentas (ID=43) and South Central Crete (ID=44) faults derive from time periods of c. 50 kyr and 125 kyr, respectively (from Gallen et al., 2014). Nevertheless, the estimated number of events on these two faults correspond to the post-glacial period (16.5 kyr). Table S1 presents uncertainties of +40% and -20% for maximum displacements derived from topography. Here we are conservative and have allowed larger errors for the maximum fault displacements to account for greater errors associated with erosion. The calculated earthquake recurrence interval (RI) in Table S1 derives from SED/Quaternary displacement rate.

opencc-by-4.0Apr 2020View details →

Dataset of "Gravity Wave Activity in the Atmosphere of Mars During the 2018 Global Dust Storm: Simulations With a High-Resolution Model" (1/2)

This dataset contains the GrADS data of high-resolution Mars GCM results used for figures in the paper "Gravity Wave Activity in the Atmosphere of Mars During the 2018 Global Dust Storm: Simulations With a High-Resolution Model" by T. Kuroda, A.S. Medvedev and E. Yiğit. Each file with the name starting 'data' contains two-dimensional (X: longitude, Y: latitude) data of surface pressure (Ps) (unit: hPa) and dust opacity in infrared wavelength (tau), and three-dimensional (X: longitude, Y: latitude, Z:sigma-level) data of temperature (T) (unit: K), zonal wind velocity (u) (unit: m/s), meridional wind velocity (v) (unit: m/s) and vertical wind velocity (w) (unit: m/s), in snapshots of every 1/6 Sol for the periods of 30 degrees in Ls per a file as described below. The dust scenario implemented for producing this dataset is taken from Montabone et al. (2020), which is based on the observed dust opacity in Mars Year 24 (MY34). data180rdc-my34.tar.xz: for Ls=180-210 (49 Sols) data210rdc-my34.tar.xz: for Ls=210-240 (47 Sols) data240rdc-my34.tar.xz: for Ls=240-270 (46 Sols) The .tar.xz files can be extracted in Linux with 'tar Jxvf' command, and .grd and .ctl files with the same stem are generated. The file 'flux61ls5-my34.tar.xz' contains the three-dimensional fluxes and physical parameters calculated from the model output with the MY34 dust scenario. The contents are (T')^2, (u')^2, (v')^2, u'v', u'w', v'w' T(bar), u(bar), v(bar), squared Brunt-Vaisala frequency, and geopotential height. (bar) denotes the sum of the total wavenumber s=0-60 components, and the dash denotes the deviation from (bar), i.e. sum of the total wavenumber s=61-106 components. There are 36 time grids between Ls=182.5 and Ls=357.5 with the step of Ls=5 degrees. Kinetic and potential energies can be derived from these values using the formulae in the paper. The file 'flux61ls5-lowdust.tar.xz' is the same as 'flux61ls5-my34.tar.xz', except the model output with the 'low-dust' scenario (Kuroda et al., 2019; Kuroda, 2019a, 2019b). The file 'scripts.zip' contains the FORTRAN scripts to derive the fluxes and physical parameters equivalent to the file 'flux61ls5-my34.tar.xz' from the model outputs in this dataset and Kuroda (2020), i.e. data180rdc-my34.tar.xz, data210rdc-my34.tar.xz, data240rdc-my34.tar.xz, data270rdc-my34.tar.xz, data300rdc-my34.tar.xz and data330rdc-my34.tar.xz. Also, the fluxes and physical parameters equivalent to the file 'flux61ls5-lowdust.tar.xz' can be derived with those scripts from the model outputs data180rdc.tar.xz, data210rdc.tar.xz, data240rdc.tar.xz, data270rdc.tar.xz, data300rdc.tar.xz and data330rdc.tar.xz which are available in Kuroda (2019a, 2019b).

opencc-by-4.0Jul 2019View details →

Endoplasmic Reticulum Associated Aminopeptidase 2 (ERAP2) Is Released in the Secretome of Activated MDMs and Reduces in vitro HIV-1 Infection

Background: Haplotype-specific alternative splicing of the endoplasmic reticulum (ER) aminopeptidase type 2 (ERAP2) gene results in either full-length (FL, haplotype A) or alternatively spliced (AS, haplotype B) mRNA. HapA/HapA homozygous (HomoA) subjects show a reduced susceptibility to HIV-1 infection, probably secondary to the modulation of the antigen processing/presenting machinery. ERAP1 was recently shown to be secreted from the plasma membrane in response to activation; we investigated whether ERAP2 can be released as well and if the secreted form of this enzyme retains its antiviral function. Methods: Human monocyte derived macrophages (MDMs) were differentiated from peripheral blood mononuclear cells (PBMCs) isolated from 6 HomoA healthy controls and stimulated with IFNγ and LPS. ERAP2-FL secretion was evaluated by mass spectrometry. PBMCs (14 HomoA and 16 HomoB) and CD8-depleted PBMCs (CD8−PBMCs) (4 HomoA and 4 HomoB) were in vitro HIV-infected in the absence/presence of recombinant human ERAP2-FL (rhERAP2) protein; p24 viral antigen quantification was used to assess viral replication. IFNγ and CD69 mRNA expression, as well as the percentage of perforin-producing CD8+ T Lymphocytes, were analyzed 3 and 7-days post in vitro HIV-1-infection, respectively. The effect of rhERAP2 addition in cell cultures on T cell apoptosis, proliferation, activation, and maturation was evaluated as well on 24 h-stimulated PBMCs. Results: ERAP2 can be secreted from human MDMs in response to IFNγ/LPS stimulation. Notably, the addition of rhERAP2 to PBMC and CD8−PBMC cultures resulted in the reduction of viral replication, though these differences were statistically significant only in PBMCs (p < 0.05 in both HomoA and HomoB). This protective effect was associated with an increase in IFNγ and CD69 mRNA expression and in the percentage of perforin-expressing CD107+CD8+ cells. RhERAP2 addition also resulted in an increase in CD8+ activated lymphocyte (CD25+HLA−DRII+) and Effector Memory/Terminally differentiated CD8+ T cells ratio. Conclusions: This is the first report providing evidence for the release of ERAP2 in the secretome of immunocompetent cells. Data herein also indicate that exogenous ERAP2-FL exerts its protective function against HIV-1 infection, even in HomoB subjects who do not genetically produce it. Presumably, this defensive extracellular feature is only partially dependent on immune system modulation.