cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4121978
title: MicroED datasets from two proteinase K lamellae using a 20 micrometre C2 condenser aperture

description: These four diffraction data sets were used to determine the proteinase K structure from two crystalline lamellae by electron diffraction, as deposited in the PDB with id 6ZEV and published in https://doi.org/10.3389/fmolb.2020.00179 A script is provided that allows indexing of the diffraction spots using DIALS 3.1. This is adapted from the commands used to process the data for the publication, which used DIALS 1.10.
description: {"references": ["Beale, E. V., Waterman, D. G., Hecksel, C., van Rooyen, J., Gilchrist, J. B., Parkhurst, J. M., \u2026 Zhang, P. (2020). A Workflow for Protein Structure Determination From Thin Crystal Lamella by Micro-Electron Diffraction. Frontiers in Molecular Biosciences, 7(August), 1\u20139. https://doi.org/10.3389/fmolb.2020.00179"]}
DOI: 10.5281/zenodo.4121977
title: MicroED datasets from two proteinase K lamellae using a 20 micrometre C2 condenser aperture

description: These four diffraction data sets were used to determine the proteinase K structure from two crystalline lamellae by electron diffraction, as deposited in the PDB with id 6ZEV and published in https://doi.org/10.3389/fmolb.2020.00179 A script is provided that allows indexing of the diffraction spots using DIALS 3.1. This is adapted from the commands used to process the data for the publication, which used DIALS 1.10.
description: {"references": ["Beale, E. V., Waterman, D. G., Hecksel, C., van Rooyen, J., Gilchrist, J. B., Parkhurst, J. M., \u2026 Zhang, P. (2020). A Workflow for Protein Structure Determination From Thin Crystal Lamella by Micro-Electron Diffraction. Frontiers in Molecular Biosciences, 7(August), 1\u20139. https://doi.org/10.3389/fmolb.2020.00179"]}
DOI: 10.5281/zenodo.4121986
title: MicroED datasets from proteinase K nanocrystals using a 20 micrometre C2 condenser aperture

description: Eight diffraction data sets were used to determine the proteinase K structure from nanocrystals by electron diffraction, as deposited in the PDB with id 6ZET and published in https://doi.org/10.3389/fmolb.2020.00179 A script is provided that allows indexing of the diffraction spots using DIALS 3.1. This is adapted from the commands used to process the data for the publication, which used DIALS 1.10.
description: {"references": ["Beale, E. V., Waterman, D. G., Hecksel, C., van Rooyen, J., Gilchrist, J. B., Parkhurst, J. M., \u2026 Zhang, P. (2020). A Workflow for Protein Structure Determination From Thin Crystal Lamella by Micro-Electron Diffraction. Frontiers in Molecular Biosciences, 7(August), 1\u20139. https://doi.org/10.3389/fmolb.2020.00179"]}
DOI: 10.5281/zenodo.4121985
title: MicroED datasets from proteinase K nanocrystals using a 20 micrometre C2 condenser aperture

description: Eight diffraction data sets were used to determine the proteinase K structure from nanocrystals by electron diffraction, as deposited in the PDB with id 6ZET and published in https://doi.org/10.3389/fmolb.2020.00179 A script is provided that allows indexing of the diffraction spots using DIALS 3.1. This is adapted from the commands used to process the data for the publication, which used DIALS 1.10.
description: {"references": ["Beale, E. V., Waterman, D. G., Hecksel, C., van Rooyen, J., Gilchrist, J. B., Parkhurst, J. M., \u2026 Zhang, P. (2020). A Workflow for Protein Structure Determination From Thin Crystal Lamella by Micro-Electron Diffraction. Frontiers in Molecular Biosciences, 7(August), 1\u20139. https://doi.org/10.3389/fmolb.2020.00179"]}
DOI: 10.6084/m9.figshare.13135934
title: Spatially selective alpha oscillations reveal moment-by-moment trade-offs between working memory and attention (Behavior)

description: Behavioral data for the experiment reported in our paper:van Moorselaar, D., Foster, J.J., Sutterer, D.W., Theeuwes, J., Olivers, C.N.L. & Awh, E (2017). Spatially selective alpha oscillations reveal moment-by-moment trade-offs between working memory and attention. Journal of Cognitive Neuroscience.All details can be found on OSF: https://osf.io/56rzh/
DOI: 10.6084/m9.figshare.13135976
title: Hundred nanosecond molecular dynamics simulation of the G domain of K-Ras4B

description: (This is a public copy of https://figshare.com/s/453b1b215cf2f9270769)<br>This is a one hundred nanosecond simulation of the G domain of K-Ras4B (UNIPROT:P01116-2, residues 1-166). The simulation was generated using GROMACS v.4.6.5 with the AMBER99SB-ILDN forcefield (altered following doi:10.1002/jcc.10262, see References), TIP3P water and 0.15 M salt. The leap-frog integrator with 2 fs timestep was used. A v-rescale thermostat was used at 310 K, with two energy groups (protein+GTP+MG and water+salt) and a time constant of 0.1 ps. PME was used with a tolerance of 1e-5 for the coulomb interactions and a cutoff was used for the VdW interactions, both with a cutoff of 1.1 nm. A Parrinello-rahman barostat was applied with a reference pressure of 1 bar and a time constant of 1 ps. For more information take a look at md.mdp. Coordinates were saved every 1 nanosecond and waters were stripped, resulting in a trajectory of 101 snapshots. <br>The initial model was made using the G-domain of GppNHp bound H-Ras (PDB ID: 4EFL). The protein was converted using MODELLER v9.16(doi:10.1002/cpbi.3 , see References) and GppNHp was converted to GTP by hand.
DOI: 10.6084/m9.figshare.13135955
title: Antarctic moisture budgets

description: This dataset contains the results from the moisture budget calculations over the Antarctic based on the ERA-Interim reanalysis and four climate models (CESM2, CESM1-LE, ACCESS1-3 and NorESM1-M). More specifically, this dataset allows analyzing the contributions of the large-scale and synoptic-scale transport to the Antarctic snow accumulation.<br>The variables included in each file (NetCDF) are:<br> -DVIq6u6: the moisture convergence (i.e. -(P-E))<br> -DVIqmum: the moisture convergence associated with the large-scale circulation<br> -DVIqpup: the moisture convergence associated with the synoptic-scale events<br>Please contact Quentin Dalaiden (quentin.dalaiden@uclouvain.be) for more information.
DOI: 10.6084/m9.figshare.13135955.v1
title: Antarctic moisture budgets

description: This dataset contains the results from the moisture budget calculations over the Antarctic based on the ERA-Interim reanalysis and four climate models (CESM2, CESM1-LE, ACCESS1-3 and NorESM1-M). More specifically, this dataset allows analyzing the contributions of the large-scale and synoptic-scale transport to the Antarctic snow accumulation.<br>The variables included in each file (NetCDF) are:<br> -DVIq6u6: the moisture convergence (i.e. -(P-E))<br> -DVIqmum: the moisture convergence associated with the large-scale circulation<br> -DVIqpup: the moisture convergence associated with the synoptic-scale events<br>Please contact Quentin Dalaiden (quentin.dalaiden@uclouvain.be) for more information.
DOI: 10.5281/zenodo.4118757
title: All bins analyzed for JORG.

description: A dataset consisting of all bins considered by JORG as part of the paper.
DOI: 10.5281/zenodo.4118756
title: All bins analyzed for JORG.

description: A dataset consisting of all bins considered by JORG as part of the paper.
DOI: 10.5281/zenodo.3686381
title: MicroED datasets of spiro-O

description: MicroED datasets of spiro-O compound were collected using Talos Arctica (200 kV) with the CMOS camera Ceta. The stage was controlled using SerialEM and diffraction images were independently collected using Velox software. For this reason, only frames with constant rotation speed should be used for data processing. Rotation step (continuous) was ~0.95 or 1.52°/frame and tilt range was +/-15 or 30°. The calibrated camera length using Al powder was 793.52 (data 190719 & 190812) or 819.71 (data 190928) mm. Crystals belonged to space group <em>P</em>-1 with a~12.4, b~15.0, c~15.3 Å, α=79.6, β=83.7, γ=87.3°. Finally 25 datasets were merged at ~0.95 Å resolution (Hamada et al., 2020; CCDC 1986103). Collection condition: gun lens 4, spot 10, C2: parallel beam condition, 0.19 e/A^2/sec, total ~15 e/A^2 Note: EMD files (hdf5 format) were transparently compressed using h5repack -f SHUF -f GZIP=4 command to reduce file size. EMD file can be processed with DIALS using this dxtbx format file. Metadata (machine parameters, stage tilt angles etc.) is stored as json format in /Data/Image/*/Metadata in emd file. See here for details.
DOI: 10.5281/zenodo.3686380
title: MicroED datasets of spiro-O

description: MicroED datasets of spiro-O compound were collected using Talos Arctica (200 kV) with the CMOS camera Ceta. The stage was controlled using SerialEM and diffraction images were independently collected using Velox software. For this reason, only frames with constant rotation speed should be used for data processing. Rotation step (continuous) was ~0.95 or 1.52°/frame and tilt range was +/-15 or 30°. The calibrated camera length using Al powder was 793.52 (data 190719 & 190812) or 819.71 (data 190928) mm. Crystals belonged to space group <em>P</em>-1 with a~12.4, b~15.0, c~15.3 Å, α=79.6, β=83.7, γ=87.3°. Finally 25 datasets were merged at ~0.95 Å resolution (Hamada et al., 2020; CCDC 1986103). Collection condition: gun lens 4, spot 10, C2: parallel beam condition, 0.19 e/A^2/sec, total ~15 e/A^2 Note: EMD files (hdf5 format) were transparently compressed using h5repack -f SHUF -f GZIP=4 command to reduce file size. EMD file can be processed with DIALS using this dxtbx format file. Metadata (machine parameters, stage tilt angles etc.) is stored as json format in /Data/Image/*/Metadata in emd file. See here for details.
DOI: 10.5281/zenodo.4122003
title: Human Stromal Antigen 1 (STAG1) Cohesin Subunit SA-1; A Target Enabling Package

description: Loss of function mutations in the cohesin subunit gene STAG2 are common in a variety of cancers (1). These cells become dependent on the paralogous cohesin subunit STAG1 (2-4). Mutants of STAG1 that disrupt the binding to the cohesin subunit RAD21 cannot complement the loss of STAG2. This TEP examines the druggability of STAG1 as a synthetic lethal strategy to treat <em>stag2<sup>-</sup></em> cancers. The TEP includes crystal structures of two domains of STAG1, alone and in complex with Rad21-rderived peptides. We performed screens of a fragment library and identified small molecules bound to pockets in the two domains of STAG1. We also developed assays for binding of RAD21 peptides to STAG1, which can be used to screen for molecules that disrupt binding.
DOI: 10.5281/zenodo.3366892
title: MicroED datasets of hemin and biotin collected on Ceta camera

description: MicroED datasets of hemin and biotin microcrystals were collected using Talos Arctica (200 kV) with the CMOS camera Ceta. The stage was controlled using SerialEM and diffraction images were independently collected using Velox software. For this reason, only frames with constant rotation speed should be used for data processing. Rotation step (continuous) was ~1.52°/frame and each dataset consisted of ~40 images (tilt range is +/-30°). The calibrated camera length using Al powder was 793.52 mm. Biotin crystals belonged to space group <em>P</em>2<sub>1</sub>2<sub>1</sub>2<sub>1</sub> with a~5.2, b~10.2, c~20.8 Å. ~14 datasets could be merged at ~0.85 Å resolution. Hemin crystals belonged to space group <em>P</em>-1 with a~10.6, b~11.1, c~13.8 Å, α~107.1°, b~99.5°, c~107.9°. ~12 datasets could be merged at ~0.9 Å resolution. Collection conditions: biotin: gun lens 8.0, spot 11, C2: parallel beam condition, 0.039e/A^2/sec, total ~3.5e/A^2 hemin: gun lens 4.0, spot 11, C2: parallel beam condition, 0.095e/A^2/sec, total ~8.6e/A^2 Note: emd files (hdf5 format) were transparently compressed using h5repack -f SHUF -f GZIP=4 command to reduce file size. EMD file can be processed with DIALS using this dxtbx format file. Metadata (machine parameters, stage tilt angles etc.) is stored as json format in /Data/Image/*/Metadata in emd file. See here for details. If you want to process data using DIALS, please see the processing note.
DOI: 10.5281/zenodo.3366891
title: MicroED datasets of hemin and biotin collected on Ceta camera

description: MicroED datasets of hemin and biotin microcrystals were collected using Talos Arctica (200 kV) with the CMOS camera Ceta. The stage was controlled using SerialEM and diffraction images were independently collected using Velox software. For this reason, only frames with constant rotation speed should be used for data processing. Rotation step (continuous) was ~1.52°/frame and each dataset consisted of ~40 images (tilt range is +/-30°). The calibrated camera length using Al powder was 793.52 mm. Biotin crystals belonged to space group <em>P</em>2<sub>1</sub>2<sub>1</sub>2<sub>1</sub> with a~5.2, b~10.2, c~20.8 Å. ~14 datasets could be merged at ~0.85 Å resolution. Hemin crystals belonged to space group <em>P</em>-1 with a~10.6, b~11.1, c~13.8 Å, α~107.1°, b~99.5°, c~107.9°. ~12 datasets could be merged at ~0.9 Å resolution. Collection conditions: biotin: gun lens 8.0, spot 11, C2: parallel beam condition, 0.039e/A^2/sec, total ~3.5e/A^2 hemin: gun lens 4.0, spot 11, C2: parallel beam condition, 0.095e/A^2/sec, total ~8.6e/A^2 Note: emd files (hdf5 format) were transparently compressed using h5repack -f SHUF -f GZIP=4 command to reduce file size. EMD file can be processed with DIALS using this dxtbx format file. Metadata (machine parameters, stage tilt angles etc.) is stored as json format in /Data/Image/*/Metadata in emd file. See here for details. If you want to process data using DIALS, please see the processing note.
DOI: 10.6084/m9.figshare.13061525.v1
title: Influence of Patient Characteristics on Chimeric Antigen Receptor T Cell Therapy in B-cell Acute Lymphoblastic Leukemia

description: This is the Source Data of the paper titled “Influence of Patient Characteristics on Chimeric Antigen Receptor T Cell Therapy in B-cell Acute Lymphoblastic Leukemia”.<br>
DOI: 10.5281/zenodo.4122023
title: Human Stromal Antigen 1 (STAG1) Cohesin Subunit SA-1; A Target Enabling Package

description: Loss of function mutations in the cohesin subunit gene STAG2 are common in a variety of cancers (1). These cells become dependent on the paralogous cohesin subunit STAG1 (2-4). Mutants of STAG1 that disrupt the binding to the cohesin subunit RAD21 cannot complement the loss of STAG2. This TEP examines the druggability of STAG1 as a synthetic lethal strategy to treat <em>stag2<sup>-</sup></em> cancers. The TEP includes crystal structures of two domains of STAG1, alone and in complex with Rad21-rderived peptides. We performed screens of a fragment library and identified small molecules bound to pockets in the two domains of STAG1. We also developed assays for binding of RAD21 peptides to STAG1, which can be used to screen for molecules that disrupt binding.
DOI: 10.5281/zenodo.3245308
title: Human Stromal Antigen 1 (STAG1) Cohesin Subunit SA-1; A Target Enabling Package

description: Loss of function mutations in the cohesin subunit gene STAG2 are common in a variety of cancers (1). These cells become dependent on the paralogous cohesin subunit STAG1 (2-4). Mutants of STAG1 that disrupt the binding to the cohesin subunit RAD21 cannot complement the loss of STAG2. This TEP examines the druggability of STAG1 as a synthetic lethal strategy to treat <em>stag2<sup>-</sup></em> cancers. The TEP includes crystal structures of two domains of STAG1, alone and in complex with Rad21-rderived peptides. We performed screens of a fragment library and identified small molecules bound to pockets in the two domains of STAG1. We also developed assays for binding of RAD21 peptides to STAG1, which can be used to screen for molecules that disrupt binding.
DOI: 10.5281/zenodo.4122025
title: Eyes wide shut: how visual cues affect brain patterns of simulated gait.

description: In the last 20 years, motor imagery (MI) has been extensively used to train motor abil- ities in sport and in rehabilitation. However, MI procedures are not all alike as much as their potential beneficiaries. Here we assessed whether the addition of visual cues could make MI performance more comparable with explicit motor performance in gait tasks. With fMRI we also explored the neural correlates of these experimental manipulations. We did this in elderly subjects who are known to rely less on kines- thetic information while favoring visual strategies during motor performance. Con- trary to expectations, we found that the temporal coupling between execution and imagery times, an index of the quality of MI, was less precise when participants were allowed to visually explore the environment. While the brain activation patterns of the gait motor circuits were very similar in both an open-eyed and eye-shut virtual walking MI task, these differed for a vast temporo-occipito-parietal additional activa- tion for open-eyed MI. Crucially, the higher was the activity in this posterior network, the less accurate was the MI performance with eyes open at a clinical test of gait. We conclude that both visually-cued and internally-cued MI are associated with the neurofunctional activation of a gait specific motor system. The less precise behavioral coupling between imagined and executed gait while keeping eyes open may be attributed to the processing load implied in visual monitoring and scanning of the environment. The implications of these observations for rehabilitation of gait with MI are discussed.
DOI: 10.5281/zenodo.4122024
title: Eyes wide shut: how visual cues affect brain patterns of simulated gait.

description: In the last 20 years, motor imagery (MI) has been extensively used to train motor abil- ities in sport and in rehabilitation. However, MI procedures are not all alike as much as their potential beneficiaries. Here we assessed whether the addition of visual cues could make MI performance more comparable with explicit motor performance in gait tasks. With fMRI we also explored the neural correlates of these experimental manipulations. We did this in elderly subjects who are known to rely less on kines- thetic information while favoring visual strategies during motor performance. Con- trary to expectations, we found that the temporal coupling between execution and imagery times, an index of the quality of MI, was less precise when participants were allowed to visually explore the environment. While the brain activation patterns of the gait motor circuits were very similar in both an open-eyed and eye-shut virtual walking MI task, these differed for a vast temporo-occipito-parietal additional activa- tion for open-eyed MI. Crucially, the higher was the activity in this posterior network, the less accurate was the MI performance with eyes open at a clinical test of gait. We conclude that both visually-cued and internally-cued MI are associated with the neurofunctional activation of a gait specific motor system. The less precise behavioral coupling between imagined and executed gait while keeping eyes open may be attributed to the processing load implied in visual monitoring and scanning of the environment. The implications of these observations for rehabilitation of gait with MI are discussed.
DOI: 10.34740/kaggle/dsv/1583651
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.6084/m9.figshare.11467374.v8
title: Supporting information. Homonyms and hemihomonyms dataset: A source of errors in the Big Data Era

description: Supporting InformationArticle: TAXONOMIC NOMENCLATURE IN THE BIG DATA ERABy: Sánchez-González, Jorge-Rubén<br>It consists on a preliminary register of existing homonyms and/or hemihomonyms.
DOI: 10.5281/zenodo.4122051
title: The Importance of Cognitive Executive Functions in Gait Recovery After Total Hip Arthroplasty

description: Objective: To determine the influence of cognitive functioning on gait recovery after total hip arthroplasty.<br> Design: Prospective cohort study.<br> Setting: Rehabilitation hospital.<br> Participants: Patients (NZ40) who underwent a total hip arthroplasty, with normal cognitive functioning and without any other relevant medical condition, were recruited and studied before surgery and at the beginning and the end of the rehabilitation program.<br> Main Outcome Measures: Gait speed (10-Meter Walk Test [10MWT]) and gait functional mobility (Timed Up and Go [TUG] test), measured at the time of discharge from the rehabilitation unit, were the primary outcomes. The candidate predictors were the cognitive and psychological variables collected in the presurgery phase, together with other potentially informative measures such as age, education, perceived pain, body mass index, presurgical gait speed and functional mobility.<br> Results: Our results suggest the existence of a direct relationship between cognitive functioning, with specific reference to high-level frontal executive functions, and the postoperative gait progress: the better the cognitive functioning in the preoperative phase, the better the course of recovery in terms of gait speed and functional mobility.<br> In particular, the performance of the Frontal Assessment Battery test, together with age, perceived pain. Presurgical gait speed and functional mobility, was the best predictor of recovery of walking measured by 10MWT and TUG.<br> Conclusions: The present study highlights the importance of cognitive functioning, together with clinical and demographic features, in the postsurgical recovery of walking, even in the absence of cognitive decline.<br> In particular, these data show the crucial role of higher-order cognitive processes, such as executive functions, involved in the formulation of motor plans and their integration with proprioceptive and visual cues.
DOI: 10.5281/zenodo.4122050
title: The Importance of Cognitive Executive Functions in Gait Recovery After Total Hip Arthroplasty

description: Objective: To determine the influence of cognitive functioning on gait recovery after total hip arthroplasty.<br> Design: Prospective cohort study.<br> Setting: Rehabilitation hospital.<br> Participants: Patients (NZ40) who underwent a total hip arthroplasty, with normal cognitive functioning and without any other relevant medical condition, were recruited and studied before surgery and at the beginning and the end of the rehabilitation program.<br> Main Outcome Measures: Gait speed (10-Meter Walk Test [10MWT]) and gait functional mobility (Timed Up and Go [TUG] test), measured at the time of discharge from the rehabilitation unit, were the primary outcomes. The candidate predictors were the cognitive and psychological variables collected in the presurgery phase, together with other potentially informative measures such as age, education, perceived pain, body mass index, presurgical gait speed and functional mobility.<br> Results: Our results suggest the existence of a direct relationship between cognitive functioning, with specific reference to high-level frontal executive functions, and the postoperative gait progress: the better the cognitive functioning in the preoperative phase, the better the course of recovery in terms of gait speed and functional mobility.<br> In particular, the performance of the Frontal Assessment Battery test, together with age, perceived pain. Presurgical gait speed and functional mobility, was the best predictor of recovery of walking measured by 10MWT and TUG.<br> Conclusions: The present study highlights the importance of cognitive functioning, together with clinical and demographic features, in the postsurgical recovery of walking, even in the absence of cognitive decline.<br> In particular, these data show the crucial role of higher-order cognitive processes, such as executive functions, involved in the formulation of motor plans and their integration with proprioceptive and visual cues.
DOI: 10.5281/zenodo.4122059
title: Meneame news dataset

description: This dataset contains 150 news scrapped from Meneame from time range 17-10-2020 to 20-10-2020
DOI: 10.5281/zenodo.4122058
title: Meneame news dataset

description: This dataset contains 150 news scrapped from Meneame from time range 17-10-2020 to 20-10-2020