Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
375
datasets available to search
ShareScore release 0.9.0
Dataset results
375 results for “compactness”
Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending
<p>This repository contains the DNA affinity purification sequencing (DAP-seq) data, for two biological replicates, as used in the following manuscript:<br><br>Yimin Hu, Samuel Schwab, Silvia Deiss, Pedro Escudeiro, Joe D. Joiner, Marcus D. Hartmann, Andrei N. Lupas, Birte Hernandez Alvarez, Vikram Alva, and Remus T. Dame. 'Bacterial Histone HBb from <i>Bdellovibrio Bacteriovorus</i> Compacts DNA by Bending'. bioRxiv, 27 September 2023. https://doi.org/10.1101/2023.02.26.530074.<br><br>There are four types of data in this repository:</p><ul><li>Paired-end FASTQ files, containing the raw Illumina reads (<i>raw_reads</i> folder).</li><li>Raw read QC reports, generated by the nf-core/chipseq pipeline (<i>fastqc</i> folder).</li><li>BAM files, generated by the nf-core/chipseq pipeline (<i>bam</i> folder).</li><li>bigWig files, generated by the nf-core/chipseq pipeline (<i>bigwig</i> folder).</li></ul><p>Abstract:<br>Histones are essential for genome compaction and transcription regulation in eukaryotes, where they assemble into octamers to form the nucleosome core. In contrast, archaeal histones assemble into dimers that form hypernucleosomes upon DNA binding. Although histone homologs have recently been identified in bacteria, their DNA-binding characteristics remain largely unexplored. Our study reveals that the bacterial histone HBb is indispensable for the survival of <i>Bdellovibrio bacteriovorus</i>, suggesting critical roles in DNA organization and gene regulation. We also elucidate the crystal structure of the HBb dimer at 1.06 Å resolution and employ various biophysico-chemical approaches to show its ability to bind and compact DNA in a sequence-independent manner. This binding induces DNA bending, similar to that observed with bacterial HU/IHF family proteins. Finally, using DNA affinity purification and sequencing, we reveal that HBb binds along the entire genomic DNA of <i>B. bacteriovorus</i> without sequence specificity. These unique DNA-binding properties of bacterial histones, distinct from their archaeal and eukaryotic counterparts, highlight the diverse roles that histones can play in DNA organization across the domains of life.<br><br>To whom correspondence should be addressed (E-mail):<br>birte.hernandez@tuebingen.mpg.de, or vikram.alva@tuebingen.mpg.de, or rtdame@chem.leidenuniv.nl</p>
DNA large fragment deleting by compact, sequence-motif-free and specific TaqTth-hpRNA assisted with the microhomology-mediated end joining pathway
<p><span>A DNA editing tool TaqTth-hpRNA was developed in this study, composed of a compact recombinant TaqTth nuclease (832 aa) and a simple hairpin-RNA guiding probe (hpRNA). <em>In vitro</em> biochemical studies showed the TaqTth-hpRNA efficiently cleaves artificially synthesized ssDNA without stringent sequence motif like PAM. It can also cleave the genomic DNA of <em>E. coli</em> with ~80% efficiency. The TaqTth-hpRNA cleavage of genomic DNA in mammalian cells generated products with large fragment deletions mediated by the microhomology-mediated end joining (MMEJ) pathway. In addition, the cleavage was sensitive to mismatches in targeted regions, which was applied to specific damage of the <em>APP<sup>lon</sup></em> mutation in Alzheimer’s disease without disrupting the <em>APP<sup>wt</sup></em> locus. It is worth mentioning that the <em>APP<sup>lon</sup></em> sequence has only one base difference from that of <em>APP<sup>wt</sup></em>. The characteristics of small size, no PAM requirement, high specificity, and large deletion products make the TaqTth-hpRNA a potential therapeutic strategy for treating autosomal dominant disorders in the future.</span></p>
Impact of New Developments in the Commissioning of Operational Radiation Protección in Compact Proton Therapy Centers (CPTC)
<p>Proton therapy is in continuous ever evolving to improve its performance. Some prominent current trends involve cutting-edge delivery methods or building compact proton centers. New developments have a direct impact in radiation protection of proton facilities and actions should be developed continuously with the aim that new centers meet all the requirements. The study of radiological protection in multi-room centers has been widely studied elsewhere, however, compact centers have specific features that pose a challenge in radiation protection, and the present work suggest different contributions to the body of knowledge in these compact facilities. Compact Proton Therapy Centers (CPTC) act out latest advances in particles: Usually have one single room, small footprint and a standard configuration, higher radiation density (Sv/m<sup>2</sup>), using the most advanced equipment and machinery to reduce their size, the delivery mode of protons is Pencil Beam Scanning (PBS), and there is a mix of professional exposed workers (clinical and technical staff) in these centers.</p> <p>The present work is framed into the project Contributions to operational radiation protection and neutron dosimetry in compact proton therapy centers (CPTC), which is focused on assessing the impact of these innovations on the operational radiation protection and commissioning of the compact facilities. Thus, several tasks have been carried out over the last three years, as checking and evaluation of shielding, comparing ambient dose equivalent of several CPTC, analyzing activation with different types of concrete, and activation in machinery, air and water of the facility, characterizing wide range rem-meters and neutron area monitors to measure neutron fields, studying new proton delivery techniques and their neutron fields, or assessing personal dosemeters, among others. The aim of the work is to present outcomes achieved in the aforementioned areas. As a result, a commissioning process of the operational radiation protection in compact centers will be suggested, lined up with the requirements by the Spanish Regulatory Body.</p> <p>Considering topics as new methods of application of dose in development (proton arc therapy, flash-therapy with protons), new materials for barriers and shielding or recent radiation monitoring equipment, future works must be carried out to study their impact on operational radiation protection and recommendations such as ICRP Publication 127, Radiological Protection in Ion Beam Radiotherapy, should be updated periodically taking into account the new methods and technologies developed.</p>
Subsoil compaction susceptibility index (SCSI)
<p>The dataset provides a global map of subsoil compaction risk of arable land by farm machinery. The calculation is detailed in the publication entitled "Farm vehicles approaching weights of sauropods exceed safe mechanical limits for soil functioning" by Thomas Keller and Dani Or.</p> <p>Three variables are available in this repository at 0.1° x 0.1° resolution (~10 km):</p> <ol> <li>the soil precompression stress at 50 cm depth (.nc)</li> <li>the soil stress at 50 cm depth (.shp)</li> <li>the subsoil compaction susceptibility index (SCSI) for arable land (.nc)</li> </ol>
Data from: Severity of topsoil compaction controls the impact of skid trails on soil ecological processes
<p>Skid trails are a major management-induced disturbance in temperate forest ecosystems with considerable impact on soil ecological processes that are so far poorly understood. In German forests, skid trails comprise 10 – 20 % of the forest area that is potentially affected by soil compaction through heavy machinery. We systematically investigated the influence of skid trails on physical, chemical, and microbiological soil parameters at 84 paired plots across four Central European forest types. In low mountain forests with steeper topography, skid trails had more drastic effects than in lowland forests. Skid trails in low mountain areas showed a decrease in the C to N ratio of microbial biomass (MBC/MBN), as well as increased microbial (MBC/SOC) and enzyme activities leading to faster carbon turnover (lower C/N, EOC/EN) and increased CO<sub>2</sub> losses (CO<sub>2</sub>/SOC) from the soil. The overall effects of the skid trails in lowland forests were small. On base-poor soils, we found an increase in the MBC/MBN ratio, while skid trails in base-rich lowland soils showed a reduction in CO<sub>2</sub>/SOC, suggesting a proportional increase in soil carbon storage. Regardless of region-specific effects, the relative increase in the bulk density of the fine soil was identified as a 'golden trait' that determined the effects of skid trails on many soil parameters, as shown by negative correlations with SOC, N, MBC, MBN, MBP, MBC/SOC and CO<sub>2</sub>/SOC and positive ones with the activities of certain hydrolytic enzymes.</p> <p>Synthesis and Applications: Our data clearly showed that carbon conversion processes and soil respiration leading to significant carbon and nutrient losses increased significantly on skid trails in low mountain regions with relatively steep slopes, which was in sharp contrast to lowland sites. The strong context dependence of our findings suggests that the mapping of soil conditions in terms of slope, substrate and moisture with high spatial resolution is mandatory to assess the vulnerability of sites to soil compaction by heavy machinery. Based on such vulnerability analysis, negative impacts can be minimized through the designation of permanently fixed skid trails, the technical adaptation of vehicles (e.g., wide base tyres) as well as careful planning and timing of management operations that should be restricted to dry weather and soil moisture conditions or periods of frost.</p>
Soil carbon maintained by perennial grasslands but lost in field crop systems over 30 years in a temperate Mollisol according to longitudinal, compaction-corrected, full-soil profile analysis
<p>To mitigate climate change, some seek to store carbon from the atmosphere in agricultural soils. However, our understanding of how agriculture affects soil organic carbon (SOC) is muddied by studies 1) lacking longitudinal data, 2) ignoring bulk density changes, or 3) sampling only surface soils. To better understand SOC trends, here we measured changes over 30 years in density-corrected, full-soil-depth (90 cm) SOC stocks under 6 cropping systems and a restored prairie in a Mollisol of southern Wisconsin, USA. Cash-grain systems and alfalfa-based systems lost SOC. Prairie and rotationally-grazed pasture maintained SOC. Average SOC losses for cash-grain and alfalfa-based systems were -0.82 (±0.12) and -0.64 (±0.17) Mg C ha<sup>-1</sup> yr<sup>-1</sup>, respectively. Sensitivity analysis showed that incomplete methodologies overestimated SOC improvements. Our findings using more comprehensive methods demonstrate the inadequacy of row-crop systems and the need for well-managed grasslands to protect SOC in productive agricultural soils of the Upper Midwest USA.</p>
IAM_COMPACT_Climate_Policy_Database
<div>This database serves as a general overview of energy and climate policies and policy targets in G20 countries, with the purpose of feeding IAMs and ESMs. The viability of applying policies may vary by model, and the type of inputs may vary from the ones displayed. Therefore, sources are included for each policy for modellers to find out the required details when necessary. In some cases, the overview displays "aspirational targets" apart from regular targets. This is because some stated targets are significantly far away from real-world advancement and the achievement of the "aspirational target" may therefore be unlikely according to tertairy sources (e.g. Climate Action Tracker).</div> <div> </div> <div>For corrections and additional policies not included, contact Dirk-Jan van de Ven: dj.vandeven@bc3research.org</div>
IAM_COMPACT_NDCs_LTTs_Database
<p>This dataset contains Nationally Determined Contributions (NDCs) for 2030, and new long-term strategies (LTSs) for 2050, which were put in place in the run-up to, during, and after the COP26 conference. </p> <ul> <li>NDC targets reflect the level of short-term ambition to which most countries are dedicated to through law or policy, but with risks of falling short if dedication is not high enough and/or changes occur in the political landscape.</li> <li>Long-term targets (LTT) reflect the level of longer-term ambition which many countries have stated to fulfil their part in mitigating climate change, but in most cases not backed with an actual policy agenda. These will come on top of pledged NDC targets, to create another increased level of proposed ambition. These pledges will be included for each separate model region as a linear pathway from the 2030 NDC target (NDC_LTT). </li> </ul> <p> </p>
Dumps and Data for 'Compaction during fragmentation and bouncing produces realistic dust grain porosities in protoplanetary discs'
<div>This dataset contains the files required to recreate the Phantom simulations run in the publication Michoulier et al. 2024, A&A 688, A31.</div> <div>We have also included the dumps required to re-create Figures 10, 11, 14, 15, 16, D.1 and E.1.</div>
gwastro/1-ogc: v1.0 of the 1-OGC Catalog of Compact Binary Merger Candidates
<p>Introduction</p> <p>This repository contains the first Open Gravitational-wave Catalog (1-OGW), which is obtained by using the public data from Advanced LIGO's first observing run to search for compact-object binary mergers. Our analysis is based on new methods that improve the separation between signals and noise in matched-filter searches for gravitational waves from the merger of compact objects.</p> <p>We make available our complete catalog of events, including the sub-threshold population of candidates. The catalog contains approximately 150,000 candidate events. We note that since the vast majority of the events in the catalog are likely to be noise, we have provided information to rank and select candidate events. The three most significant signals in our catalog correspond to the binary black hole mergers <a href="https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.061102">GW150914</a>, <a href="https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.241103">GW151226</a>, and <a href="https://journals.aps.org/prd/abstract/10.1103/PhysRevD.93.122003">LVT151012</a>, respectively. We observe these signals at a true discovery rate of 99.92%. We find that LVT151012 alone has a 97.6% probability of being astrophysical in origin. No other significant binary black hole candidates are found, nor did we observe any significant binary neutron star or neutron star--black hole candidates.</p> <p>The catalog is stored in the file '1-OGC.hdf'. There are a variety of tools to access <a href="https://www.hdfgroup.org/">hdf files</a> from numerous computing languages. Here we will focus on access through python and <a href="www.h5py.org">h5py</a>.</p> <p>Analysis Details</p> <p>Details of the analysis are available in this <a href="https://arxiv.org/abs/1811.01921">preprint paper</a> and the configuration files needed to create the analysis workflows are provided in the <a href="https://github.com/gwastro/1-ogc/tree/master/workflow/configuration">workflow/configuration</a> directory.</p>
The OmegaWhite Survey for Short-period Variable Stars. V. Discovery of an Ultracompact Hot Subdwarf Binary with a Compact Companion in a 44-minute Orbit
<p>MESA inlists and run_star_extras associated with <a href="https://ui.adsabs.harvard.edu/?#abs/2017ApJ...851...28K">Kupfer et al. (2017)</a>. MESA version 9793.</p> <p>Publication DOI: <a href="https://doi.org/10.3847/1538-4357/aa9522">10.3847/1538-4357/aa9522</a></p>
Stylized urban landscapes optimized for compactness, climate regulation and vascular plant species richness
<p>The data set provides the output of a genetic algorithm optimizing a stylized urban region with respect to three target functions: urban compactness, climate regulation as an exemplary ecosystem service and vascular plant species richness as a measure of biodiversity.</p> <p>The optimisation varies the spatial allocation of three types of land cover blocks in a stylized urban region: high- and low-density and park blocks which consist of green and/or built-up cells. We systematically vary landscape composition at the block level, but keep city size constant.</p> <p>The data set is related to a publication submitted to Frontiers in Environmental Science.</p>
Neutrino Quantum Kinetics in Compact Objects
<p>This contains the codebase and data from "Neutrino Quantum Kinetics in<br> Compact Objects" by Sherwood Richers, Gail McLaughlin, Alexey<br> Vlasenko, and James P. Kneller. (2019, submitted to PrD)</p> <p>======================<br> All f.h5 file contents<br> ======================<br> r(cm) - proxy for the time (r=ct)<br> dr_block(cm) - proxy for the block timestep (dr=cdt). Stored for<br> recovery purposes<br> dr_int(cm) - proxy for the interaction integration timestep<br> (dr=cdt). Stored for recovery purposes.<br> dr_osc(cm) - proxy for the oscillation integration timestep<br> (dr=cdt). Stored for recovery purposes.<br> fmatrixf - dimensionless distribution function. Accessed with<br> [time][helicity][energy][flavor1][flavor2][0=real,1=imaginary]</p> <p>==================<br> Directory contents<br> ==================</p> <p>fiducial - simulation output from the fiducial case of a background<br> with rho=1e10g/ccm, T=10MeV, Ye=0.3, the HShen EOS, including<br> oscillations, neutrino absorption on nucleons and nuclei, inelastic<br> electron scattering, elastic nucleon scattering, electron-positron<br> pair production, effective-absorption nucleon-nucleon bremsstrahlung,<br> and neutrino-neutrino scattering and pair processes. Using 25 energy<br> bins covering up to 100 MeV.</p> <p>noosc_full - simulation output from the fiducial case with the same<br> circumstanses as above, except without oscillations and using 50<br> energy bins up to 100 MeV.</p> <p>noosc_supernova_background.dat - snapshot from a 1D core-collapse<br> supernova simulation. The only relevant<br> quantities are the radius (col. 2), density<br> (col. 3), electron fraction (col. 4),<br> temperature (col. 5), electron chemical<br> potential (col. 9), proton chemical potential<br> (col. 10), and neutron chemical potential<br> (col. 11)<br> <br> noosc_*_tdecohere.dat - decoherence time (col. 4) for neutrinos at<br> every radial point (col. 1), each helicity<br> (col. 2), and every energy (col. 3), using 50<br> energy bins at integer multiples of 2 MeV.</p> <p> full - calculations done including the full set of<br> collision interactions listed in fiducial.</p> <p> nonu4 - calculations done including the full set of<br> collision interactions listed in fiducial<br> except neutrino-neutrino scattering/pair<br> processes.</p>
Fundamental Limits From Chaos On Instability Time Predictions In Compact Planetary Systems
<p>REBOUND SimulationArchives analysed in Hussain & Tamayo (2019) Fundamental Limits From Chaos On Instability Time Predictions In Compact Planetary Systems. Dataset consists of a set of compact planetary configurations, and large ensembles of shadow trajectories from N-body simulations with initial conditions perturbed near machine precision to investigate the spread in instability times. Instructions and scripts for extracting the data and generating the plots in the paper can be found at https://github.com/Naireen/StabilitySetImage</p>
Energetic Compact Strokes as the Major Source of Downward Terrestrial Gamma-ray Flashes in Winter Thunderstorms
<p>ECS-TGF_10km.csv contains a list of ECSs in Figure 1. Raw FALMA waveforms of these ECSs are in FALMA_wave.zip. For each ECS, waveforms of one or two seconds recorded at one FALMA site are provided. Some waveform data contain a PPS pulse. See PPS_pulse.txt in FALMA_wave.zip for more details. The format of waveform data is described at https://tingwu.info/pylab/lab05.html.</p> <p>ECS_100km.csv contains a list of ECSs in Figure 5.</p>
IAM_COMPACT_Study_3_Geopolitics
<p>This dataset contains the underling raw data of IAM COMPACT "Study 3 - Geopolitics". </p> <p>This study aims to respond to the research question “What are the different cost, energy security and resilience metrics and how do they compare for different scenarios?” (it groups 4 policy questions) by assessing the effectiveness of transformational responses to Climate Change through a comparative analysis of socio-economic outcomes across different resilience scenarios. </p> <p>Disruptive events pose significant risks to socio-economic systems, necessitating a comprehensive framework to understand and address their potential impacts. Part of this study builds upon van Ginkel et al. proposed dimensions of transformational response and resilience to socio-economic impact, to create a novel matrix for exploring climate-related extremes and their socio-economic consequences.</p> <p>The resulting scenario matrix yields four distinct narratives: Business as Usual, Unadaptive Transformation, Incremental Resilience, and Effective Transformation. These narratives represent varying combinations of transformational response and resilience to socio-economic impacts, offering a nuanced perspective on potential future pathways. The Business as Usual scenario depicts a society with low transformation and resilience, while the Unadaptive Transformation narrative illustrates the pitfalls of narrow focus in climate change mitigation efforts. Incremental Resilience represents a society that achieves high resilience through expanding existing capacities rather than transformative changes. Finally, the Effective Transformation scenario embodies the ideal resilient future, characterized by significant, well-rounded transformations and high resilience to socio-economic impacts.</p> <p>This framework provides a valuable tool for policymakers, researchers, and stakeholders to assess the complex interplay between climate change tipping points and socio-economic systems, facilitating more informed decision-making and strategy development in the face of climate uncertainties.</p> <div></div> <p>Results of the study have been documented in D5.4 - Modelling out-of-ordinary extremes (DOI <a href="../doi/10.5281/zenodo.13840866">10.5281/zenodo.13840866</a>)</p>
IAM_COMPACT_Study_6_Interest_rates
<p>This dataset contains the underling raw data of IAM COMPACT "Study 6 - Interest rates".</p> <p>Models used to assess decarbonisation pathways typically assume a uniform cost of capital; such assumption, however, does not do justice to real-world conditions and may therefore lead to inaccurate policy recommendations. The study aims to explore how non-uniform weighted average cost of capital (WACC), i.e., the discount rate a company uses to estimate its net present value, could influence global decarbonisation pathways. </p> <p>The study builds on empirically calibrated WACC values by region and technology in global IAMs and expands the modelling analysis by exploring stakeholder-driven pathways of de-risking clean energy technologies and risking fossil fuels. As one of the largest uncertainties lies in the way WACC values are expected to evolve over time, the empirical estimates of baseline WACC values are combined with an expert-based approach to produce forward-looking scenarios of evolving WACCs over time. The study also attempts to incorporate a corrective justice dimension in its narratives, by assessing the impacts of risk underwriting for low-carbon investments through taxing corporate windfall profits for 2022 and distributing the revenue as subsidies towards high-risk regions.</p> <p>Results of the study have been documented in D5.6 - Behaviour, social and disruptive innovation (DOI <a href="../doi/10.5281/zenodo.12751959">10.5281/zenodo.12751959</a>)</p>
Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging
<p>Source data of paper "Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging" published on Nature Methods.</p>
Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging
<p>Source data of paper "Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging" published on Nature Methods.</p>
MargNet: Photometric identification of compact galaxies, stars and quasars
<p>This page contains the accompanying deep learning models, dataset and code for the paper on MargNet, titled "Photometric identification of compact galaxies, stars and quasars using multiple neural networks".</p> <p><strong>Deep Learning Models</strong>:</p> <p>MargNet is a deep learning-based classifier for identifying stars, quasars and compact galaxies using photometric parameters and images from the Sloan Digital Sky Survey. MargNet consists of a combination of Convolutional Neural Network (CNN) and Artificial Neural Network (ANN) architectures. The deep learning Keras model for each experiment was saved as an h5 file after training. All saved models (organised by different experiments, as described in the paper) are available in SavedModels.zip.</p> <p><strong>Dataset</strong>:</p> <p>Our dataset consists of 240,000 compact objects and an additional 150,000 faint objects consisting of an equal number of stars, galaxies and quasars. This data is available as NumPy arrays and CSV files, as described below:</p> <ul> <li>SDSS ObjID of each object (objlist.npy)</li> <li>SDSS 5-band images of each object cropped to 32*32 pixels (X.npy)</li> <li>The set of 24 photometric features for each object (dnnx.npy)</li> <li>The classification label for each object (y.npy)</li> <li>SDSS spreadsheet containing all the features from dnnx, labels from y, ObjIDs from objlist and a couple of more SDSS specific parameters (photofeatures.csv)</li> </ul> <p>The complete dataset (organised by different experiments, as described in the paper) is available in Dataset.zip.<br> (Note: objlist, X, dnnx and y are in the same order. So, objlist[0], X[0], dnnx[0] and y[0] correspond to the same object.)</p> <p><strong>Code</strong>:</p> <p>All our code was written in Python in the form of Jupyter Notebooks. A copy of our code has also been made available on <a href="https://github.com/sidchaini/MargNet">GitHub</a>, but not all files could be included on GitHub due to the storage limit. So a complete copy of the repository has also been mirrored here on Zenodo and is contained in MargNet_RepositoryMirror.tgz</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.