cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17617/3.soot50
title: Comparative analysis of surface phase diagrams in aqueous environment: implicit vs explicit solvation models

description: This dataset contains relevant data for the paper "Comparative analysis of surface phase diagrams in aqueous environment: implicit vs explicit solvation models" (J. Chem. Phys. 160, (2024); doi: 10.1063/5.0190304). It consists of two files. dft_data.tar.gz contains the raw DFT data, which is created with pyiron and vasp. phase_diagram.tar.gz contains the pandas table which summarizes the data and the jupyter notebook used to create the figures. The pandas tables and jupyter notebooks can also be found on github: https://github.com/eisenforschung/Mg-surface-phase-diagram.
description: pyiron, 0.5.2
description: VASP, 5.4.4
DOI: 10.17617/3.p3zab1
title: Data for the manuscript entitled "Importance of the semimetallic state for the quantum Hall effect in HfTe5"

description: This dataset contains the experimental data used in the manuscript entitled "Importance of the semimetallic state for the quantum Hall effect in HfTe5". It is composed by longitudinal and Hall resistivity curves as a function of temperature and/or magnetic field at different pressures. It also contains the transition temperatures, activation energies, cross sectional area of the Fermi surface, carriers density and mobility as a function of pressure. Finally, the X-ray diffaction and the lattice parameters are also present in this dataset.
DOI: 10.17617/3.6oxues
title: How light at night sets the circalunar clock in the marine midge Clunio marinus

description: Datasets underlying figures in the manuscript titled "How light at night sets the circalunar clock in the marine midge Clunio marinus".
DOI: 10.17617/3.tmg46z
title: Measuring the Spin-Forbidden Transition in Iron(IV)-oxo Catalysts Relevant to Two-State Reactivity

description: 2p3d resonant inelastic x-ray scattering, magnetic circular dichroism, and orca input files and structures for iron(IV)-oxos and iron(II) complexes
DOI: 10.17617/3.bnghvs
title: Mouse de novo genes trigger a largely unique transcriptomic response

description: Proteins that emerge de novo from non-coding DNA contribute to the generation of evolutionary novelty. To study de novo genes in a heterologous context, we have expressed several different mouse de novo genes (Mdngs) in a human cell line from a defined genomic integration site. Each of the mouse de novo genes triggers a largely unique transcriptomic response, indicating specific, rather than generalized effects. Enrichment of different Gene Ontology terms associated with the transcriptomic response for each Mdng further supports their functional diversity.
description: Trimmomatic, 0.39
description: HISAT2, 2.2.1
description: StringTie version, 2.2.1
description: Samtools, 1.15.1
description: DESeq2, 1.36
DOI: 10.17617/3.mazxuw
title: Data repository for the paper "Plastic deformation and heat-enabled structural recovery of monolithic silica aerogels"

description: This data repository contains the raw and processed data related to the manuscript "Plastic deformation and heat-enabled structural recovery of monolithic silica aerogels". 

Users willing to download the complete dataset could do so by using automated download tools. This would allow them to conserve more easily the structure of the dataset, and to bypass the downloading cap of Edmond for a single download (46.6 GB). We suggest using the python package DVuploader (https://github.com/gdcc/python-dvuploader). Alternatively, pyDataverse (https://pydataverse.readthedocs.io/en/latest/user/basic-usage.html#download-and-save-a-dataset-to-disk) can be used.
description: Python, 3.9
description: Dragonfly, 2022.2
DOI: 10.17617/3.t5buww
title: The Allure of Rome Maarten van Heemskerck draws the City - Medienstation App

description: Code of the Exist-DB Application, using part of the TEI-Publisher libraries, used for the Medienstation and Web page of the exhibition “The Allure of Rome. Maarten van Heemskerck Draws the City” hosted at the Kupferstichkabinett – Staatliche Museen zu Berlin and developed in cooperation with the Bibliotheca Hertziana – Max-Planck-Institut for Art History.
Images are not provided with the app.
DOI: 10.21233/tvbm-v641
title: Cheeseboro Lake diatom dataset

description: Raw data for the Cheeseboro Lake diatom dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.17617/3.64v3mf
title: IPv6-IPv4 Hypergiant Infrastructure Measurement Data and Analysis

description: Data and Analysis for the study on uncovering major hypergiants' offnet deployments.
DOI: 10.17617/3.wvkkxl
title: Evolutionary dynamics of plant cell wall-degrading enzymes in weevils: A comparative study across Curculionoidea

description: Weevils of the superfamily Curculionoidea arguably represent the most diverse group of herbivorous beetles. Most of the 62,000 described species feed on live plants, some on rotten wood, and others on wood-decaying fungi. They include economically important pests like bark beetles (Scolytinae), grain weevils (Sitophilus spp.), and the boll weevil (Anthonomus grandis). Previous research suggests that enzymes breaking down plant cell wall polysaccharides may have influenced weevil diversification. However, our understanding of the distribution of plant cell wall-degrading enzymes (PCWDEs) and their evolution in Curculionoidea is limited to a few species, primarily within Curculionidae. Herein, using transcriptome and genome data, we analyzed PCWDE-encoding genes in 45 weevil species representative of the majority of families within Curculionoidea. Our investigation revealed the presence of 13 families of PCWDEs, including the description of putative endo-α-1,5-L-arabinanases from subfamily 6 of glycoside hydrolase family 43 (GH43_6) in animals for the first time. Different weevil species possessed varying numbers of PCWDE families, ranging from one to nine. Notably, species associated with wood-decaying fungi, including ambrosia beetles (Scolytinae), exhibited a reduced set of PCWDEs compared to closely related species that primarily feed on plants. Our study provides valuable insights into the distribution and diversity of PCWDEs within Curculionoidea, reinforcing the role played by horizontal gene transfer, gene duplication and gene loss in the evolution of these enzyme families.
DOI: 10.17617/3.ektkpo
title: ICON: Towards vertical-integrated model configurations for numerical weather prediction, climate predictions and projections

description: This dataset provides additional information for the related publication (see below). Details for the content are given in the README.pdf file.
DOI: 10.17617/3.ye7u5m
title: Self-organization of filamentous cyanobacteria

description: Supplementary Videos
PhD Thesis, Maximilian Kurjahn, "Self-organization of filamentous cyanobacteria", Georg-August-Universität Göttingen (2024)
DOI: 10.17617/3.pwpuu0
title: Dormancy-inducing 3D-engineered matrix uncovers mechanosensitive and drug protective FHL2-p21 signaling axis

description: Resected tumors frequently relapse with distant metastasis, despite systemic treatment. Cellular dormancy has been identified as an important mechanism underlying such drug resistance enabling late relapse. Nonetheless, hurdles associated with detection and isolation of disseminated cancer cells (DCCs) in disease-free patients urge the need for in vitro models of dormant cells suited for drug discovery. Here, we explore dormancy-inducing 3D-engineered matrices, which generate mechanical confinement and induce growth arrest and survival against chemotherapy in cancer cells. We characterized the dormant phenotype of solitary cells by P-ERKlow:P-p38high dormancy signaling ratio, along with Ki67- expression. As underlying mechanism, we identified stiffness-dependent nuclear localization of the four-and-a-half LIM domains 2 (FHL2) protein, leading to p53-independent high p21Cip1/Waf1 nuclear expression, validated in murine and human tissue. Suggestive of a resistance-causing role, cells in the dormancy-inducing matrix became sensitive against chemotherapy upon FHL2 downregulation. Thus, our biomaterial-based approach will enable systematic screens for novel compounds suited to eradicate potentially relapsing, dormant cancer cells.
DOI: 10.17617/3.h44en5
title: MPI-ESM 1.2.01p7

description: CMIP6 version of the Max Planck Institute for Meteorology's Earth System Model, ported to the HLRE4 HPC system of the German Climate Computing Center (DKRZ).
Includes model components atmosphere ECHAM 6.3.05p3-rc1, land surface JSBACH 3.20p1, ocean MPIOM 1.6.3p5-rc1, biogeochemistry HAMOCC; infrastructure components coupling tool set OASIS3-MCT 2.0@r722 (modified), experiment configurator MakeExperiments! 1.1.5rc2, visualization tool Plot'em ESMs 1.0.5
DOI: 10.17617/3.fxc12w
title: Data and code for Immigrant birds use payoff biased social learning in spatially variable environments

description: The repository contains the data and code to reproduce the study "Immigrant birds use payoff biased social learning in spatially variable environments". Please consult the readme file for file descriptions and locations, and descriptions of variable names. We simulated immigration events between captive experimental populations of great tits (Parus major) to test whether spatial variability in environmental cues or payoffs affected the degree to which immigrant birds used social information. We analyzed birds' preferences before and after immigration, and used Bayesian learning models to understand the mechanisms behind change (or lack-thereof) in preferences. Behavioral data was collected using automated puzzle boxes in an experiment using captive wild-caught great tits (Parus major). The experiment took place over 2 periods: Jan-March 2021, and Jan-March 2022. All work was conducted by under a nature conservation permit and animal ethics permit from the Regierungsprasidium Freiburg, no.35-9185.81/G-20/100.
DOI: 10.17617/3.zrzube
title: Investigation of bSSFP frequency response changes during a functional experiment at 9.4 T

description: All data was acquired using an accelerated 3D stack-of-spirals sequence at a Siemens Magnetom 9. 4 T human MRI scanner. A resting-state phase-cycling experiment to assess data quality and two functional phase-cycling experiments with temporally shifted paradigm (see Figure 4) to obtain SSFP profiles for active and resting conditions. An additional passband experiment (TR= 10 ms, 1 mm iso, volume TR= 1.4 s) was performed for identifying the activated voxels.
DOI: 10.17617/3.uqrssa
title: EGAP50000000094

description: Harmonised Data Access Agreement (hDAA) for Controlled Access Data
DOI: 10.17617/3.cwguul
title: Code Generation in ORCA with AGE II. Calculation Data.

description: Repository containing the ORCA, MRCC and CFOUR output files that showcase the new capabilities of the ORCA's code generator, the Automated Generator Environment (AGE).
DOI: 10.17617/3.i0ecy9
title: The Nonlinear Frequency Response Method for the Diagnosis of the PEM Water Electrolyzer Performance

description: A better grasp of the underlying phenomena occurring in electrochemical technologies is crucial for their further development and, consequently, a much-needed step forward to a greener economy. Diagnostic methods that can reliably determine the state of health and causes of the performance shortcomings are indispensable. The ease of obtaining electrochemical data makes the analysis of current and voltage responses the preferred diagnostic approach. Traditional techniques, like steady-state polarization and electrochemical impedance spectroscopy are limited by their inability to distinguish between different processes due to the constraints of steady-state and linearity of system response, respectively. The nonlinear frequency response (NFR) method is an advanced diagnostic method that has the potential to overcome these issues. In this work, the NFR method was applied both experimentally and theoretically to study polymer electrolyte membrane water electrolysis (PEMWE). The model-based analysis provides insights into the losses in the PEMWE at different current densities. It shows that the contributions of the cathode to the overpotential losses at high current densities cannot be neglected. This has been much discussed in the literature and was often attributed only to mass transport losses. The contribution of mass transport has also been identified at higher current densities but is less pronounced than the kinetic contributions. Furthermore, we show that including the nonlinear dynamics in the analysis was crucial for identifying the appropriate parameter set. Overall, this work showed a considerable potential of the NFR method for the diagnosis of PEMWE due to its prospects of identifying different processes occurring within.
description: Matlab, R2019b
DOI: 10.17617/3.onemor
title: Understanding Anomalous Gas-Phase Peak Shifts in Dip-and-Pull Ambient Pressure XPS Experiments

description: Detre Teschner, Julius Plescher, Simone Piccinin, Travis E. Jones, Adnan Hammud, Franz Schmidt, Axel Knop-Gericke, Hendrik Bluhm, and Andrey Shavorskiy: Understanding Anomalous Gas-Phase Peak Shifts in Dip-and-Pull Ambient Pressure XPS Experiments; https://doi.org/10.1021/acs.jpcc.4c00113
DOI: 10.17617/3.45s7ep
title: The Iron Nitrogenase Reduces Carbon Dioxide to Formate and Methane under Physiological Conditions: A Route to Feedstock Chemicals

description: Experimental data of the manuscript "The Iron Nitrogenase Reduces Carbon Dioxide to Formate and Methane under Physiological Conditions: A Route to Feedstock Chemicals "
DOI: 10.17617/3.od2ike
title: ICON version used for investigation of permafrost cloud feedback

description: Data set contain code of icon version related to the publication "Permafrost cloud feedback may amplify climate change" by de Vrese et al. (submitted to GRL). ICON-A and ICON-O versions are similar to ICON Earth System Model Version 1.0, described in Junglcaus et al. (2022: https://doi.org/10.1029/2021MS002813). ICON-Land uses JSBACH 4 which has been modified to include a scheme to account for the interaction of laterally coupled tiles.
DOI: 10.17617/3.nwoker
title: Physics-Based Synthetic Data Model for Automated Segmentation in Catalysis Microscopy

description: This is the source code and data used in the publication "Physics-Based Synthetic Data Model for Automated Segmentation in Catalysis Microscopy" by Maurits Vuijk, Gianmarco Ducci, Luis Sandoval, Markus Pietsch, Karsten Reuter, Thomas Lunkenbein and Christoph Scheurer.
DOI: 10.17617/3.sftzip
title: Source data for the manuscript: "Quantitative trait locus mapping in field plant populations reveals a genetic basis for frequency- and spatially-specific fungal pathosystem resistance"

description: This folder contains data and other information supporting the results described in the manuscript.
DOI: 10.17617/3.fgiuet
title: Identifiability analysis of frequency response functions for the diagnosis of PEMFC

description: The repository contains the data relative to the article "Assessment of Frequency Response Techniques in Diagnosing Polymer Electrolyte Membrane Fuel Cells"
DOI: 10.21233/kdez-7x94
title: Bison Lake pollen dataset

description: Raw data for the Bison Lake pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.17617/3.ca8mqy
title: SSU rRNA and PacBio HiFi metagenome-derived data for "Seasonal recurrence and modular assembly of an Arctic marine pelagic microbiome"

description: This entry contains all of the necessary derived data files required to reproduce the analysis and recreate the figures presented in the manuscript titled "Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome". 

The scripts required to process the data files along with a detailed description on the analysis can be found here - https://github.com/tpriest0/Fram_Strait_WSC_time_series_2016-2020

The raw sequence data from which these derived files were generated are available at ENA - see 'Related Datasets' below.
DOI: 10.17617/3.a1kmub
title: Data and R codes from "Pertussis vaccines, epidemiology and evolution"

description: Data and R codes from the review article, "Pertussis vaccines, epidemiology and evolution", published in Nature Reviews Microbiology.
description: R, 4.1.2
description: R, 4.3.1
DOI: 10.17617/3.izm9ha
title: Dataset for publication "Determining the absolute number density of a thermal vapor via photon correlations"

description: Repository containing the datasets and LaTeX code to reproduce the figures 2 to 6 of the manuscript "Determining the absolute number density of a thermal vapor via photon correlations".
DOI: 10.17617/3.tazdxc
title: Structural color in the bacterial domain: the ecogenomics of a 2-dimensional optical phenotype

description: Structural colour is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural colour is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here we collected and sequenced a set of 87 structurally coloured bacterial isolates, and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two dimensional packing capable of producing SC. Pan-genome-wide association approaches were used to identify genes associated with structural colour. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilisation and metabolism, were found to be involved. Using this information, we constructed a classifier to predict structural colour directly from bacterial genome sequences, validated it by scoring 100 strains that were not involved in creating the structural colour classifier, and predicted that photonic structures are widely distributed within Gram-negative bacteria. Analysis of over 13 thousand assembled metagenomes predicted that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides the first large-scale ecogenomics view of structural colour in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon.
DOI: 10.17617/3.wrnnzh
title: Schroeter et al DOM HR-MS raw data

description: 866 Mzml files of direct infusion MS1 mass spectra recorded on an Orbitrap Elite at the Max Planck Institute for Biogeochemistry. Data contain groundwater samples, soil seepage samples, blanks, and in-house reference DOM.
DOI: 10.17617/3.yzvpxb
title: Euroleon nostras genome assembly

description: Genome assembly of the Neuropteran insect Euroleon nostras (antlion). The genome assembly is based on PacBio HiFi reads and was assembled using Hifiasm (v0.16.0). The primary assembly was then checked for potential contaminants using Blobtools and TaxIdent. The final assembly contains 1,481,991,678 nucleotides and an N50 contig size of 97,627,798 with a total of 52 contigs.
DOI: 10.17617/3.brsgla
title: Demo data for Quantitative imaging of species-specific lipid transport in mammalian cells.

description: This repository contains a minimal data set to run the scripts that were used in the image analysis of the data for: "Quantitative imaging of species-specific lipid transport in mammalian cells."
DOI: 10.17617/3.wpvjhq
title: Data for paper 'A cytokinetic ring-driven cell rotation achieves Hertwig's rule in early development'

description: Raw microscopy data for 'A cytokinetic ring-driven cell rotation achieves Hertwig's rule in early development', accepted for publication in PNAS, 2024. The data is organized by figure/subfigure and for each figure there is a separate 'notes.txt' file with explanatory text.
DOI: 10.17617/3.xy5a6u
title: Codes for "Muted Amazon rainfall response to deforestation in a global storm-resolving model"

description: Codes for figures and analysis from "Muted Amazon rainfall response to deforestation in a global storm-resolving model"
DOI: 10.17617/3.fv4qyx
title: Data for Inserting Three-Coordinate Nickel into [4Fe-4S] Clusters

description: Experimental and computational data supporting the publication "Inserting Three-Coordinate Nickel into [4Fe-4S] Clusters", published October 2024 in ACS Central Science: https://doi.org/10.1021/acscentsci.4c00985. Experimental data include Mössbauer, XAS, UVVIS, IR, EPR, NMR, CV, EA, XRC, and SQUID magnetometry measurements. Computational data include DFT results and input files for the ORCA program.
DOI: 10.17617/3.nqdslw
title: Ectocarpus sp7 version 5 genome and annotation

description: Sex chromosomes are unique genomic regions displaying structural and evolutionary features that distinguish them markedly from autosomes. Although nuclear three dimensional (3D) folding of chromatin structure is important for gene expression regulation and correct developmental programs, very little is known about the 3D architecture of sex chromosomes within the nucleus, and how that impacts their function in sex determination. Here, we determine the sex-specific 3D organization of the model brown alga Ectocarpus chromosomes at 2 kb resolution, by comprehensively mapping long-range chromosomal interactions using Hi-C coupled with Oxford Nanopore long reads. We report that Ectocarpus interphase chromatin exhibits a non-Rabl conformation, with strong contacts among telomeres and among centromeres, which feature centromere-specific LTR retrotransposons. The Ectocarpus chromosomes do not contain large local interactive domains that resemble TADs described in animals, but their 3D genome organization is largely shaped by post-translational modifications of histone proteins that regulate chromatin compaction and mediate transcriptional regulation. We describe the spatial conformation and sub-nuclear positioning of the sex determining region (SDR) within the U and V chromosomes and show that these regions are very insulated and span the centromeres. Moreover, we link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of U and V chromosomes. Finally, we uncover the unique conformation of a large genomic region on chromosome 6 harboring an endogenous viral element (EVE), providing insights regarding the functional significance of the chromatin organisation of latent giant dsDNA virus.
DOI: 10.17617/3.jk4anf
title: BGU Pattern-Cutting Dataset (BGU-PatCut)

description: The BGU Pattern-Cutting Dataset (BGU-PatCut) contains the raw data for the publication "Augmenting Robot-Assisted Pattern Cutting with Periodic Perturbations – Can We Make Dry Lab Training More Realistic?"
&lt;br&gt;
The dataset comprises data from 54 participants who performed 24 repetitions of a robot-assisted pattern-cutting surgical task under various conditions. For each repetition, we share kinematic data, video recordings, and manual labels for the different stages of the task. Detailed information on data collection is available in the Methods section of the manuscript.
&lt;br&gt;
The dataset includes a PDF file describing the data and separate folders for each experiment:&lt;br&gt;
1. PatternCuttingForcePerturbation 
&lt;br&gt;
2. PatternCuttingMotionPerturbations
&lt;br&gt; 
We recommend using the "Tree" view instead of the "Table" view to view the files organized by folder.