cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17617/3.gqapeu
title: Revealing a hidden conducting state in KV10.1 mutants

description: The KCNH family of potassium channels serves relevant physiological functions in both excitable and non-excitable cells, reflected in the massive consequences of mutations or pharmacological manipulation of their function. This group of channels shares structural homology with other voltage-gated K&lt;sup&gt;+&lt;/sup&gt; channels, but the mechanisms of gating in this family show significant differences with respect to the canonical electromechanical coupling in these molecules. In particular, the large intracellular domains of KCNH channels play a crucial role in gating that is still only partly understood. Using KCNH1(K&lt;sub&gt;V&lt;/sub&gt;10.1) as a model, we have characterized the behavior of a series of modified channels that could not be explained by the current models. With electrophysiological and biochemical methods combined with mathematical modeling, we show that the uncovering of an open state can explain the behavior of the mutants. This open state, which is not detectable in wild-type channels, appears to lack the rapid flicker block of the conventional open state. Because it is accessed from deep closed states, it elucidates intermediate gating events well ahead of channel opening in the wild type. This allowed us to study gating steps prior to opening, which, for example, explain the mechanism of gating inhibition by Ca&lt;sup&gt;2+&lt;/sup&gt;-Calmodulin and generate a model that describes the characteristic features of KCNH channels gating.
description: Igor Pro, 9.05
DOI: 10.17617/3.iiuvr9
title: Molecular Hybrid Materials for Selective CO2 Electroreduction to Multicarbon Products

description: X-ray absorption spectroscopy: RAW data
description: Athena
DOI: 10.17617/3.itpoi5
title: Atmospheric health burden across the century and the accelerating impact of temperature compared to pollution

description: Anthropogenic emissions alter atmospheric composition and therefore the climate, 
with implications for air pollution- and climate-related human health. 
Mortality attributable to air pollution and non-optimal temperature is a major concern, 
which is subject to change in the future under different climate change and socioeconomic scenarios. 

The goal of the study is to assess future changes in mortality attributable 
to long-term exposure to both non-optimal temperature and air pollution simultaneously, 
using model outputs from the recent Intergovernmental Panel on Climate Change multi-institution simulations. 

We show that, under a moderate scenario (SSP2-4.5), end-of-century mortality could quadruple from present-day values 
to around 30 (confidence level 95%:12-53) million/year.
While pollution-related mortality is projected to increase five-fold by the end of the century in a moderate scenario, 
temperature-related mortality will experience a seven-fold rise.
This increase causes non-optimal temperature to become a more important health risk factor than air pollution for at least 20% of the world's population. 
Population aging emerges as the primary driver of increased mortality, countering efforts 
to improve air quality and mitigate climate change.

These findings underscore the urgency not only to improve air quality but, more importantly, 
to simultaneously implement more effective climate change policies. 
This will prevent significant loss of life in the future, which could offset 
the gain obtained by air quality improvements.
DOI: 10.17617/3.tg4to4
title: Tables for Neandertal ancestry breakpoint analysis with the high-coverage Ranis13, Zlaty kun, and other ancient and modern human genomes

description: Input and output tables of an analysis of Neandertal breakpoints in high-coverage ancient and present-day human genomes.
DOI: 10.15468/dl.9wtpap
title: Occurrence Download

description: A dataset containing 391578 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is KSA Flora Survey 2013"
 ]
}

 The dataset includes 391578 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021498-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17617/3.4ntbxl
title: :unav

description: :unav
DOI: 10.17617/3.gvzjrt
title: MPIESM-1.2 model version and scripts used to examine convective mass flux and Walker circulation changes

description: The dataset contains model source code and scripts used to prepare, run and analyze the experiments performed to study "Common and distinct drivers of convective mass flux and Walker circulation changes" by Kang et al. 2024 (submitted to GRL).
The MPI-ESM1.2 model version used is almost identical to the code version in https://edmond.mpg.de/dataset.xhtml?persistentId=doi:10.17617/3.H44EN5 with a few minor differences concerning model handling and additional options for the land component (not used here).
DOI: 10.17617/3.dboplj
title: Physiological and behavioral data on the experience of different classical concert formats

description: This dataset contains physiological and behavioural data from N = 802 participants watching one of eleven live classical chamber music concerts that differed regarding their formats. To test whether the audience experience differs depending on the format, physiological measures were obtained via portable sensors (heart and respiration activity, electrodermal activity), facial expression (valence, intensity) was extracted from video recordings, and subjective appreciation and experience was assessed with a post-concert survey. All dependent variables are z-standardized.
DOI: 10.17617/3.ghaalo
title: HLA alignment files for two ancient high-coverage genomes: Ranis13 and Zlaty kun

description: HLA alignment files for the high-coverage genomes Ranis13 and Zlaty kun. Sequence data were mapped to the HLA reference file, accessible at https://targt-pipeline.sourceforge.io/, using Bowtie2.
DOI: 10.17617/3.1oauep
title: The Roots Go Deep: NLNOG RING Active DNS Root Server Measurements

description: This repository contains the active measurement data for The Roots Go Deep: Measuring ‘.’ Under Change. 
For more information, see our paper: 

Florian Steurer, Daniel Wagner, Danny Lachos, Anja Feldmann, and Tobias Fiebig. 2024. The Roots Go Deep: Measuring ‘.’ Under Change. In Proceedings of the 2024 ACM Internet Measurement Conference (IMC ’24),
November 4–6, 2024, Madrid, Spain. ACM, New York, NY, USA
DOI: 10.17617/3.u13lnz
title: DNp03 recordings and optogenetic activation during flight in Drosophila

description: This data set contains the raw data for whole-cell patch-clamp recordings from the descending neuron DNp03 and simultaneously recorded wing stroke amplitude data during visual stimulus presentation, as well as flight trajectories of freely flying Drosophila during optogenetic activation of descending neurons.
DOI: 10.17617/3.egkv28
title: Eigenstrat files for genome-wide shotgun data of ancient and present-day individuals

description: Eigenstrat files used for genome-wide f-statistics calculations, that are based on the shotgun data of analysed individuals. Includes a small perl script for converting vcf files into eigenstrat file format.
DOI: 10.15468/dl.bcvxkq
title: Occurrence Download

description: A dataset containing 477 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Deparia pterorachis (Christ) M.Kato",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2010",
 "HasCoordinate is true"
 ]
}

 The dataset includes 477 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021510-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17617/3.wufmfn
title: Data repository for "High-resolution observations of NO2 and CO2 emission plumes from space"

description: This data set presents all EnMAP results and data used to create the figures and values in the study.&lt;br&gt;

- fit_samples.zip: Sample spectra for the creation of Fig. S1.&lt;br&gt;
&lt;br&gt;
- fluxes.zip: zipped folder contains the calculated NO2 and CO2 fluxes from the EnMAP measurements as well as the corresponding NO2/CO2 ratio as a function of distance from the respective source for each use case. &lt;br&gt;
&lt;br&gt;
The individual netcdf files (.nc) contain the following variables for each use case of the study:&lt;br&gt;
- Longitude &lt;br&gt;
- Latitude &lt;br&gt;
- RGB Channel Information &lt;br&gt;
- SWIR Information &lt;br&gt;
- EnMAP NO2 dVCD &lt;br&gt;
- EnMAP CO2 dVCD &lt;br&gt;
- Plume Mask &lt;br&gt;
- NO2/CO2 ratio &lt;br&gt;
- TROPOMI NO2 dVCD &lt;br&gt;
- EnMAP NO2 dVCD resampled to TROPOMI resolution &lt;br&gt;
- Wind speed
DOI: 10.17617/3.bsxxsq
title: Script and code for "Bayesian reinforcement learning models reveal how great-tailed grackles improve their behavioral flexibility in serial reversal learning experiments"

description: This file contains the R script for the analyses presented in Lukas et al. (2024) https://doi.org/10.32942/osf.io/4ycps
description: R, 4.3.3
DOI: 10.17617/3.eznkyv
title: Sample Dataset for YOLO-Behaviour: A simple, flexible framework to automatically quantify animal behaviours from videos

description: Sample dataset and weights for YOLO-Behaviour framework. Required to run demo code in the documentation. Also provided bounding box datasets for 4 case studies in YOLO format. The human dataset is not included due to privacy concerns.

Code: https://github.com/alexhang212/YOLO_Behaviour_Repo
Documentation: https://alexhang212.github.io/YOLO_Behaviour_Repo/
DOI: 10.17617/3.ypxug0
title: Imprinted atomic displacements drive spin-orbital order in a vanadate perovskite

description: The experimental data shown in all relevant figures of the publication "Imprinted atomic displacements drive spin-orbital order in a vanadate perovskite" can be found in the data files named Fig*.csv. The file format is CSV with delimiter ','. Please see the README.docx file for further explanation of the data file names.
DOI: 10.17617/3.npidk2
title: Scripts for data analysis of "Chromosome architecture and low cohesion bias acrocentric chromosomes towards aneuploidy during mammalian meiosis"

description: This code data set is associated to a publication. The code has been used to process and analyze microscopy images of mammalian oocytes during meiosis. In particular the code allowed to track chromosomes in time lapse images, morphometrics and segmentation of kinetochores.
description: Fiji
description: Matlab
description: R
DOI: 10.21233/88em-9j92
title: Chalahuites vertebrate fauna dataset

description: Raw data for the Chalahuites vertebrate fauna 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.b8i2lj
title: Experimentally assessing the electronic structure and spin state energetics in MnFe dimers using 1s3p resonant inelastic X-ray scattering

description: Data set per figure.
DOI: 10.17617/3.k7zdg5
title: Rising atmospheric levels of fine particulate matter reduce the degree of linear polarisation of light

description: Many insects utilise optical information in linearly polarised light for navigation, with the degree of linear polarisation (DoLP) determining whether the ‘visibility’ of such optical information is available to them. However, changes in degree of linear polarisation in response to increased atmospheric levels of fine particulate matter (PM2.5) are poorly understood. Here, we specifically use honeybees as a representative case to illustrate how these changes may impact insect navigation. We present analyses based on both ground-based monitoring and particulate matter modelling, establishing a quantitative relationship between PM2.5 mass concentration and the DoLP. We apply this relationship to a global PM2.5 projection for 2050 and estimate the increase in number and spatial extent of low visibility days for honeybees. We find an increase by up to 20% in the geographical extent of low visibility days in 2050, with an augmented frequency of low visibility days across an area exceeding 0.75 million km2 in India and 2 million km2 in China. More frequent and widespread low visibility conditions can reduce the ability of insects to navigate, especially in hotspot regions.
description: R
DOI: 10.17617/3.rxjpsa
title: Supplemental material for the PhD thesis " Detection and functional annotation of unique genomic regions"

description: Supplementary material for the thesis "Detection and functional annotation of unique genomic regions"
Available at:
DOI: 10.17617/3.svhtrh
title: APEXLD WP FFT 2024

description: Electron wall probe frequency data from APEX LD
DOI: 10.17617/3.2gbqwy
title: DNA sequences for the manuscript "New-to-nature, CO2-dependent acetyl-CoA assimilation enabled by an engineered B12-dependent acyl-CoA mutase"

description: DNA sequences from the manuscript "New-to-nature, CO2-dependent acetyl-CoA assimilation enabled by an engineered B12-dependent acyl-CoA mutase"
DOI: 10.17617/3.hqtv1j
title: Post-processed data and scripts for "Pattern scaling of simulated vegetation change in North Africa during glacial cycles"

description: This dataset provides information needed to reproduce numbers and figures in the
study entitled "Pattern scaling of simulated vegetation change in North Africa during glacial cycles". It includes post-processed model output from the MPI-ESM 1.2 climate model (at T31 resolution) and respective processing Python scripts. It also contains a small set of proxy data obtained from other studies which are publicly available online (external web resources). Please refer to the original data sources of the proxy data as they are cited in the accompanying manuscript of this dataset.
DOI: 10.17617/3.qrixln
title: Three dimensionally printed microstructured alginate scaffolds for neural tissue engineering

description: Raw data for the paper
DOI: 10.17617/3.blyngq
title: This dataset contains the experimental diffraction frames for compound 4-I used in the manuscript entitled "Polymorphism and whole-molecule disorder of an antitubercular 8-nitrobenzothiazinone" by Rüdiger W. Seidel, Richard Goddard, Tom Schlegel, Adrian Richter, Ines Rudolph, Peter Imming.

description: This dataset contains the experimental data used in the manuscript entitled "Polymorphism and whole-molecule disorder of an antitubercular 8-nitrobenzothiazinone". The dataset contains raw diffraction data in the Bruker AXS .sfrm format.
description: APEX3, v2018.7-2
DOI: 10.17617/3.8wofvw
title: This dataset contains the experimental diffraction frames for compound 1-II used in the manuscript entitled "Polymorphism and whole-molecule disorder of an antitubercular 8-nitrobenzothiazinone" by Rüdiger W. Seidel, Richard Goddard, Tom Schlegel, Adrian Richter, Ines Rudolph, Peter Imming.

description: This dataset contains the experimental data used in the manuscript entitled "Polymorphism and whole-molecule disorder of an antitubercular 8-nitrobenzothiazinone". The dataset contains raw diffraction data in the Bruker AXS .sfrm format.
description: APEX5, Software Version: v2023.9-4
DOI: 10.17617/3.qxuamn
title: Supplemental data for "3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization"

description: Sex chromosomes are unique genomic regions displaying structural and evolutionary features that markedly distinguish them from autosomes. Although nuclear three dimensional (3D) folding of chromatin structure has been linked to 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 role 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 insulated and span the centromeres. Moreover, we link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of the 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 impact of a latent giant dsDNA virus on the host genome’s 3D chromosomal folding.
DOI: 10.17617/3.s0hj48
title: Source Data for "Frequent transitions in self-assembly across the evolution of a central metabolic enzyme"

description: Source data for the manuscript "Frequent transitions in self-assembly across the evolution of a central metabolic enzyme" including MP spectra, kinetic traces, growth curves and AF2-predicted models as well as phylogenetic trees, alignments, ancestral sequences.
DOI: 10.15468/dl.cfa9pu
title: Occurrence Download

description: A dataset containing 1832 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cantharellus cibarius Fr.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Geometry POLYGON ((-20 20, -20 75, 45 75, 45 20, -20 20))"
 ]
}

 The dataset includes 1832 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021495-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17617/3.vasy8p
title: Brachinus crepitans - Transcriptomic Data - Supplemental File S2

description: Transcriptome assembly of Brachinus crepitans combining body and gland RNAseq data. The Excel file contains the contig IDs, sequences, annotation and relative gene expression levels for all RNAseq samples.
DOI: 10.17617/3.wo4cvd
title: Brachinus crepitans - Transcriptomic Data - Supplemental File S1

description: Transcriptome assembly of Brachinus crepitans gland RNAseq data. The Excel file contains the contig IDs, sequences, annotation and relative gene expression levels for all RNAseq samples.
DOI: 10.17617/3.epu9pq
title: Mechanism of sensor kinase CitA transmembrane signaling

description: NMR spectra for CitA
DOI: 10.21233/13xt-xq80
title: Queen Lake water chemistry dataset

description: Raw data for the Queen Lake water chemistry 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.dqs7sb
title: Source data for The mitochondrial citrate synthase from Tetrahymena thermophila does not form an intermediate filament

description: Epifluorescence microscopy files for Tetrahymena thermophila strep_tag mutants conjugating with wild-type cells. 
SIM microscopy files for Tetrahtyemna thermophila strep GFP mutants under fed, starving, and conjugating conditions.
Mass photometry measurements report in .csv format.
DOI: 10.17617/3.pjseul
title: The expansion and diversification of epigenetic regulatory networks underpins major transitions in the evolution of land plants

description: Epigenetic silencing is essential for regulating gene expression and cellular diversity in eukaryotes. While transposable elements (TEs) are mostly silenced with DNA and H3K9 methylation, gene silencing is mediated by H3K27me3, an epigenetic mark deposited by the Polycomb repressive complex 2 (PRC2). Despite the major role epigenetic silencing plays in the development of multicellular eukaryotes, little is known about how epigenetically-controlled regulatory networks were shaped over evolutionary time. Here, we analyse epigenomes from a diverse group of species across the green lineage and infer the chronological epigenetic recruitment of genes that occurred during land plant evolution. We first reveal the nature of plant heterochromatin in the unicellular green microalga Chlorella sorokiniana and identify a substantial number of genes marked with H3K27me3, highlighting the deep origin of PRC2-regulated genes in the green lineage. By incorporating genomic phylostratigraphy, we show how genes of differing evolutionary age are partitioned into distinct epigenetic states in plants, with evolutionarily young genes incorporated into developmental programs controlled by H3K9 methylation in Arabidopsis. We further reveal a major wave of PRC2 recruitment to genes that emerged during land terrestrialisation and flowering plant evolution, and identify an ancestral PRC2 network with a shared functional topology in green algae through to land plants, providing a glimpse of the earliest types of genes regulated by PRC2 during the course of plant evolution. Finally, we analyse the potential regulation of these ancestral PRC2 target genes and find a strong enrichment of motifs bound by ancient AP2/ERF transcription factors (TFs) known to interact with PRC2, which we hypothesise were key determinants in shaping some of the first gene regulatory networks controlled by PRC2 in plants. Our data thus reveal pivotal epigenetic adaptations that occurred during a significant period in the evolutionary history of plants, which likely contributed to key regulatory innovations that influenced major morphological and developmental change into the modern-day. More broadly, our findings offer insight into the evolutionary dynamics and molecular triggers that drive the adaptation and elaboration of epigenetic regulation, laying the groundwork for its future consideration in other major eukaryotic lineages.
DOI: 10.17617/3.w1nniv
title: Symbiosis and horizontal gene transfer promote herbivory in the megadiverse leaf beetles

description: Beetles that feed on the nutritionally depauperate and recalcitrant tissues provided by the leaves, stems, and roots of living plants comprise one quarter of herbivorous insect species. Among the key adaptations for herbivory are plant cell wall degrading enzymes (PCWDEs) that break down the fastidious polymers in the cell wall and grant access to the nutritious cell content. While largely absent from the non-herbivorous ancestors of beetles, such PCWDEs were occasionally acquired via horizontal gene transfer (HGT) or by the uptake of digestive symbionts. However, the macro-evolutionary dynamics of PCWDEs and their impact on evolutionary transitions in herbivorous insects remained poorly understood. Through genomic and transcriptomic analyses of 74 leaf beetle species and 50 symbionts, we show that multiple independent events of microbe-to-beetle horizontal gene transfer and specialized symbioses drove convergent evolutionary innovations in approximately 21,000 and 13,500 leaf beetle species, respectively. Enzymatic assays indicate that these events significantly expanded the beetles’ digestive repertoires and thereby contributed to their adaptation and diversification. Our results exemplify how recurring HGT and symbiont acquisition catalyzed digestive and nutritional adaptations to herbivory and thereby contributed to the evolutionary success of a megadiverse insect taxon.