cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29673470
title: Large-scale multi-omics unveils host-microbiome interactions driving root development and nitrogen acquisition

description: The microbiome influences the performance and fitness of the host plant. Nevertheless, the biotic interaction between host genetic variation, gene regulation and the impact of the microbiome on the host phenotype remain unknown. Here, we generated 1,341 paired datasets, including root transcriptomes, rhizosphere prokaryotic taxa, and root ionomes, to conduct multi-omics analyses of the host-microbe associations at the root-soil interface using 175 rapeseed (Brassica napus L.) ecotypes that were resequenced and evaluated at two field environments. We observed the high prediction ability of nitrogen uptake, with a prediction accuracy of 0.67, accounting for about 45% of the variance in nitrogen levels among natural ionomic variations. This significant proportion of explained variance was driven by the overall transcriptome-wide gene expression and 203 highly heritable microbial amplicon sequence variants (ASVs). These microbial variations were strongly associated with root nitrogen uptake, underscoring the role of the microbiome in plant nutrition. We also identified significant genome-wide associations for the 203 heritable ASVs at multiple genetic loci, regulated by eQTL hotspots, particularly those involved in carbon and nitrogen metabolism. These associations involved a dominant bacterial genus, Sphingopyxis, which exhibited a strong gene regulatory effect on its variation, regulated by the eQTL hotspots. In addition, we performed high-throughput bacterial cultivation from rapeseed roots and subjected the isolated bacterial isolate to whole-genome sequencing. Finally, targeted plant metabolite profiling of auxin biosynthesis and root confocal imaging assays demonstrated that Sphingopyxis regulates lateral root development and impacts plant nitrogen nutrition. These results suggest a host-microbiome regulatory effect that connects bacterial abundance with plant root architecture and nutrient acquisition. In summary, this study reveals the genetic basis of host-microbiome trait associations across transcriptional, nutritional and environmental domains and suggests that the potential of bacterial microbiome might have consistent effects on root development with implications towards the breeding of nutrient-efficient crops.
DOI: 10.6084/m9.figshare.29673470.v4
title: Large-scale multi-omics unveils host-microbiome interactions driving root development and nitrogen acquisition

description: The microbiome influences the performance and fitness of the host plant. Nevertheless, the biotic interaction between host genetic variation, gene regulation and the impact of the microbiome on the host phenotype remain unknown. Here, we generated 1,341 paired datasets, including root transcriptomes, rhizosphere prokaryotic taxa, and root ionomes, to conduct multi-omics analyses of the host-microbe associations at the root-soil interface using 175 rapeseed (Brassica napus L.) ecotypes that were resequenced and evaluated at two field environments. We observed the high prediction ability of nitrogen uptake, with a prediction accuracy of 0.67, accounting for about 45% of the variance in nitrogen levels among natural ionomic variations. This significant proportion of explained variance was driven by the overall transcriptome-wide gene expression and 203 highly heritable microbial amplicon sequence variants (ASVs). These microbial variations were strongly associated with root nitrogen uptake, underscoring the role of the microbiome in plant nutrition. We also identified significant genome-wide associations for the 203 heritable ASVs at multiple genetic loci, regulated by eQTL hotspots, particularly those involved in carbon and nitrogen metabolism. These associations involved a dominant bacterial genus, Sphingopyxis, which exhibited a strong gene regulatory effect on its variation, regulated by the eQTL hotspots. In addition, we performed high-throughput bacterial cultivation from rapeseed roots and subjected the isolated bacterial isolate to whole-genome sequencing. Finally, targeted plant metabolite profiling of auxin biosynthesis and root confocal imaging assays demonstrated that Sphingopyxis regulates lateral root development and impacts plant nitrogen nutrition. These results suggest a host-microbiome regulatory effect that connects bacterial abundance with plant root architecture and nutrient acquisition. In summary, this study reveals the genetic basis of host-microbiome trait associations across transcriptional, nutritional and environmental domains and suggests that the potential of bacterial microbiome might have consistent effects on root development with implications towards the breeding of nutrient-efficient crops.
DOI: 10.6084/m9.figshare.29673470.v5
title: Large-scale multi-omics unveils host-microbiome interactions driving root development and nitrogen acquisition

description: The microbiome influences the performance and fitness of the host plant. Nevertheless, the biotic interaction between host genetic variation, gene regulation and the impact of the microbiome on the host phenotype remain unknown. Here, we generated 1,341 paired datasets, including root transcriptomes, rhizosphere prokaryotic taxa, and root ionomes, to conduct multi-omics analyses of the host-microbe associations at the root-soil interface using 175 rapeseed (Brassica napus L.) ecotypes that were resequenced and evaluated at two field environments. We observed the high prediction ability of nitrogen uptake, with a prediction accuracy of 0.67, accounting for about 45% of the variance in nitrogen levels among natural ionomic variations. This significant proportion of explained variance was driven by the overall transcriptome-wide gene expression and 203 highly heritable microbial amplicon sequence variants (ASVs). These microbial variations were strongly associated with root nitrogen uptake, underscoring the role of the microbiome in plant nutrition. We also identified significant genome-wide associations for the 203 heritable ASVs at multiple genetic loci, regulated by eQTL hotspots, particularly those involved in carbon and nitrogen metabolism. These associations involved a dominant bacterial genus, Sphingopyxis, which exhibited a strong gene regulatory effect on its variation, regulated by the eQTL hotspots. In addition, we performed high-throughput bacterial cultivation from rapeseed roots and subjected the isolated bacterial isolate to whole-genome sequencing. Finally, targeted plant metabolite profiling of auxin biosynthesis and root confocal imaging assays demonstrated that Sphingopyxis regulates lateral root development and impacts plant nitrogen nutrition. These results suggest a host-microbiome regulatory effect that connects bacterial abundance with plant root architecture and nutrient acquisition. In summary, this study reveals the genetic basis of host-microbiome trait associations across transcriptional, nutritional and environmental domains and suggests that the potential of bacterial microbiome might have consistent effects on root development with implications towards the breeding of nutrient-efficient crops.
DOI: 10.15468/dl.6rp7uj
title: Occurrence Download

description: A dataset containing 646 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Specimen)",
 "Country is Mexico",
 "TaxonKey is Centurio senex",
 {
 "or" : [
 "Year 1982-1982",
 "Year 1980-2025"
 ]
 }
 ]
}

 The dataset includes 646 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009914-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15775838
title: U2-intron strand displacement towards branch helix

description: Datasets from the U2-intron strand displacement simulations



U2_BPH_data - simulation setup data, input files, reference structures, analysis files (see also this repo)

trajectories/* - trajectory data (all without water) and the respective topologies (*.parm7). All trajectories are strided with 1 frame per 1 ns


in the strand_displacement_*/  directories:    nomod_* are trajectories with no force-field modification    hbf_* are trajectories with HBfix    hbfstf_* are trajectories with HBfix and stafix

in the metadynamics/ directories:    rep_*cut.xtc are non-stroden trajectories with spurious parts cut out (see SI for details). These were used to calculate energies (and correspond to the deposited HILLS files)    rep*_full_strode.xtc are trajectories strode without the cut-outs



HILLS - HILLS files from the metadynamics, raw and averaged, where applicable.
DOI: 10.5281/zenodo.15775839
title: U2-intron strand displacement towards branch helix

description: Datasets from the U2-intron strand displacement simulations



U2_BPH_data - simulation setup data, input files, reference structures, analysis files (see also this repo)

trajectories/* - trajectory data (all without water) and the respective topologies (*.parm7). All trajectories are strided with 1 frame per 1 ns


in the strand_displacement_*/  directories:    nomod_* are trajectories with no force-field modification    hbf_* are trajectories with HBfix    hbfstf_* are trajectories with HBfix and stafix

in the metadynamics/ directories:    rep_*cut.xtc are non-stroden trajectories with spurious parts cut out (see SI for details). These were used to calculate energies (and correspond to the deposited HILLS files)    rep*_full_strode.xtc are trajectories strode without the cut-outs



HILLS - HILLS files from the metadynamics, raw and averaged, where applicable.
DOI: 10.15468/dl.nj7rh5
title: Occurrence Download

description: A dataset containing 382 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Bambusa balcooa"
 ]
}

 The dataset includes 382 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009915-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.27967.98729
title: International Certificate Irina Vasileva. Has received this award for successfully completing the course. Leadership and Management for Managers. The Continuing Professional Development (CPD). Certified. Certification Service. Alison. 29th October, 2025. Certificate 5050-47454999. UK
DOI: 10.5281/zenodo.17113746
title: Geodetic Deformation, DPM products, and source imaging results in "Bimaterial Effect and Favorable Energy Ratio Enabled Supershear Rupture in the 2025 Mandalay Earthquake" (Xu et al., 2025, Science, DOI: 10.1126/science.ady6100)

description: This repository contains the geodetic deformation, DPM products, and source imaging results (including the finite fault inversion and back-projection) in "Bimaterial Effect and Favorable Energy Ratio Enabled Supershear Rupture in the 2025 Mandalay Earthquake" (Xu et al., 2025, Science). Please refer to readme.txt file for the detailed description.

Please cite our paper "Bimaterial Effect and Favorable Energy Ratio Enabled Supershear Rupture in the 2025 Mandalay Earthquake" (Xu et al., 2025, Science, DOI: 10.1126/science.ady6100) if you use any of our data. Feel free to contact me (xuliuw1997@ucla.edu) if you have any questions.

We thank the European Space Agency, China Centre for Resources Satellite Data and Application, and Aerospace Exploration Agency of Japan (JAXA) for providing the Sentinel-­1, LuTan-­1, and ALOS-­2 SAR imagery.
DOI: 10.5517/ccdc.csd.cc2khb0f
title: CCDC 2368214: Experimental Crystal Structure Determination

description: Related Article: Qiang Wen, Melissa Tan, Ofir Eisenberg, Hadar Nasi, Vlad Brumfeld, Akash Tiwari, Hai-Mu Ye, Bart Kahr, Linda J. W. Shimon, Michal Lahav, Milko E. van der Boom|2025|Nat.Commun.|16|8441|doi:10.1038/s41467-025-62889-2
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: 10.5281/zenodo.17113310
title: Geodetic Deformation, DPM products, and source imaging results in "Bimaterial Effect and Favorable Energy Ratio Enabled Supershear Rupture in the 2025 Mandalay Earthquake" (Xu et al., 2025, Science, DOI: 10.1126/science.ady6100)

description: This repository contains the geodetic deformation, DPM products, and source imaging results (including the finite fault inversion and back-projection) in "Bimaterial Effect and Favorable Energy Ratio Enabled Supershear Rupture in the 2025 Mandalay Earthquake" (Xu et al., 2025, Science). Please refer to readme.txt file for the detailed description.

Please cite our paper "Bimaterial Effect and Favorable Energy Ratio Enabled Supershear Rupture in the 2025 Mandalay Earthquake" (Xu et al., 2025, Science, DOI: 10.1126/science.ady6100) if you use any of our data. Feel free to contact me (xuliuw1997@ucla.edu) if you have any questions.

We thank the European Space Agency, China Centre for Resources Satellite Data and Application, and Aerospace Exploration Agency of Japan (JAXA) for providing the Sentinel-­1, LuTan-­1, and ALOS-­2 SAR imagery.
DOI: 10.5517/ccdc.csd.cc2n5y4y
title: CCDC 2448570: Experimental Crystal Structure Determination

description: Related Article: Xiao‐Feng Xie, Ya-Yu Dong, Guo-Ping Yang|2025|Tungsten|||doi:10.1007/s42864-025-00360-x
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: 10.15468/dl.75gtjm
title: Occurrence Download

description: A dataset containing 5488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "OccurrenceStatus is Present",
 "TaxonKey is Lontra canadensis",
 "Year 1996-2025"
 ]
}

 The dataset includes 5488 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009916-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e239462
title: COEP Replication Package for 'Nurse Practitioner Scope of Practice Law and Safety Net Participation: Evidence from WIC'

description: Given that nurse practitioners (NPs) are likely to practice
in underserved areas, NP scope of practice reform may have spillover effects on
safety net program participation. Leveraging the staggered rollout of NP full
practice authority (FPA) across states, we estimate the effect of NP FPA on WIC
participation. We find that starting 4-5 years after FPA, WIC participation
increases by 4.1%, rising to 7.4% a decade post-FPA. The increase is driven by
the enrollment of women and children and may be attributable to the patient-centered care delivery of NPs, which reduces
the stigma and information costs associated with WIC participation.<b></b>
DOI: 10.5281/zenodo.17475744
title: Supported data for manuscript "Fingerprints of Mott and Slater gaps in the core-level photoemission spectra of antiferromagnetic iridates"

description: Supported data for manuscript "Fingerprints of Mott and Slater gaps in the core-level photoemission spectra of antiferromagnetic iridates" in Phys. Rev. B 111, 195114 (2025).
DOI: 10.5281/zenodo.17475743
title: Supported data for manuscript "Fingerprints of Mott and Slater gaps in the core-level photoemission spectra of antiferromagnetic iridates"

description: Supported data for manuscript "Fingerprints of Mott and Slater gaps in the core-level photoemission spectra of antiferromagnetic iridates" in Phys. Rev. B 111, 195114 (2025).
DOI: 10.15468/dl.t5prbe
title: Occurrence Download

description: A dataset containing 345 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mozambique_Fish_Collections"
 ]
}

 The dataset includes 345 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009921-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48366/r1559306
title: Comparative Analysis of Transfer Learning-Based Malware Detection Approaches

description: This work reflects a comparative research of literature concerning authors who rely on transfer learning to develop solutions to detect malware
DOI: 10.15468/dl.tadfpm
title: Occurrence Download

description: A dataset containing 357 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Physalaemus signifer"
 ]
}

 The dataset includes 357 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009922-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/dans-zqp-fxwj
title: Kindertransporten: 'Joodse kinderen in kamp Vught' - documentaire (2007) WAT KUNNEN ZE NOU MET ONS DOEN

description: &lt;p&gt;Dit is een korte educatieve documentaire, gebaseerd op de interviews met bovenstaande getuigen, en gemaakt voor de doelgroep 11-14 jaar. Af en toe zijn foto’s (historische beelden en privéfoto’s van o.a. familieleden) te zien.&lt;br&gt;Het verhaal over de bezetting, de deportaties, kamp Vught en andere kampen wordt door de getuigen min of meer chronologisch verteld. De sprekers wisselen elkaar af in snelle, korte montages. De interviewfragmenten worden doorsneden met hedendaagse beelden van spelende kinderen.&lt;/p&gt;&lt;p&gt;De geïnterviewden zijn: Koos Valk, Lotty Veffer, Ernst Verduin, Kitty Wurms&lt;/p&gt;&lt;p&gt;De getuigen vertellen over hun herinneringen aan de inval, en de verwachtingen die zij koesterden over wat er met de Joden in Nederland zou gebeuren. Over het algemeen was de gedachte dat ze naar werkkampen moesten. ‘Wat kunnen ze nou met ons doen?’&lt;br&gt;Om hen heen werden steeds meer Joden van huis gehaald. Tot ook het moment daar was dat zij zelf aan de beurt waren.&lt;br&gt;De tocht van station Vught naar het kamp maakte veel indruk. De mannen, vrouwen en kinderen werden van elkaar gescheiden en in aparte barakken ondergebracht. De omstandigheden in het kamp waren vreselijk: te weinig eten, slechte hygiëne, agressieve bewaking. Veel kinderen werden ziek. Twee van de getuigen waren zelf nog kind: Koos Valk (9), Ernst Verduin (15). Koos was erg in paniek omdat hij alleen werd gelaten. Kitty vertelt over het spaarzame contact met haar vader, en hoe ze zag dat hij een keer kreupel geslagen was. Koos werd ziek, belandde in de ziekenbarak en trof hier zijn broertje. Aanvankelijk herkenden ze elkaar niet eens, zo mager waren ze.&lt;br&gt;Bij het Kindertransport van 6 en 7 juni 1943 moesten de ouders en jongste zusjes van Kitty en Lotty mee. Het afscheid was dramatisch. Lotty, Kitty en Ernst werden enige tijd later naar Auschwitz gedeporteerd, en vertellen kort over hun aankomst daar.&lt;/p&gt;
DOI: 10.15468/dl.t4kj48
title: Occurrence Download

description: A dataset containing 500 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Unio crassus crassus"
 ]
}

 The dataset includes 500 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009924-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13569077
title: Autistic Children Emotions - Dr. Fatma M. Talaat
DOI: 10.15468/dl.mr3bw7
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "TaxonKey is Staminodianthus rosae"
 ]
}

 The dataset includes 28 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009928-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r9xz5h
title: Occurrence Download

description: A dataset containing 4635481 species occurrences available in GBIF matching the query:
{
 "GadmGid" : [
 "is one of (BEL.3_1)"
 ]
}

 The dataset includes 4635481 records from 672 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009893-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/776-t89-1dl
title: Amaranthus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/yf8-aew-2gb
title: Rubiaceae

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/rrf-4dz-tj6
title: Amaranthus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/z63-9g6-atz
title: Apiaceae Lindl.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/tm6-f48-9be
title: Achyranthes aspera L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/hjr-6av-96j
title: Amaranthus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/t65-3ts-kh2
title: Achyranthes aspera L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/w2k-ztd-ynw
title: Achyranthes aspera L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/yxe-fmk-sv8
title: Orchidaceae

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/asz-hm5-npd
title: Amaranthus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/jjq-7lc-6b4
title: Achyranthes aspera L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/9br-w34-gyn
title: Achyranthes aspera L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/qsh-ryy-sr4
title: Amaranthus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/305-75x-vnj
title: Amaranthus spinosus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/3z0-q0s-vyt
title: Amaranthus spinosus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/q5w-ws4-96p
title: Amaranthus spinosus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/0da-87f-k78
title: Amaranthus spinosus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/1f2-8ds-9m2
title: Fagaceae

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/7mg-jal-764
title: Erigeron acris subsp. pycnotrichus (F. Vierh.) Grierson

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.