cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5851379
title: ClevrTex: A Texture-Rich Benchmark for Unsupervised Multi-Object Segmentation

description: There has been a recent surge in methods that aim to decompose and segment scenes into multiple objects in an unsupervised manner, i.e., unsupervised multi-object segmentation. Performing such a task is a long-standing goal of computer vision, offering to unlock object-level reasoning without requiring dense annotations to train segmentation models. Despite significant progress, current models are developed and trained on visually simple scenes depicting mono-colored objects on plain backgrounds. The natural world, however, is visually complex with confounding aspects such as diverse textures and complicated lighting effects. In this study, we present a new benchmark called ClevrTex, designed as the next challenge to compare, evaluate and analyze algorithms. ClevrTex features synthetic scenes with diverse shapes, textures and photo-mapped materials, created using physically based rendering techniques. ClevrTex has 50k examples depicting 3-10 objects arranged on a background, created using a catalog of 60 materials, and a further test set featuring 10k images created using 25 different materials. We benchmark a large set of recent unsupervised multi-object segmentation models on ClevrTex and find all state-of-the-art approaches fail to learn good representations in the textured setting, despite impressive performance on simpler data. We also create variants of the ClevrTex dataset, controlling for different aspects of scene complexity, and probe current approaches for individual shortcomings. Project webpage: https://www.robots.ox.ac.uk/~vgg/data/clevrtex/ These are <strong>the variant datasets</strong>. Please see project page for links to the main dataset.
DOI: 10.25345/c5zg35
title: MassIVE MSV000088684 - MicroID: A Novel Biotin Ligase Enables Rapid Proximity Ligation Proteomics
title: Identifying protein-protein interactions is central to dissecting signaling and regulatory processes in cells. BioID is a proximity ligation method that uses a promiscuous biotin ligase to detect protein&#45;protein interactions in cells in a highly reproducible manner. Recent advancements in proximity ligation tools have improved efficiency and timing of labeling, allowing for measurement of interactions on a cellular timescale. However&#44; issues of size, stability&#44; and background labeling of these constructs persist. Here we modified the structure of BioID2 to create a smaller&#44; highly active&#44; biotin ligase that we named MicroID. Truncation of the c&#45;terminal of BioID2 and mutations to alleviate blockage of biotin&#47;ATP binding at the active site of BioID2 resulted in a smaller&#44; highly active construct with lower baseline labeling. Several additional point mutations improved the function of our modified MicroID construct compared to BioID2 and other biotin ligases&#44; including TurboID and miniTurbo. MicroID is the smallest biotin ligase &#40;180 AA for microID vs. 257 AA for miniTurbo and 338 AA for TurboID&#41; yet it demonstrates only slightly less labeling activity than TurboID and outperforms miniTurboID. MicroID also had lower background labeling than TurboID. For experiments where precise temporal control of labeling is essential, we developed a MicroID mutant that has lower labeling efficiency&#44; but significantly reduced biotin scavenging compared to BioID2. Finally&#44; we demonstrate utility of MicroID in mass spectrometry experiments by localizing MicroID constructs to subcellular organelles and measuring protein-protein interactions.
DOI: 10.6084/m9.figshare.18441998
title: Cellular Lifespan Study Data

description: The current study provides a multimodal molecular map across the entire replicative lifespan of primary human fibroblast cell lines from n=6 healthy male and female donors and n=3 donors with lifespan-altering mitochondrial disease caused by mutations in the SURF1 gene. These data include cytological (cell size, morphology), bioenergetic (energy expenditure, derived ATP synthesis rates from Seahorse), secreted proteins, telomere length, and whole-genome sequencing (WGS) data. These datasets can be integrated with other omic measures collected in parallel along the cellular lifespan, including gene expression (RNA sequencing) and DNA methylation (GSE179849).This dataset also includes experimental manipulations with treatments targeting oxidative phosphorylation (OXPHOS) and glycolysis, and glucocorticoid signaling, providing an opportunity to examine the influence of stress and bioenergetics on human aging biology. All processed data can be accessed and browsed at our webtool: https://columbia-picard.shinyapps.io/shinyapp-Lifespan_Study/. A detailed description of the study and associated methods can be found at: https://www.biorxiv.org/content/10.1101/2021.11.12.468448
DOI: 10.6084/m9.figshare.18441998.v1
title: Lifespan Study Data

description: The current study provides a multimodal molecular map across the entire replicative lifespan of primary human fibroblast cell lines from n=6 healthy male and female donors and n=3 donors with lifespan-altering mitochondrial disease caused by mutations in the SURF1 gene. These data include cytological (cell size, morphology), bioenergetic (energy expenditure, derived ATP synthesis rates from Seahorse), secreted proteins, telomere length, and whole-genome sequencing (WGS) data. These datasets can be integrated with other omic measures collected in parallel along the cellular lifespan, including gene expression (RNA sequencing) and DNA methylation (GSE179849).This dataset also includes experimental manipulations with treatments targeting oxidative phosphorylation (OXPHOS) and glycolysis, and glucocorticoid signaling, providing an opportunity to examine the influence of stress and bioenergetics on human aging biology. All processed data can be accessed and browsed at our webtool: https://columbia-picard.shinyapps.io/shinyapp-Lifespan_Study/. A detailed description of the study and associated methods can be found at: https://www.biorxiv.org/content/10.1101/2021.11.12.468448
DOI: 10.5281/zenodo.4750616
title: 20210512_JGRplanets_UranusMoonInduction

description: This dataset entails the Matlab .fig files containing the data illustrated in the draft manuscript submitted to JGR Planets on May 12, 2021, titled, "In Search of Subsurface Oceans within the Uranian Moons".
DOI: 10.5281/zenodo.5484442
title: 20210907_JGRplanets_TritonOceanDetection

description: This dataset contains the Matlab .mat structure files and associated .m script to produce the data illustrated in the manuscript submitted to JGR Planets in Sept. 2021, titled, "Single- and Multi-Pass Magnetometric Subsurface Ocean Detection and Characterization in Icy Worlds Using Principal Component Analysis: Application to Triton".
DOI: 10.5281/zenodo.5484441
title: 20210907_JGRplanets_TritonOceanDetection

description: This dataset contains the Matlab .mat structure files and associated .m script to produce the data illustrated in the manuscript submitted to JGR Planets in Sept. 2021, titled, "Single- and Multi-Pass Magnetometric Subsurface Ocean Detection and Characterization in Icy Worlds Using Principal Component Analysis: Application to Triton".
DOI: 10.5281/zenodo.5851676
title: Interpolated depth to water table (groundwater) maps for the continental United States

description: <strong>DATA:</strong> This is a collection of depth to water table maps with uncertainty estimates for the continental United States for years 1989 and 2019. Data used to create these maps were obtained from the National Ground-Water Monitoring Network (NGWMN). Data included 14,351 sites and 17,632,047 observations for the years 1989-2019. To improve our inference a set of auxiliary variables proven to have a relation with depth to water table were included. We paired point estimates of depth to water table data with environmental data, as well as terrain variables derived out of a base digital elevation model (DEM) created by NASA at a 1x1km resolution. Climatic layers (temperature, precipitation, and snow melt equivalent) for 1989-2019 were obtained from Daymet (Version 4), which provides a continuous grid of historical monthly and annual weather data, with a 1x1km spatial resolution (Thornton et al., 2020). Out of the DEM, primary (slope, aspect) and secondary terrain attributes (curvatures, upslope contributing areas) were used to calculate a compound topographic index (CTI). <strong>MODELING FRAMEWORK:</strong> Water table depth analyses were conducted using a three-step interpolation approach: 1) we utilized gradient boosted regression trees (GBRT) to make predictions, 2) we used kriging interpolation on GBRT residuals to reduce bias from spatial autocorrelation, to incorporate a spatial correlation structure and to create uncertainty maps, and 3) we then combined the GBRT and kriging predictions for the final map. This method is equivalent to a Universal Kriging, where in our case, we evaluated the trend using GBRT. Model metrics were calculated for the training (80% of the data) and validation (20% of the data) datasets to evaluate overall performance. *** Uncertainty is greater surrounding the 1989 interpolations due to a lower number of observations.
description: Please contact one of the co-authors for more information about this dataset.
DOI: 10.5281/zenodo.5851675
title: Interpolated depth to water table (groundwater) maps for the continental United States

description: <strong>DATA:</strong> This is a collection of depth to water table maps with uncertainty estimates for the continental United States for years 1989 and 2019. Data used to create these maps were obtained from the National Ground-Water Monitoring Network (NGWMN). Data included 14,351 sites and 17,632,047 observations for the years 1989-2019. To improve our inference a set of auxiliary variables proven to have a relation with depth to water table were included. We paired point estimates of depth to water table data with environmental data, as well as terrain variables derived out of a base digital elevation model (DEM) created by NASA at a 1x1km resolution. Climatic layers (temperature, precipitation, and snow melt equivalent) for 1989-2019 were obtained from Daymet (Version 4), which provides a continuous grid of historical monthly and annual weather data, with a 1x1km spatial resolution (Thornton et al., 2020). Out of the DEM, primary (slope, aspect) and secondary terrain attributes (curvatures, upslope contributing areas) were used to calculate a compound topographic index (CTI). <strong>MODELING FRAMEWORK:</strong> Water table depth analyses were conducted using a three-step interpolation approach: 1) we utilized gradient boosted regression trees (GBRT) to make predictions, 2) we used kriging interpolation on GBRT residuals to reduce bias from spatial autocorrelation, to incorporate a spatial correlation structure and to create uncertainty maps, and 3) we then combined the GBRT and kriging predictions for the final map. This method is equivalent to a Universal Kriging, where in our case, we evaluated the trend using GBRT. Model metrics were calculated for the training (80% of the data) and validation (20% of the data) datasets to evaluate overall performance. *** Uncertainty is greater surrounding the 1989 interpolations due to a lower number of observations.
description: Please contact one of the co-authors for more information about this dataset.
DOI: 10.5281/zenodo.5851687
title: Reddit WSB Annotated Dataset 2021

description: This is a WIP randomized sample of comments from the Wallstreetbets community on Reddit during the GameStop event during the 2021 rise. The sample contains 5000 observations of which 3000 were annotated and agreed upon by two annotators. The next 600 were annotated by two authors but due to time constraints, only 1 author corrected them. The remaining 1400 have only been annotated by one author and have not been compared. Annotations are broken into two main categories, support (the comment indicates some level of support for either the company GameStop, the stock price, or the narrative of 'us' vs 'them'.). Support can be either Y= Yes, N= No, U= Unsure, I= Informative. The second category, 'intent' indicates the individual has expressed intentions or interest in the stock, or has already purchased the stock during the event period. Intent can be either Y= Yes, N= No, M= Maybe, U= Unsure, or I= Informative.
DOI: 10.6084/m9.figshare.18429239.v1
title: VeroInf24h.all.fastq.tar.gz

description: The Chlorocebus sabaeus sample VeroInf24h.fastq is downloaded from https://osf.io/8f6n9/ on the Open Science Framework.
DOI: 10.6084/m9.figshare.18429239
title: VeroInf24h.all.fastq.tar.gz

description: The Chlorocebus sabaeus sample VeroInf24h.fastq is downloaded from https://osf.io/8f6n9/ on the Open Science Framework.
DOI: 10.5281/zenodo.5851689
title: Reddit WSB Annotated Dataset 2021

description: This is a WIP randomized sample of comments from the Wallstreetbets community on Reddit during the GameStop event during the 2021 rise. The sample contains 5000 observations of which 3000 were annotated and agreed upon by two annotators. The next 600 were annotated by two authors but due to time constraints, only 1 author corrected them. The remaining 1400 have only been annotated by one author and have not been compared. The second file is the annotation ruleset used to annotate the dataset, we briefly summarize the rules here: Annotations are broken into two main categories, support (the comment indicates some level of support for either the company GameStop, the stock price, or the narrative of 'us' vs 'them'.). Support can be either Y= Yes, N= No, U= Unsure, I= Informative. The second category, 'intent' indicates the individual has expressed intentions or interest in the stock, or has already purchased the stock during the event period. Intent can be either Y= Yes, N= No, M= Maybe, U= Unsure, or I= Informative.
DOI: 10.6084/m9.figshare.3761562.v2104
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.21227/s1gy-3v36
title: Learned Stereo

description: We present a passive stereo depth system that produces dense and accurate point clouds optimized for human environments, including dark, textureless, thin, reflective and specular surfaces and objects, at 2560x2048 resolution, with 384 disparities, in 30 ms. The system consists of an algorithm combining learned stereo matching with engineered filtering, a training and data-mixing methodology, and a sensor hardware design. Our architecture is 15x faster than approaches that perform similarly on the Middlebury and Flying Things Stereo Benchmarks. To effectively supervise the training of this model, we combine real data labelled using off-the-shelf depth sensors, as well as a number of different rendered, simulated labeled datasets. We demonstrate the efficacy of our system by presenting a large number of qualitative results in the form of depth maps and point-clouds, experiments validating the metric accuracy of our system and comparisons to other sensors on challenging objects and scenes. We also show the competitiveness of our algorithm compared to state-of-the-art learned models using the Middlebury and FlyingThings datasets.
DOI: 10.6084/m9.figshare.18444731
title: Brightfield Images for Cellular Lifespan Study

description: The current imaging dataset (n=~4000) provides brightfield images of cultured primary human fibroblasts (in vitro) aged through the cellular lifespan. The dataset was generated using the Fisherbrand™ Inverted Infinity and Phase Contrast Microscope (Fisher Scientific #11350119). Images were taken at 10x and 20x magnification before each passage. This provides morphological trajectories collected at high temporal frequency (every 5 days, ~21timepoints per a donor) across the entire replicative lifespan of fibroblast cell lines from n=6 healthy donors and n=3 donors with mitochondrial disease caused by mutations in the SURF1 gene. The dataset can be integrated with other measures collected in parallel along the lifespan, including bioenergetic, gene expression (RNA sequencing, GSE179848), DNA methylation(GSE179847), and whole-genome sequencing (WGS) data. All processed data can be accessed and browsed at our webtool: https://columbia-picard.shinyapps.io/shinyapp-Lifespan_Study/. The study is described in detail at: https://www.biorxiv.org/content/10.1101/2021.11.12.468448
DOI: 10.5281/zenodo.5849616
title: Dados da pesquisa denominada "DESAFIOS E NOVAS COMPETÊNCIAS DEMANDADAS NO CONTEXTO EDUCACIONAL DA PANDEMIA DE COVID-19"

description: Os dados foram coletados por intermédio do questionário online respondido por 146 professores, elaborado pelo Google Forms, com perguntas abertas e fechadas, encaminhado via e-mail. Aos moldes da Resolução nº 510 de 2016, foi ofertado aos participantes o Termo de Consentimento Livre Esclarecido (TCLE) e o projeto foi aprovado pelo CEP com CAAE N 43947821.8.0000.5188 e Número do Parecer 4.740.147.<br>
DOI: 10.5281/zenodo.5849615
title: Dados da pesquisa denominada "DESAFIOS E NOVAS COMPETÊNCIAS DEMANDADAS NO CONTEXTO EDUCACIONAL DA PANDEMIA DE COVID-19"

description: Os dados foram coletados por intermédio do questionário online respondido por 146 professores, elaborado pelo Google Forms, com perguntas abertas e fechadas, encaminhado via e-mail. Aos moldes da Resolução nº 510 de 2016, foi ofertado aos participantes o Termo de Consentimento Livre Esclarecido (TCLE) e o projeto foi aprovado pelo CEP com CAAE N 43947821.8.0000.5188 e Número do Parecer 4.740.147.<br>
DOI: 10.5281/zenodo.5851704
title: Supplementary Data for the manuscript 'The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia'

description: This dataset contains the supplementary data files for the manuscript titled 'The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia'.
description: This versions includes .md5 checksum files and fixes the broken archives from version 1.0 (due to a faulty SSD).
DOI: 10.5281/zenodo.5848247
title: Rivermead assessment of somatosensory performance: Italian normative data

description: Raw data collected and analysed for the paper 'Rivermead assessment of somatosensory performance: Italian normative data', published in Neurological Sciences (2021) 42:5149–5156
DOI: 10.5281/zenodo.5848246
title: Rivermead assessment of somatosensory performance: Italian normative data

description: Raw data collected and analysed for the paper 'Rivermead assessment of somatosensory performance: Italian normative data', published in Neurological Sciences (2021) 42:5149–5156
DOI: 10.34740/kaggle/dsv/3044895
title: US counties COVID 19 dataset
DOI: 10.5281/zenodo.5849252
title: Increased Cardiac Pi/PCr in the Diabetic Heart Observed Using Phosphorus Magnetic Resonance Spectroscopy at 7T

description: The uploaded data relate to the work of Valkovič et al. entitled "Increased Cardiac Pi/PCr in the Diabetic Heart Observed Using Phosphorus Magnetic Resonance Spectroscopy at 7T." submitted in 2022<br> The data consist of the anonymised in vivo data of healthy volunteers and T2DM patients, in Siemens DICOM format, acquired as described in the manuscript. The uploaded data also include all analysed STEAM data results with visualised MR spectra and fitted values of PCr and Pi, used for Pi/PCr calculation.
description: LV and CTR are funded by Sir Henry Dale Fellowships awarded jointly by the Wellcome Trust and the Royal Society [221805/Z/20/Z and 098436/Z/12/B, respectively]. AA is funded by a British Heart Foundation clinical research training fellowship [FS/17/18/32449]. AIS is funded by the Austrian Science Fund (FWF) Schrödinger Fellowship [J 4043]. SN acknowledges support from the Oxford NIHR Biomedical Research Centre and the Oxford British Heart Foundation Centre of Research Excellence. DJT acknowledges support from a British Heart Foundation Senior Fellowship (FS/19/18/34252). Support of the Slovak Grant Agencies VEGA [2/0003/20] and APVV [#19–0032] is also gratefully acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
DOI: 10.5281/zenodo.5849251
title: Increased Cardiac Pi/PCr in the Diabetic Heart Observed Using Phosphorus Magnetic Resonance Spectroscopy at 7T

description: The uploaded data relate to the work of Valkovič et al. entitled "Increased Cardiac Pi/PCr in the Diabetic Heart Observed Using Phosphorus Magnetic Resonance Spectroscopy at 7T." submitted in 2022<br> The data consist of the anonymised in vivo data of healthy volunteers and T2DM patients, in Siemens DICOM format, acquired as described in the manuscript. The uploaded data also include all analysed STEAM data results with visualised MR spectra and fitted values of PCr and Pi, used for Pi/PCr calculation.
description: LV and CTR are funded by Sir Henry Dale Fellowships awarded jointly by the Wellcome Trust and the Royal Society [221805/Z/20/Z and 098436/Z/12/B, respectively]. AA is funded by a British Heart Foundation clinical research training fellowship [FS/17/18/32449]. AIS is funded by the Austrian Science Fund (FWF) Schrödinger Fellowship [J 4043]. SN acknowledges support from the Oxford NIHR Biomedical Research Centre and the Oxford British Heart Foundation Centre of Research Excellence. DJT acknowledges support from a British Heart Foundation Senior Fellowship (FS/19/18/34252). Support of the Slovak Grant Agencies VEGA [2/0003/20] and APVV [#19–0032] is also gratefully acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
DOI: 10.5281/zenodo.5851717
title: Results of statistical analyses of the comparison of phosphorous measurement laboratory methods

description: The study in the related article compares the phosphorus (P) analysis methods of ammonium lactate (AL), Mehlich 3 (M3); water extraction (P-WA(P)&P-WA(PO<sub>4</sub>)), cobalt hexamine (CoHex) and X-ray fluorescence (XRF, as an estimate of total soil P). The ratio of the P-content/XRF was calculated and compared with the whole dataset first. Based on the comparison of all the data there were significant differences between the results of P-WA(P) and P-WA(PO<sub>4</sub>) vs M3 and AL, CoHex vs M3 and CoHex vs AL methods (p&lt;0.001). The influencing factors were also analysed for a more in-depth understanding of their role (CaCO<sub>3</sub>-content, pH, soil texture and clay content). The file contains the results of the statistical analyses.
DOI: 10.5281/zenodo.5851716
title: Results of statistical analyses of the comparison of phosphorous measurement laboratory methods

description: The study in the related article compares the phosphorus (P) analysis methods of ammonium lactate (AL), Mehlich 3 (M3); water extraction (P-WA(P)&P-WA(PO<sub>4</sub>)), cobalt hexamine (CoHex) and X-ray fluorescence (XRF, as an estimate of total soil P). The ratio of the P-content/XRF was calculated and compared with the whole dataset first. Based on the comparison of all the data there were significant differences between the results of P-WA(P) and P-WA(PO<sub>4</sub>) vs M3 and AL, CoHex vs M3 and CoHex vs AL methods (p&lt;0.001). The influencing factors were also analysed for a more in-depth understanding of their role (CaCO<sub>3</sub>-content, pH, soil texture and clay content). The file contains the results of the statistical analyses.
DOI: 10.25345/c5v008
title: MassIVE MSV000088685 - Analysis of GELFrEE-prefractionated E. coli MG1655 whole cell lysate
title: Analysis of whole cell lysate from E. coli MG1655 prefractionated with a 10% GELFrEE cartridge.