cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7510587
title: Dry Bench Skills for the Researcher

description: The practice of biological inquiry has evolved so that a biological researcher's training must include both wet-lab and dry lab experimental and computational approaches. This course seeks to lay a broad foundation for the dry bench researcher. It is clear that "data literacy is a key skill in the modern world." This course will introduce the trainee to the computational techniques that enable data analysis locally on their laptop and as well as how to enable these same analysis techniques in the cloud. In this workshop, we will also introduce the learner to the concept of team science. The learner will obtain critical skills in effective collaboration that is imperative in a world where the amount of data available is beyond a single lab's walls. Over 10 hours of instruction, spread over two weeks, we seek to introduce the learner to RNAseq analysis and demystify concepts in RNAseq analysis. By the end of the course, the learner can successfully use tools involved in these analyses collaboratively and independently. This course aims to go broad and point the learner to learn more and take their knowledge deeper. Through their participation in the class, learners will acquire experience in a full suite of tools essential to any bioinformatics analysis. They will learn and understand FAIR best practices. They will obtain and use their GitHub, Docker, and ORCID ids. They will know where to find Nextflow workflows and run them to generate results that are further explored through interactive Jupyter Lab notebooks. They will learn about publicly available datasets downloadable from cloud resources and the ever-growing datasets that may aid their research. They will learn about using flexible, powerful, and community-based workflow languages such as Nextflow and how the resulting workflows use containerization to modularize and simplify bioinformatic analysis. Such workflows will be run using cloud-accessible data in the cloud and on their laptop. The course's final day will focus on pulling together all these resources into a single end-to-end example to empower the trainee to apply new knowledge towards their specific use case.
DOI: 10.5281/zenodo.6959427
title: Data & model products from "Identification of carbon dioxide in an exoplanet atmosphere"

description: Associated Publication: https://www.nature.com/articles/s41586-022-05269-w<br> <br> OVERVIEW: Carbon dioxide (CO2) is a key chemical species that is found in a wide range of planetary atmospheres. In the context of exoplanets, CO2 is an indicator of the metal enrichment (i.e., elements heavier than helium, also called “metallicity”), and thus formation processes of the primary atmospheres of hot gas giants. It is also one of the most promising species to detect in the secondary atmospheres of terrestrial exoplanets. Previous photometric measurements of transiting planets with the Spitzer Space Telescope have given hints of the presence of CO2, but have not yielded definitive detections due to the lack of unambiguous spectroscopic identification. Here we present the detection of CO2 in the atmosphere of the gas giant exoplanet WASP-39b from transmission spectroscopy observations obtained with JWST as part of the Early Release Science Program (ERS). The data used in this study span 3.0 - 5.5 µm in wavelength and show a prominent CO2 absorption feature at 4.3 µm (26σ significance). The overall spectrum is well matched by one-dimensional, 10x solar metallicity models that assume radiative-convective-thermochemical equilibrium and have moderate cloud opacity. These models predict that the atmosphere should have water, carbon monoxide, and hydrogen sulfide in addition to CO2, but little methane. Furthermore, we also tentatively detect a small absorption feature near 4.0 µm that is not reproduced by these models.
description: Includes NIRSpec Prism 3-5.5 um transmission spectra from multiple reductions as well as model fits as described in the corresponding publication. These can be used to reconstruct Figures 2 and 3. A CSV file to reconstruct the light curves shown in Figure 1 is also included.
DOI: 10.5281/zenodo.6959426
title: Data & model products from "Identification of carbon dioxide in an exoplanet atmosphere"

description: Associated Publication: https://www.nature.com/articles/s41586-022-05269-w<br> <br> OVERVIEW: Carbon dioxide (CO2) is a key chemical species that is found in a wide range of planetary atmospheres. In the context of exoplanets, CO2 is an indicator of the metal enrichment (i.e., elements heavier than helium, also called “metallicity”), and thus formation processes of the primary atmospheres of hot gas giants. It is also one of the most promising species to detect in the secondary atmospheres of terrestrial exoplanets. Previous photometric measurements of transiting planets with the Spitzer Space Telescope have given hints of the presence of CO2, but have not yielded definitive detections due to the lack of unambiguous spectroscopic identification. Here we present the detection of CO2 in the atmosphere of the gas giant exoplanet WASP-39b from transmission spectroscopy observations obtained with JWST as part of the Early Release Science Program (ERS). The data used in this study span 3.0 - 5.5 µm in wavelength and show a prominent CO2 absorption feature at 4.3 µm (26σ significance). The overall spectrum is well matched by one-dimensional, 10x solar metallicity models that assume radiative-convective-thermochemical equilibrium and have moderate cloud opacity. These models predict that the atmosphere should have water, carbon monoxide, and hydrogen sulfide in addition to CO2, but little methane. Furthermore, we also tentatively detect a small absorption feature near 4.0 µm that is not reproduced by these models.
description: Includes NIRSpec Prism 3-5.5 um transmission spectra from multiple reductions as well as model fits as described in the corresponding publication. These can be used to reconstruct Figures 2 and 3. A CSV file to reconstruct the light curves shown in Figure 1 is also included.
DOI: 10.25800/jd3p-fs02
title: DSA-110 Data for Candidate Fast Radio Burst 220319aaeb

description: Data associated with DSA-110 candidate transient.
DOI: 10.5281/zenodo.7508426
title: Data from: Membrane phase separation drives responsive assembly of receptor signaling domains

description: Plasma membrane heterogeneity has been tied to a litany of cellular functions and is often explained by analogy to membrane phase separation, yet models based on phase separation alone fall short of describing the rich organization available within cell membranes. We present comprehensive experimental evidence motivating an updated model of plasma membrane heterogeneity in which membrane domains assemble in response to protein scaffolds. Quantitative super-resolution nanoscopy measurements in live B lymphocytes detect membrane domains that emerge upon clustering B cell receptors (BCR). These domains enrich and retain membrane proteins based on their preference for the liquid-ordered phase. Unlike phase separated membranes that consist of binary phases with defined compositions, membrane composition at BCR clusters is modulated through the protein constituents in clusters or the composition of the membrane overall. This tunable domain structure is detected through the variable sorting of membrane probes and impacts the magnitude of BCR activation.
description: a readme file is included with detailed information about the dataset. Funding provided by the NIH (GM110052), the NSF (MCB1552439), and the American Cancer Society (PF1800401CCE)
DOI: 10.5281/zenodo.7508425
title: Data from: Membrane phase separation drives responsive assembly of receptor signaling domains

description: Plasma membrane heterogeneity has been tied to a litany of cellular functions and is often explained by analogy to membrane phase separation, yet models based on phase separation alone fall short of describing the rich organization available within cell membranes. We present comprehensive experimental evidence motivating an updated model of plasma membrane heterogeneity in which membrane domains assemble in response to protein scaffolds. Quantitative super-resolution nanoscopy measurements in live B lymphocytes detect membrane domains that emerge upon clustering B cell receptors (BCR). These domains enrich and retain membrane proteins based on their preference for the liquid-ordered phase. Unlike phase separated membranes that consist of binary phases with defined compositions, membrane composition at BCR clusters is modulated through the protein constituents in clusters or the composition of the membrane overall. This tunable domain structure is detected through the variable sorting of membrane probes and impacts the magnitude of BCR activation.
description: a readme file is included with detailed information about the dataset. Funding provided by the NIH (GM110052), the NSF (MCB1552439), and the American Cancer Society (PF1800401CCE)
DOI: 10.5281/zenodo.7510586
title: Phantom imaging data and analysis macros for the article "Monochromatic computed tomography using laboratory-scale setup"

description: The raw and processed data and analysis macros of the article <em>A.-P.</em> <em>Honkanen et S. J. Huotari, Monochromatic computed tomography using laboratory-scale setup, Scientific Reports (2023), doi:10.1038/s41598-023-27409-6</em> The data set consists of the raw and reconstructed computed tomography projection data taken of an PMMA phantom embedded with three different chemical species of selenium taken with a monochromatic X-ray imaging setup based on a laboratory-scale Johann-type crystal X-ray spectrometer. In addition to the imaging data, the set contains also the Jupyter Notebooks used to process and analyse the data. The details of the instrument and the analysis are presented in the article. The dataset is licensed under Creative Commons Attribution 4.0 International License https://creativecommons.org/licenses/by/4.0/
DOI: 10.5281/zenodo.7510585
title: Phantom imaging data and analysis macros for the article "Monochromatic computed tomography using laboratory-scale setup"

description: The raw and processed data and analysis macros of the article <em>A.-P.</em> <em>Honkanen et S. J. Huotari, Monochromatic computed tomography using laboratory-scale setup, Scientific Reports (2023), doi:10.1038/s41598-023-27409-6</em> The data set consists of the raw and reconstructed computed tomography projection data taken of an PMMA phantom embedded with three different chemical species of selenium taken with a monochromatic X-ray imaging setup based on a laboratory-scale Johann-type crystal X-ray spectrometer. In addition to the imaging data, the set contains also the Jupyter Notebooks used to process and analyse the data. The details of the instrument and the analysis are presented in the article. The dataset is licensed under Creative Commons Attribution 4.0 International License https://creativecommons.org/licenses/by/4.0/
DOI: 10.15139/s3/ccc0qi
title: Arkansas Poll 2022

description: 2022 Arkansas Poll raw data
DOI: 10.5281/zenodo.7510274
title: Data Set for Predicting the Performance of ATL Model Transformations

description: Model transformation languages are special-purpose languages, which are designed to define transformations as comfortably as possible, i.e., often in a declarative way. With the increasing use of transformations in various domains, the complexity and size of input models are also increasing. However, developers often lack suitable models for performance testing. We have therefore conducted experiments in which we predict the performance of model transformations based on characteristics of input models using machine learning approaches. This dataset contains our raw and processed input data, the scripts necessary to repeat our experiments, and the results we obtained. Our input data consists of the time measurements for six different transformations defined in the Atlas Transformation Language (ATL), as well as the collected characteristics of the real-world input models that were transformed. We provide the script that implements our experiments. We predict the execution time of ATL transformations using the machine learning approaches linear regression, random forests and support vector regression using a radial basis function kernel. We also investigate different sets of characteristics of input models as input for the machine learning approaches. These are described in detail in the provided documentation.pdf. The results of the experiments are provided as raw data in individual cvs files. Additionally, we calculated the mean absolute percentage error in % and the 95th percentile of the absolute percentage error in % for each experiment and provide these results. Furthermore, we provide our Eclipse plugin, which collects the characteristics for a set of given models, the Java projects used to measure the execution time of the transformations, and other supporting scripts, e.g. for the analysis of the results. A short introduction with a quick start guide can be found in README.md and a detailed documentation in documentaion.pdf.
description: The authors acknowledge support by the state of Baden-Württemberg through bwHPC.
DOI: 10.6084/m9.figshare.21834111
title: Docking calculation

description: Docking calculation by autodock vina
DOI: 10.6084/m9.figshare.21834111.v1
title: Docking calculation

description: Docking calculation by autodock vina
DOI: 10.5519/qd.ts8givqa
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (216 records)
DOI: 10.6084/m9.figshare.21834123
title: dorcervicalincidencia.sav

description: Research data from project funded by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), under protocol number 2011/20123-4.
DOI: 10.6084/m9.figshare.21834123.v1
title: dorcervicalincidencia.sav

description: Research data from project funded by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), under protocol number 2011/20123-4.
DOI: 10.15784/601639
title: Computed fetch for project study sites

description: This csv dataset includes the fetch distances for the 15 study sites visited by projects ANT-1744550, -1744570, -1744584, and -1744602 during ARSV Laurence M. Gould cruise LMG 19-04 in April and May 2019. The fetch distances were computed for each of the following eight cardinal directions (0°,45°,90°,135°,180°,225°,270°,315°). The fetches are all reported in meters (m). Fetch was determined by computing the distance along each of the eight directions to the nearest shoreline based on a 100 m resolution land/water grid. The grid was constructed using a vector-to-raster conversion of the Scientific Council of Antarctic Research (SCAR) Antarctic Digital Database’s High resolution vector polylines of the Antarctic coastline. The fetch computations utilized an ArcGIS toolbox based on code by Finlayson (2006) that computes fetch using the recommended procedures from the US Army Corp of Engineers Shore Protection Manual (USACE, 1984). Finlayson, D.P. 2006. The geomorphology of Puget Sound beaches. Ph.D. dissertation. University of Washington, Seattle. 216 p. Gerrish, L., Fretwell, P., & Cooper, P. (2021). High resolution vector polylines of the Antarctic coastline (7.4) [Data set]. UK Polar Data Centre, Natural Environment Research Council, UK Research & Innovation. https://doi.org/10.5285/e46be5bc-ef8e-4fd5-967b-92863fbe2835'. USACE, 1984. Shore Protection Manual, Coastal Engineering Research Center, Fort Belvoir, Virginia.
DOI: 10.5281/zenodo.7510668
title: Supplementary Material - Marine animal forests in turbid environments are overlooked seascapes in urban areas

description: Figures S1, S2, and S3 of the manuscript "Marine animal forests in turbid environments are overlooked seascapes in urban areas" accepted in the open-access journal Ocean and Coastal Research (Soares et al. 2023)
description: {"references": ["Soares et al. Marine animal forests in turbid environments are overlooked seascapes in urban areas"]}
DOI: 10.5281/zenodo.7510667
title: Supplementary Material - Marine animal forests in turbid environments are overlooked seascapes in urban areas

description: Figures S1, S2, and S3 of the manuscript "Marine animal forests in turbid environments are overlooked seascapes in urban areas" accepted in the open-access journal Ocean and Coastal Research (Soares et al. 2023)
description: {"references": ["Soares et al. Marine animal forests in turbid environments are overlooked seascapes in urban areas"]}
DOI: 10.15784/601649
title: Five year mean annual and summer sea ice concentration grids for the Western Antarctic Peninsula from AMSR2, National Ice Center Charts and the Sea Ice Index

description: This dataset comprises a series of geotiff files containing mean annual or summer (October-February) gridded sea ice concentrations for five-year periods developed from available Sea Ice Concentration Datasets (AMSR2, the Sea Ice Index, and National Ice Center Charts). The grids encompass a portion of the Western Antarctic Peninsula. This dataset was developed in support of projects ANT-1744550, -1744570, -1744584, and -1744602.
DOI: 10.5281/zenodo.3710459
title: MICrONS Layer 2/3 Data Tables

description: These are data tables released as part of the MICrONS project, and contain annotations on the EM data and reconstructions. You can find more information about the dataset and the project at microns-explorer.org.
DOI: 10.5281/zenodo.3710458
title: MICrONS Layer 2/3 Data Tables

description: These are data tables released as part of the MICrONS project, and contain annotations on the EM data and reconstructions. You can find more information about the dataset and the project at microns-explorer.org.
DOI: 10.5281/zenodo.4029612
title: MICrONS Layer 2/3 Data Tables

description: These are data tables released as part of the MICrONS project, and contain annotations on the EM data and reconstructions. You can find more information about the dataset and the project at microns-explorer.org.
DOI: 10.5281/zenodo.5579388
title: MICrONS Layer 2/3 Data Tables

description: These are data tables released as part of the MICrONS project, and contain annotations on the EM data and reconstructions. You can find more information about the dataset and the project at microns-explorer.org.
DOI: 10.5281/zenodo.5646567
title: MICrONS Layer 2/3 Data Tables

description: These are data tables released as part of the MICrONS project, and contain annotations on the EM data and reconstructions. You can find more information about the dataset and the project at microns-explorer.org.
DOI: 10.5281/zenodo.6363348
title: MICrONS Layer 2/3 Data Tables

description: These are data tables released as part of the MICrONS project, and contain annotations on the EM data and reconstructions. You can find more information about the dataset and the project at microns-explorer.org.
DOI: 10.5281/zenodo.7510511
title: MICrONS Layer 2/3 Data Tables

description: These are data tables released as part of the MICrONS project, and contain annotations on the EM data and reconstructions. You can find more information about the dataset and the project at microns-explorer.org.
DOI: 10.5281/zenodo.7296176
title: Inflammation-controlled anti-inflammatory hydrogels

description: Dataset to the publication <strong>Inflammation-controlled anti-inflammatory hydrogels</strong> Tina Helmecke, Dominik Hahn, Nadine Matzke, Lisa Ferdinand, Lars Franke, Sebastian Kühn, Gunter Fischer, Carsten Werner, Manfred F. Maitz Advanced Science 2022, 2206412. https://doi.org/10.1002/advs.202206412
description: The research was funded by the Federal Ministry of Education and Research (BMBF) within the project Zwanzig20 RESPONSE – Partnerschaft für Innovation in der Implantattechnologie.
DOI: 10.5281/zenodo.7296177
title: Inflammation-controlled anti-inflammatory hydrogels

description: Dataset to the publication <strong>Inflammation-controlled anti-inflammatory hydrogels</strong> Tina Helmecke, Dominik Hahn, Nadine Matzke, Lisa Ferdinand, Lars Franke, Sebastian Kühn, Gunter Fischer, Carsten Werner, Manfred F. Maitz Advanced Science 2022, 2206412. https://doi.org/10.1002/advs.202206412
description: The research was funded by the Federal Ministry of Education and Research (BMBF) within the project Zwanzig20 RESPONSE – Partnerschaft für Innovation in der Implantattechnologie.
DOI: 10.17909/4cgv-j876
title: Data from paper "GOALS-JWST: Revealing the Buried Star Clusters in the Luminous Infrared Galaxy VV 114"

description: NIRCam F150W observation from the GOALS ERS program (ID 1328) "A JWST Study of the Starburst-AGN Connection in Merging LIRGs"
DOI: 10.17909/kd6r-2b69
title: Data from paper "GOALS-JWST: Revealing the Buried Star Clusters in the Luminous Infrared Galaxy VV 114"

description: NIRCam F200W observation from the GOALS ERS program (ID 1328) "A JWST Study of the Starburst-AGN Connection in Merging LIRGs"
DOI: 10.6084/m9.figshare.21834264
title: Copula based Cox proportional hazards models for dependent censoring

description: Most existing copula models for dependent censoring in the literature assume that the parameter defining the copula is known. However, prior knowledge on this dependence parameter is often unavailable. In this paper we propose a novel model under which the copula parameter does not need to be known. The model is based on a parametric copula model for the relation between the survival time (<i>T</i>) and the censoring time (<i>C</i>), whereas the marginal distributions of <i>T</i> and <i>C</i> follow a semiparametric Cox proportional hazards model and a parametric model, respectively. We show that this model is identified, and propose estimators of the nonparametric cumulative hazard and the finite-dimensional parameters. It is shown that the estimators of the model parameters and the cumulative hazard function are consistent and asymptotically normal. We also investigate the performance of the proposed method using finite-sample simulations. Finally, we apply our model and estimation procedure to a follicular cell lymphoma data set.
DOI: 10.6084/m9.figshare.21834264.v1
title: Copula based Cox proportional hazards models for dependent censoring

description: Most existing copula models for dependent censoring in the literature assume that the parameter defining the copula is known. However, prior knowledge on this dependence parameter is often unavailable. In this paper we propose a novel model under which the copula parameter does not need to be known. The model is based on a parametric copula model for the relation between the survival time (<i>T</i>) and the censoring time (<i>C</i>), whereas the marginal distributions of <i>T</i> and <i>C</i> follow a semiparametric Cox proportional hazards model and a parametric model, respectively. We show that this model is identified, and propose estimators of the nonparametric cumulative hazard and the finite-dimensional parameters. It is shown that the estimators of the model parameters and the cumulative hazard function are consistent and asymptotically normal. We also investigate the performance of the proposed method using finite-sample simulations. Finally, we apply our model and estimation procedure to a follicular cell lymphoma data set.
DOI: 10.5281/zenodo.7510627
title: Databases of dereplicated vOTUs and MAGs recovered from a rewetting experiment on grassland soils

description: Databases of dereplicated viral operational taxonomic units (vOTUs) and metagenome-assembled genomes (MAGs) recovered from a rewetting experiment on grassland soils.
DOI: 10.5281/zenodo.7510626
title: Databases of dereplicated vOTUs and MAGs recovered from a rewetting experiment on grassland soils

description: Databases of dereplicated viral operational taxonomic units (vOTUs) and metagenome-assembled genomes (MAGs) recovered from a rewetting experiment on grassland soils.