cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6557385
title: X-ray scattering data from Norway spruce at different moisture conditions

description: This data includes small and wide-angle X-ray scattering (SAXS, WAXS) intensities measured for Norway spruce (<em>Picea abies</em>) wood. The experiments were done in perpendicular transmission geometry, with the wood fiber axis roughly vertical and the radial direction of the wood tissue parallel to the X-ray beam, using a Xenocs Xeuss 3.0 C SAXS/WAXS device and Cu K-alpha radiation (wavelength 1.542 Å). The scattering patterns were recorded using an EIGER2 R 1M detector (pixel size 75 µm). The wood sample was measured first in wet state (saturated with water; "Wet"), and then equilibrated at different relative humidities (RH) in the following order: 95% ("RH95_1st"), 85% ("RH85"), 70% ("RH70"), 50% ("RH50_1st"), 20% ("RH20"), 10% ("RH10"), 50% ("RH50_2nd"), 95% ("RH95_2nd"). The sample-to-detector distance was 0.4139 m in SAXS, and 0.1528 m for the first 4 conditions (until "RH70") and 0.1525 m for the remaining 5 conditions in WAXS. Beam center (in detector pixels) was at x=540.6, y=667.0 (except y=635.0 in "RH70") in SAXS and x=1540, y=1521 in WAXS. For each of the 9 moisture conditions, files corresponding to 3 different processing steps are provided: "_bgsub_saxs.txt" and "_bgsub_waxs.txt" are ASCII files that contain the normalized and background-subtracted detector images (intensity in units mm^-1) corresponding to SAXS and WAXS, respectively. Pixels to be masked have the value "nan". "_bgsub_saxs_pol90.txt" and "_bgsub_waxs_pol90.txt" contain azimuthally regrouped images (90 bins in azimuthal angle) based on "_bgsub_saxs.txt" and "_bgsub_waxs.txt", respectively. PNG image files "_bgsub_saxs_pol.png" and "_bgsub_waxs_pol.png" are provided for reference. "_bgsub_pol90_ibg.txt" and "_bgsub_waxs_pol90_vert_ibg.txt" contain the equatorial and meridional anisotropic intensities, respectively, which were obtained from the azimuthally regrouped images by subtracting the isotropic scattering from the equatorial or meridional intensity (sector width 25°) at each value of the scattering vector <em>q</em>. The equatorial anisotropic intensities from SAXS and WAXS were merged by scaling the SAXS intensity, and the meridional anisotropic intensity is provided for the WAXS range only. The files contain columns for the magnitude of the scattering vector (q, unit Å<sup>-1</sup>), anisotropic intensity (I_ani, unit mm<sup>-1</sup>), error of anisotropic intensity (dI_ani, unit mm<sup>-1</sup>), and isotropic intensity (I_iso, unit mm<sup>-1</sup>). More detailed descriptions of the sample, the measurement, and the data processing can be found in the following reference:<br> Antti Paajanen, Aleksi Zitting, Lauri Rautkari, Jukka A. Ketoja, Paavo A. Penttilä. Nanoscale mechanism of moisture-induced swelling in wood microfibril bundles. <em>Nano Letters</em> 2022, 22(13): 5143–5150, DOI: 10.1021/acs.nanolett.2c00822
DOI: 10.5281/zenodo.6557384
title: X-ray scattering data from Norway spruce at different moisture conditions

description: This data includes small and wide-angle X-ray scattering (SAXS, WAXS) intensities measured for Norway spruce (<em>Picea abies</em>) wood. The experiments were done in perpendicular transmission geometry, with the wood fiber axis roughly vertical and the radial direction of the wood tissue parallel to the X-ray beam, using a Xenocs Xeuss 3.0 C SAXS/WAXS device and Cu K-alpha radiation (wavelength 1.542 Å). The scattering patterns were recorded using an EIGER2 R 1M detector (pixel size 75 µm). The wood sample was measured first in wet state (saturated with water; "Wet"), and then equilibrated at different relative humidities (RH) in the following order: 95% ("RH95_1st"), 85% ("RH85"), 70% ("RH70"), 50% ("RH50_1st"), 20% ("RH20"), 10% ("RH10"), 50% ("RH50_2nd"), 95% ("RH95_2nd"). The sample-to-detector distance was 0.4139 m in SAXS, and 0.1528 m for the first 4 conditions (until "RH70") and 0.1525 m for the remaining 5 conditions in WAXS. Beam center (in detector pixels) was at x=540.6, y=667.0 (except y=635.0 in "RH70") in SAXS and x=1540, y=1521 in WAXS. For each of the 9 moisture conditions, files corresponding to 3 different processing steps are provided: "_bgsub_saxs.txt" and "_bgsub_waxs.txt" are ASCII files that contain the normalized and background-subtracted detector images (intensity in units mm^-1) corresponding to SAXS and WAXS, respectively. Pixels to be masked have the value "nan". "_bgsub_saxs_pol90.txt" and "_bgsub_waxs_pol90.txt" contain azimuthally regrouped images (90 bins in azimuthal angle) based on "_bgsub_saxs.txt" and "_bgsub_waxs.txt", respectively. PNG image files "_bgsub_saxs_pol.png" and "_bgsub_waxs_pol.png" are provided for reference. "_bgsub_pol90_ibg.txt" and "_bgsub_waxs_pol90_vert_ibg.txt" contain the equatorial and meridional anisotropic intensities, respectively, which were obtained from the azimuthally regrouped images by subtracting the isotropic scattering from the equatorial or meridional intensity (sector width 25°) at each value of the scattering vector <em>q</em>. The equatorial anisotropic intensities from SAXS and WAXS were merged by scaling the SAXS intensity, and the meridional anisotropic intensity is provided for the WAXS range only. The files contain columns for the magnitude of the scattering vector (q, unit Å<sup>-1</sup>), anisotropic intensity (I_ani, unit mm<sup>-1</sup>), error of anisotropic intensity (dI_ani, unit mm<sup>-1</sup>), and isotropic intensity (I_iso, unit mm<sup>-1</sup>). More detailed descriptions of the sample, the measurement, and the data processing can be found in the following reference:<br> Antti Paajanen, Aleksi Zitting, Lauri Rautkari, Jukka A. Ketoja, Paavo A. Penttilä. Nanoscale mechanism of moisture-induced swelling in wood microfibril bundles. <em>Nano Letters</em> 2022, 22(13): 5143–5150, DOI: 10.1021/acs.nanolett.2c00822
DOI: 10.21227/yk0j-e526
title: Benchmark dataset for depth estimation from lightfield images

description: We propose a real world data set comprising light field images of 19 objects captured with the Lytro Illum camera in outdoor scenes and their corresponding 3D point clouds, as ground truth, captured with the 3dMD scanner. This data set allows more precise 3D pointcloud level comparison of algorithms for the task of depth estimation or 3D point cloud reconstruction from light field images.
DOI: 10.5281/zenodo.5721233
title: Supporting data to the paper "Modelling charge profiles of electric vehicles based on charges data"

description: This dataset contains the<em> underling data</em> and the <em>extended data</em> for the paper Modelling charge profiles of electric vehicles based on charges data”, submitted for consideration and open review in Open Research Europe. In the follow the description of the files is reported: HISTORIC DATA 2019 ELECTROLINERES AMB.csv: contains information on the charge events at the public charging points managed by the municipality in the metropolitan area of Barcelona in 2019. Fields are: charging point name; connector typology and number; charge start time; charge stop time; charge duration in minutes, energy delivered in kWh; vehicle manufacturer (optional); vehicle model (optional). STATIC INFORMATION CHARGING POINTS AMB 29042020.csv: contains the information about the public charging points of the metropolitan area of Barcelona. Fields are: charger typology (Quick/Normal); Charging point name and address; OCCP version; charger location; longitude; latitude; 7 flag fields for the connector type; observations; charging point maker. Lataustapahtumat, julkiset latauslaitteet 2019.csv: contains the information about the Turku Energia charge events for the city of Turku in 2019. Fields are: date of record creation, Station ID, Station name, charge start time, charge stop time, charge duration in minutes, energy delivered in Wh, Plug type (AC 22 kW/DC 50 kW), Cumulative energy delivered in the year (Wh), Average charge power (W) EV.csv: containes data on battery size retrived from vehicle datasheet or manufacturer website. Fields are: record ID, vehicle manufacturer ; vehicle model; battery size in kWh. Charge2019_EV_AMB.csv: contains the data on charge requests ( HISTORIC DATA 2019 ELECTROLINERES AMB.csv ) combined with the information on vehicle battery (EV.csv).
DOI: 10.5281/zenodo.5721232
title: Supporting data to the paper "Modelling charge profiles of electric vehicles based on charges data"

description: This dataset contains the<em> underling data</em> and the <em>extended data</em> for the paper Modelling charge profiles of electric vehicles based on charges data”, submitted for consideration and open review in Open Research Europe. In the follow the description of the files is reported: HISTORIC DATA 2019 ELECTROLINERES AMB.csv: contains information on the charge events at the public charging points managed by the municipality in the metropolitan area of Barcelona in 2019. Fields are: charging point name; connector typology and number; charge start time; charge stop time; charge duration in minutes, energy delivered in kWh; vehicle manufacturer (optional); vehicle model (optional). STATIC INFORMATION CHARGING POINTS AMB 29042020.csv: contains the information about the public charging points of the metropolitan area of Barcelona. Fields are: charger typology (Quick/Normal); Charging point name and address; OCCP version; charger location; longitude; latitude; 7 flag fields for the connector type; observations; charging point maker. Lataustapahtumat, julkiset latauslaitteet 2019.csv: contains the information about the Turku Energia charge events for the city of Turku in 2019. Fields are: date of record creation, Station ID, Station name, charge start time, charge stop time, charge duration in minutes, energy delivered in Wh, Plug type (AC 22 kW/DC 50 kW), Cumulative energy delivered in the year (Wh), Average charge power (W) EV.csv: containes data on battery size retrived from vehicle datasheet or manufacturer website. Fields are: record ID, vehicle manufacturer ; vehicle model; battery size in kWh. Charge2019_EV_AMB.csv: contains the data on charge requests ( HISTORIC DATA 2019 ELECTROLINERES AMB.csv ) combined with the information on vehicle battery (EV.csv).
DOI: 10.5281/zenodo.6546361
title: Full-Length Spatial Transcriptomics Reveals the Unexplored Isoform Diversity of the Myocardium Post-MI

description: We introduce Single-cell Nanopore Spatial Transcriptomics (scNaST), a software suite to facilitate the analysis of spatial gene expression from second- and third-generation sequencing, allowing to generate a full-length near-single-cell transcriptional landscape of the tissue microenvironment. Taking advantage of the Visium Spatial platform, we adapted a strategy recently developed to assign barcodes to long-read single-cell sequencing data for spatial capture technology. Here, we demonstrate our workflow using four short axis sections of the mouse heart following myocardial infarction. We constructed a <em>de novo</em> transcriptome using long-read data, and successfully assigned 19,794 transcript isoforms in total, including clinically-relevant, but yet uncharacterized modes of transcription, such as intron retention or antisense overlapping transcription. We showed a higher transcriptome complexity in the healthy regions, and identified intron retention as a mode of transcription associated with the infarct area. Our data revealed a clear regional isoform switching among differentially used transcripts for genes involved in cardiac muscle contraction and tissue morphogenesis. Molecular signatures involved in cardiac remodeling integrated with morphological context may support the development of new therapeutics towards the treatment of heart failure and the reduction of cardiac complications.
description: The data presented here contains all the files necessary to reproduce the analyses, as well as the published results. References to code and scripts are in the published manuscript. The file "gffcmp.multi_exons.annotated.gtf" is the de novo annotation. The file "satuRn_scnast_fact_regs.RDS" contains the results for the DTU analyses.
DOI: 10.5281/zenodo.6546360
title: Full-Length Spatial Transcriptomics Reveals the Unexplored Isoform Diversity of the Myocardium Post-MI

description: We introduce Single-cell Nanopore Spatial Transcriptomics (scNaST), a software suite to facilitate the analysis of spatial gene expression from second- and third-generation sequencing, allowing to generate a full-length near-single-cell transcriptional landscape of the tissue microenvironment. Taking advantage of the Visium Spatial platform, we adapted a strategy recently developed to assign barcodes to long-read single-cell sequencing data for spatial capture technology. Here, we demonstrate our workflow using four short axis sections of the mouse heart following myocardial infarction. We constructed a <em>de novo</em> transcriptome using long-read data, and successfully assigned 19,794 transcript isoforms in total, including clinically-relevant, but yet uncharacterized modes of transcription, such as intron retention or antisense overlapping transcription. We showed a higher transcriptome complexity in the healthy regions, and identified intron retention as a mode of transcription associated with the infarct area. Our data revealed a clear regional isoform switching among differentially used transcripts for genes involved in cardiac muscle contraction and tissue morphogenesis. Molecular signatures involved in cardiac remodeling integrated with morphological context may support the development of new therapeutics towards the treatment of heart failure and the reduction of cardiac complications.
description: The data presented here contains all the files necessary to reproduce the analyses, as well as the published results. References to code and scripts are in the published manuscript. The file "gffcmp.multi_exons.annotated.gtf" is the de novo annotation. The file "satuRn_scnast_fact_regs.RDS" contains the results for the DTU analyses.
DOI: 10.5281/zenodo.6790211
title: Dataset for a physical model characterizing visualization of the cervix during pelvic exams

description: This dataset accompanies our manuscript draft: <em>A physical model for improving visualization of the cervix during pelvic exams: A steppingstone towards reducing disparities in women's health</em>. <strong>Manuscript Draft Abstract</strong> Pelvic exams are frequently complicated by collapse of the lateral vaginal walls, obstructing the physician’s view of the cervix. A commonly utilized method in the clinical setting, passed down from mentors to trainees, is repurposing either a condom or a glove as a sheath placed over the speculum blades to retract the lateral vaginal walls during the exam. Despite their regular use in clinical practice, little research has been done comparing the relative efficacy of these methods. Better visualization of the cervix can benefit patients by decreasing examination-related discomfort, aiding in cancer screening, and preventing the need to move the examination to the operating room under general anesthesia. This study presents a physical model that simulates vaginal pressure being exerted around a speculum. Using it, we then compare the efficacy of different condom types, glove materials, glove sizes, and methods of application onto the speculum. The results showed that condoms provided minimal lateral wall retraction, while vinyl-material gloves with the speculum placed into the third finger had the best lateral wall retraction. However, the nitrile-material gloves are overall preferred over the vinyl gloves as they provided adequate lateral wall retraction without applying a significant vertical compressive effect on the speculum, and thus had overall better cervical visualization. Glove size had minimal impact. This study serves as a guide for clinicians as they use tools commonly found in a clinical setting to perform difficult pelvic exams. We recommend that clinicians consider the use of a nitrile glove as a sheath around a speculum. Additionally, this study demonstrates proof-of-concept of a physical model that can quantitatively describe different materials on their ability to improve cervical visualization. This model can be used in future research with more speculum and material combinations, including with materials custom-designed materials for this purpose.
DOI: 10.5281/zenodo.6790210
title: Dataset for a physical model characterizing visualization of the cervix during pelvic exams

description: This dataset accompanies our manuscript draft: <em>A physical model for improving visualization of the cervix during pelvic exams: A steppingstone towards reducing disparities in women's health</em>. <strong>Manuscript Draft Abstract</strong> Pelvic exams are frequently complicated by collapse of the lateral vaginal walls, obstructing the physician’s view of the cervix. A commonly utilized method in the clinical setting, passed down from mentors to trainees, is repurposing either a condom or a glove as a sheath placed over the speculum blades to retract the lateral vaginal walls during the exam. Despite their regular use in clinical practice, little research has been done comparing the relative efficacy of these methods. Better visualization of the cervix can benefit patients by decreasing examination-related discomfort, aiding in cancer screening, and preventing the need to move the examination to the operating room under general anesthesia. This study presents a physical model that simulates vaginal pressure being exerted around a speculum. Using it, we then compare the efficacy of different condom types, glove materials, glove sizes, and methods of application onto the speculum. The results showed that condoms provided minimal lateral wall retraction, while vinyl-material gloves with the speculum placed into the third finger had the best lateral wall retraction. However, the nitrile-material gloves are overall preferred over the vinyl gloves as they provided adequate lateral wall retraction without applying a significant vertical compressive effect on the speculum, and thus had overall better cervical visualization. Glove size had minimal impact. This study serves as a guide for clinicians as they use tools commonly found in a clinical setting to perform difficult pelvic exams. We recommend that clinicians consider the use of a nitrile glove as a sheath around a speculum. Additionally, this study demonstrates proof-of-concept of a physical model that can quantitatively describe different materials on their ability to improve cervical visualization. This model can be used in future research with more speculum and material combinations, including with materials custom-designed materials for this purpose.
DOI: 10.34740/kaggle/dsv/4014402
title: Dutch News Articles
DOI: 10.5281/zenodo.6947782
title: Training material for Genome assembly quality control (Galaxy Training Network tutorial)

description: This Zenodo repository includes the required datasets for following the GTN: Genome assembly quality control.
DOI: 10.5281/zenodo.6947781
title: Training material for Genome assembly quality control (Galaxy Training Network tutorial)

description: This Zenodo repository includes the required datasets for following the GTN: Genome assembly quality control.
DOI: 10.17036/researchdata.aston.ac.uk.00000575
title: Bandwidth extension in a mid-link optical phase conjugation using higher order Raman amplification with a single FBG
DOI: 10.5281/zenodo.5559624
title: openSAHE: Open Source Statistical Anatomical Atlas of the Human head for Electrophysiology Applications (precomputed atlases)

description: Computed anatomical atlases of the human head at 100Hz, 1kHz 10kHz 100kHz and 1MHz. Electrical properties: resistivity, conductivity and relative permittivity in SI units. This dataset is part of the article 'Anatomical atlas of the upper part of the human head for electroencephalography and bioimpedance applications' by Moura, F, Beraldo R, Ferreira, L and Siltanen S, Physiological Measurement, Volume 42, Number 10, 2021. If you use any of these files, please add a reference to this article. Source code available at https://github.com/fsmMLK/openSAHE
description: {"references": ["Fernando S Moura et al 2021 Physiol. Meas. 42 105015"]}
DOI: 10.5281/zenodo.5559623
title: openSAHE: Open Source Statistical Anatomical Atlas of the Human head for Electrophysiology Applications (precomputed atlases)

description: Computed anatomical atlases of the human head at 100Hz, 1kHz 10kHz 100kHz and 1MHz. Electrical properties: resistivity, conductivity and relative permittivity in SI units. This dataset is part of the article 'Anatomical atlas of the upper part of the human head for electroencephalography and bioimpedance applications' by Moura, F, Beraldo R, Ferreira, L and Siltanen S, Physiological Measurement, Volume 42, Number 10, 2021. If you use any of these files, please add a reference to this article. Source code available at https://github.com/fsmMLK/openSAHE
description: {"references": ["Fernando S Moura et al 2021 Physiol. Meas. 42 105015"]}
DOI: 10.6084/m9.figshare.20410837
title: Python Jupyter Notebook from The Elbert range of magnetostrophic convection. I. Linear theory

description: The supplementary Python Jupyter Notebook allows the reader to recreate the main plots and to calculate the critical Rayleigh numbers, wave numbers and frequencies for stationary, oscillatory, and wallmode onset.
DOI: 10.6084/m9.figshare.20410837.v1
title: Python Jupyter Notebook from The Elbert range of magnetostrophic convection. I. Linear theory

description: The supplementary Python Jupyter Notebook allows the reader to recreate the main plots and to calculate the critical Rayleigh numbers, wave numbers and frequencies for stationary, oscillatory, and wallmode onset.