cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8333110
title: Growth Chamber mesocosm experiment to assess the effects of the OSS decoupled from the presence of G. senegalensis (PRJNA930014)

description: The Sahel region of West Africa is a vulnerable eco-region where a growing population and climate-change induced drought threaten food security. The subsistence farmers here grow pearl millet (Pennisetum glaucum) without fertilizers or irrigation. Local and biologically-based means of maintaining yields are needed, and an agroforestry system in Senegal - the Optimized Shrub-intercropping System (OSS) - provides a solution. In the OSS, the shrub Gueira senegalensis performs hydraulic lift, distributing deep subsurface water to neighboring millet plants. The shrub also supports a distinct microbial community and significantly improves carbon storage and nutrient dynamics. Here, we aimed to test whether shrub-impacted soils differed in microbiome and millet outcomes under simulated early-season drought in a growth chamber. Shrub impact was separated into residual impacts on microbiome and soil, versus ongoing shrub-derived organic matter (OM) input. decoupled from the effects of the growing shrub. Methods: We characterized the microbiota through dry-down and rewetting periods, with particular attention to lineages with known plant growth promoting (PGP) properties, via amplicon sequencing of the 16S rRNA gene V3-V4 region and the ITS2, . Results: Both bacterial and fungal communities were significantly altered by imposed drought, OM amendment, and original soil type (+/-OSS). The largest significant bacterial community impact under dry down occurred for +shrub/-OM treatments, and under rewetting for -OM treatment regardless of +/- OSS. Known bacterial PGP lineages were only enriched under drought in +OSS/-OM treatments. The fungal community behaved differently with a significant dry-down impact only in +OSS/+OM treatments, while rewetting enriched for fungal pathogens but only in -OSS/+OM soils. Decoupled from ongoing shrub growth, both residual shrub impacts and shrub OM inputs altered microbiota and increased millet biomass under drought. These results are part of a growing body of work aimed at understanding microbiome roles in increasing ecological resilience and combating food insecurity. Metagenomic and amplicon sequencing data are publicly available via NCBI PRJNA930014. Here we present all associated soil chemical, enzyme, and plant physical and chemical data
DOI: 10.5281/zenodo.8333109
title: Growth Chamber mesocosm experiment to assess the effects of the OSS decoupled from the presence of G. senegalensis (PRJNA930014)

description: The Sahel region of West Africa is a vulnerable eco-region where a growing population and climate-change induced drought threaten food security. The subsistence farmers here grow pearl millet (Pennisetum glaucum) without fertilizers or irrigation. Local and biologically-based means of maintaining yields are needed, and an agroforestry system in Senegal - the Optimized Shrub-intercropping System (OSS) - provides a solution. In the OSS, the shrub Gueira senegalensis performs hydraulic lift, distributing deep subsurface water to neighboring millet plants. The shrub also supports a distinct microbial community and significantly improves carbon storage and nutrient dynamics. Here, we aimed to test whether shrub-impacted soils differed in microbiome and millet outcomes under simulated early-season drought in a growth chamber. Shrub impact was separated into residual impacts on microbiome and soil, versus ongoing shrub-derived organic matter (OM) input. decoupled from the effects of the growing shrub. Methods: We characterized the microbiota through dry-down and rewetting periods, with particular attention to lineages with known plant growth promoting (PGP) properties, via amplicon sequencing of the 16S rRNA gene V3-V4 region and the ITS2, . Results: Both bacterial and fungal communities were significantly altered by imposed drought, OM amendment, and original soil type (+/-OSS). The largest significant bacterial community impact under dry down occurred for +shrub/-OM treatments, and under rewetting for -OM treatment regardless of +/- OSS. Known bacterial PGP lineages were only enriched under drought in +OSS/-OM treatments. The fungal community behaved differently with a significant dry-down impact only in +OSS/+OM treatments, while rewetting enriched for fungal pathogens but only in -OSS/+OM soils. Decoupled from ongoing shrub growth, both residual shrub impacts and shrub OM inputs altered microbiota and increased millet biomass under drought. These results are part of a growing body of work aimed at understanding microbiome roles in increasing ecological resilience and combating food insecurity. Metagenomic and amplicon sequencing data are publicly available via NCBI PRJNA930014. Here we present all associated soil chemical, enzyme, and plant physical and chemical data
DOI: 10.5281/zenodo.8356264
title: Supplementary Data: An evaluation of the General Bathymetric Chart of the Ocean (GEBCO) in shoreline-crossing geomorphometric investigations of volcanic islands

description: Supplementary data for the titular publication. Consists of .csv and .gpkg files with the results of geomorphometric parameter extraction of volcanic islands from shoreline-crossing DEMs of various resolution, the calculation of the deviation of these parameters depending on the source DEM, as well as basic statistical distribution of these parameters. See publication for more detailed information.
DOI: 10.5281/zenodo.8356263
title: Supplementary Data: An evaluation of the General Bathymetric Chart of the Ocean (GEBCO) in shoreline-crossing geomorphometric investigations of volcanic islands

description: Supplementary data for the titular publication. Consists of .csv and .gpkg files with the results of geomorphometric parameter extraction of volcanic islands from shoreline-crossing DEMs of various resolution, the calculation of the deviation of these parameters depending on the source DEM, as well as basic statistical distribution of these parameters. See publication for more detailed information.
DOI: 10.6084/m9.figshare.21365532
title: Source data for Brabham, Gomez De La Cruz et al.

description: Source data for Brabham, Gomez De La Cruz et al. (2022) bioRxiv that includes raw data, uncropped images, replicated experiments, and scripts used for data analysis and figure preparation. Updated on September 18th, 2023 with additional figures based on peer review.
DOI: 10.6084/m9.figshare.21365532.v2
title: Source data for Brabham, Gomez De La Cruz et al.

description: Source data for Brabham, Gomez De La Cruz et al. (2022) bioRxiv that includes raw data, uncropped images, replicated experiments, and scripts used for data analysis and figure preparation. Updated on September 18th, 2023 with additional figures based on peer review.
DOI: 10.6084/m9.figshare.21365532.v1
title: Source data for Brabham, Gomez De La Cruz et al. (2022)

description: Source data for Brabham, Gomez De La Cruz et al. (2022) that includes raw data, uncropped images, replicated experiments, and scripts used for data analysis and figure preparation.
DOI: 10.5281/zenodo.8356068
title: Clinical subtyping of cancer from plasma based on comprehensive epigenomic profiling

description: <strong><em>Peak bed files.</em></strong> While circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1mL of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors, and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling could unlock clinically actionable information that is currently accessible only via direct tissue sampling.
DOI: 10.5281/zenodo.8356067
title: Clinical subtyping of cancer from plasma based on comprehensive epigenomic profiling

description: <strong><em>Peak bed files.</em></strong> While circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1mL of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors, and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling could unlock clinically actionable information that is currently accessible only via direct tissue sampling.
DOI: 10.5281/zenodo.8333762
title: The potential impact of climate change on European renewable energy droughts

description: The file contains a supplementary material for an article entitled <em>The potential impact of climate change on European renewable energy droughts</em> (currently under review): The projected change of the total number of drought days for a wind, solar and hybrid generator in relation to the reference period as predicted by the models considered
DOI: 10.5281/zenodo.8333761
title: The potential impact of climate change on European renewable energy droughts

description: The file contains a supplementary material for an article entitled <em>The potential impact of climate change on European renewable energy droughts</em> (currently under review): The projected change of the total number of drought days for a wind, solar and hybrid generator in relation to the reference period as predicted by the models considered
DOI: 10.25925/20230901
title: Multi-laboratory compilation of atmospheric carbon dioxide data for the year 2023; obspack_co2_1_NRT_v9.0_2023-09-16

description: This product is constructed using the Observation Package (ObsPack) framework [Masarie et al., 2014; www.earth-syst-sci-data.net/6/375/2014/]. The framework is designed to bring together atmospheric greenhouse gas (GHG) observations from a variety of sampling platforms, prepare them with specific applications in mind, and package and distribute them in a self-consistent and well-documented product. ObsPack products are intended to support GHG budget studies and represent a new generation of cooperative value-added GHG data products.
DOI: 10.25345/c5v40k90q
title: MassIVE MSV000092887 - Exploring the Metabolic Consequences of SARSCoV2 Infection A comprehensive IDA and SWATH DIA Lipidomics and Metabolomics dataset
title: Exploring the Metabolic Consequences of SARS-CoV-2 Infection A comprehensive IDA and SWATH-DIA Lipidomics and Metabolomics dataset In this work, we generated an extensive dataset describing the metabolome and lipidome of 39 SARS-CoV-2 infected patients versus age- and gender-matched 39 healthy controls. We implemented state of the art acquisition techniques including IDA and SWATH-DIA to ensure a holistic insight in the lipidome and metabolome, ensuring a future-proof repurposable dataset
DOI: 10.5517/ccdc.csd.cc23gjy2
title: CCDC 1950394: Experimental Crystal Structure Determination

description: Related Article: Saira Manzoor, Rana Adnan Tahir, Muhammad Adnan Younis, Wen-Li Cao, Qamar-un-nisa Tariq, Amjad Ali, Naushad Ahmad, Chuntian Qiu, Bingbing Tian, Jian-Guo Zhang|2023|Bioorg.Chem.|140|106822|doi:10.1016/j.bioorg.2023.106822
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.24156654
title: Unlocking the Future: Navigating 6G Research with Scientometrics and Emerging Trends

description: The advent of 6G, an emerging technology, has ushered in transformative changes across multiple industries. Its numerous benefits have paved the way for extensive research opportunities, thereby capturing the attention of the scholarly community. Given the swift proliferation of 6G-related research, there is a pressing need for a comprehensive examination of the existing knowledge landscape in this domain.
DOI: 10.6084/m9.figshare.24156654.v1
title: Unlocking the Future: Navigating 6G Research with Scientometrics and Emerging Trends

description: The advent of 6G, an emerging technology, has ushered in transformative changes across multiple industries. Its numerous benefits have paved the way for extensive research opportunities, thereby capturing the attention of the scholarly community. Given the swift proliferation of 6G-related research, there is a pressing need for a comprehensive examination of the existing knowledge landscape in this domain.
DOI: 10.6069/qsmg-5m62
title: AD-BXD Mouse Hippocampus Proteomics

description: The AD-BXD mouse population is a powerful emerging model for studying AD resilience. AD-BXD mice query two different levels of genetic information: genometypes and genotypes. The genetically diverse BXD genometypes are a mosaic of the approximately 6 million segregating single nucleotide polymorphisms between C57BL/6J and DBA/2J mice. The transgenic genotype of the 5 times familial Alzheimer’s disease (5xFAD) transgene, which includes human APP carrying three pathogentic variants and human PSEN1 carrying two pathogenic, can be contrasted with non-transgenic control animals (Ntg). Reproducible BXD genometypes allow repeated measurement of the same mosaic genomes, a strategy that boosts the mappable heritability of genetic loci (cite ). This property facilitates QTL mapping of the relatively lower effect size variants that modify susceptibility to Alzheimer’s-like cognitive phenotypes in 5xFAD animals. Further, the same cognitive phenotype can be measured in both 5xFAD and Ntg mice within the same genometype. The ability to contrast a genometype’s performance with different AD genotypes facilitates the measurement of novel and interesting derived phenotypes based upon the property of trait correlation (cite ). Because of these properties, our lab has successfully leveraged AD-BXD mice to identify genetic modifiers of AD-related phenotypes in recent years. We quantified resilience using a novel regression-based metric. We utilized this measure to map resilience to a locus, then leveraged proteomics data to identify a putative molecular mechanism for the genetic resilience factor. We found potential novel targets for AD by querying elements coregulated in trans to the putative molecular mechanism. Finally, we implicated differential expression of networked synaptic proteins as the likeliest downstream consequences of differences in resilience.
DOI: 10.6084/m9.figshare.24156726.v1
title: The long-term flux of the solar wind suprathermal ions that precipitate on the lunar surface

description: This online supplementary material contains numerical values for the Figures of the article "The long-term flux of the solar wind suprathermal ions that precipitate on the lunar surface". It also contains additional maps for the anisotropy of the long-term fluxes of protons, He++, O6+, and Fe10+ ions.<br>
DOI: 10.5066/p9lct8dz
title: Harmonized continuous water quality data in support of modeling harmful algal blooms in the United States, 2005 - 2022

description: Harmful algal blooms (HABs) are overgrowths of algae or cyanobacteria in water and can be harmful to humans and animals directly via toxin exposure or indirectly via changes in water quality and related impacts to ecosystems services, drinking water characteristics, and recreation. While HABs occur frequently throughout the United States, the driving conditions behind them are not well understood, especially in flowing waters. In order to facilitate future national model development and characterization of HABs, this data release publishes a synthesized and cleaned collection of HABs-related water quality and quantity data for river and stream sites across the United States. It includes nutrients, major ions, sediment, physical properties, streamflow, chlorophyll and other types of water data. This data release contains files of harmonized data from the USGS National Water Information System (NWIS). Continuous sensor data for 132 parameters (35 of which returned data) between January 1, 2005 and December 31, 2022 were downloaded from NWIS programmatically. All data were harmonized into a shared format and grouped by generic parameters; data are in files named "daily_{parameter_grp}.csv", and the "pcode_group_xwalk.csv" maps parameter codes to parameter groups. Lastly, we include a "site_metadata.csv" containing site identification and location information for all sites with water quality and quantity data, and mappings to the National Hydrography Dataset flowlines where available. This work was completed as part of the USGS Proxies Project, an effort supported by the Water Mission Area (WMA) Water Quality Processes program to develop estimation methods for PFAS, harmful algal blooms, and metals, at multiple spatial and temporal scales.
DOI: 10.5281/zenodo.8356350
title: lepidocolaptes_lacrymiger_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8356349
title: lepidocolaptes_lacrymiger_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8356355
title: Supplementary information to "What does ChatGPT know about natural science and engineering?"

description: This Excel workbook contains the survey data and data analysis from the manuscript "What does ChatGPT know about natural science and engineering?" by Schulze Balhorn et al.
DOI: 10.5281/zenodo.8356354
title: Supplementary information to "What does ChatGPT know about natural science and engineering?"

description: This Excel workbook contains the survey data and data analysis from the manuscript "What does ChatGPT know about natural science and engineering?" by Schulze Balhorn et al.
DOI: 10.6084/m9.figshare.24156741
title: Raw data

description: The individual raw values used for analysis in the study. Note that the change scores were used for statistical analysis by subtracting the baseline value from the timepoint of interest.
DOI: 10.6073/pasta/3460bfd1905d76470151c759d533801b
title: MCR LTER: Coral Reef: 3D photogrammetry improves measurement of growth and biodiversity patterns in branching corals; data for Curtis 2023, Coral Reefs

description: These data and code were generated in support of the manuscript: Curtis JS, Galvan JW, Primo A, Osenberg CW, and AC Stier, Coral Reefs. We collected manual and photogrammetry-based measurements of coral size and volume to examine which method best described short-term coral growth and links between coral habitat and biodiversity of CAFI (coral-associated fishes and invertebrates). This study was completed between August and December 2019 on an experimental array located in the back reef off the south shore of Moorea, French Polynesia. These data were published in Coral Reefs, analyses and full methods descriptions of this model can be found in the manuscript “3D photogrammetry improves measurement of growth and biodiversity patterns in branching corals”. This manuscript uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2023).
DOI: 10.25919/cspk-3d25
title: Parkes observations for project P1171 semester 2023APRS_14

description: The origin of Fast Radio Bursts (FRBs) is still unclear with a plethora of theoretical models for their origin. Several models predict associated multi-wavelength emission, but previous searches for optical, X-ray or gamma-ray counterparts of FRBs have not led to any detection. The Galactic magnetar SGR 1935+2154A has been observed to simultaneously emit FRB-like bursts and X-ray flares, which suggests that also extragalactic FRB sources may exhibit X-ray counterparts. Because of the high cost of X-ray satellites and in face of the relatively low FRB detection probability in their small field of view, coordinated radio and X-ray observations are logistically very difficult to set up. We propose a new approach using the X-ray satellite XMM-Newton and the Parkes/Murriyang radio telescope to put constraints on the theoretical models: We aim to conduct shadowing observations with the Parkes telescope to search for new FRBs in fields that are simultaneously covered by XMM-Newton. We hereby target regular XMM observations of nearby (low-z) galaxies, to increase our detection chances of possibly associated X-ray emission. In case of an FRB detection in the radio band, we will have guaranteed simultaneous X-ray coverage and will get detailed information about the associated X-ray spectrum and light curve since all XMM-Newton data will become public a year after the observation.