cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7909660
title: rCRUX Generated Kelly Metazoan 16S Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Kelly Metazoan 16S<br> Gene: 16S<br> Length of Target: 114-160<br> get_seeds_local() minimum length: 80<br> get_seeds_local() maximum length: 195<br> blast_seeds() minimum length: 50<br> blast_seeds() maximum length: 168<br> max_to_blast: 100<br> Forward Sequence (5'-3'): AGTTACYYTAGGGATAACAGCG<br> Reverse Sequence (5'-3'): CCGGTCTGAACTCAGATCAYGT<br> Reference: Kelly, R. P., O’Donnell, J. L., Lowell, N. C., Shelton, A. O., Samhouri, J. F., Hennessey, S. M., ... & Williams, G. D. (2016). Genetic signatures of ecological diversity along an urbanization gradient. PeerJ, 4, e2444. https://doi.org/10.7717/peerj.2444 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909670
title: rCRUX Generated MiDeca Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: MiDeca<br> Gene: 16S<br> Length of Target: 154-184<br> get_seeds_local() minimum length: 105<br> get_seeds_local() maximum length: 230<br> blast_seeds() minimum length: 66<br> blast_seeds() maximum length: 191<br> max_to_blast: 50<br> Forward Sequence (5'-3'): GGACGATAAGACCCTATAAA<br> Reverse Sequence (5'-3'): ACGCTGTTATCCCTAAAGT<br> Reference: Komai, T., Gotoh, R.O., Sado, T. and Miya, M., 2019. Development of a new set of PCR primers for eDNA metabarcoding decapod crustaceans. Metabarcoding and Metagenomics, 3, p.e33835. https://doi.org/10.3897/mbmg.6.76534 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.6084/m9.figshare.23903094
title: Evolutionary and ecological forces shape nutrient strategies of mycorrhizal woody plants

description: The associations of arbuscular mycorrhizal (AM) or ectomycorrhiza (EcM) fungi with plants have sequentially evolved and significantly contributed to enhancing plant nutrition. Nonetheless, how evolutionary and ecological forces drive nutrient acquisition strategies of AM and EcM plants remains poorly understood. Our global analysis of woody species revealed that, over divergence time, AM plants evolved faster nitrogen mineralization rates without changes in nitrogen resorption. However, EcM plants exhibited an increase in nitrogen mineralization but a decrease in nitrogen resorption, indicating a shift towards a more inorganic nutrient economy. Despite this alteration, when evaluating present-day woody species, AM plants still display faster nitrogen mineralization and lower nitrogen resorption than EcM plants. This inorganic nutrient economy allows AM plants to thrive in warm environments with a faster litter decomposition rate. Our findings indicate that the global pattern of nutrient acquisition strategies in mycorrhizal plants is shaped by the interplay between phylogeny and climate.
DOI: 10.6084/m9.figshare.23903094.v3
title: Evolutionary and ecological forces shape nutrient strategies of mycorrhizal woody plants

description: The associations of arbuscular mycorrhizal (AM) or ectomycorrhiza (EcM) fungi with plants have sequentially evolved and significantly contributed to enhancing plant nutrition. Nonetheless, how evolutionary and ecological forces drive nutrient acquisition strategies of AM and EcM plants remains poorly understood. Our global analysis of woody species revealed that, over divergence time, AM plants evolved faster nitrogen mineralization rates without changes in nitrogen resorption. However, EcM plants exhibited an increase in nitrogen mineralization but a decrease in nitrogen resorption, indicating a shift towards a more inorganic nutrient economy. Despite this alteration, when evaluating present-day woody species, AM plants still display faster nitrogen mineralization and lower nitrogen resorption than EcM plants. This inorganic nutrient economy allows AM plants to thrive in warm environments with a faster litter decomposition rate. Our findings indicate that the global pattern of nutrient acquisition strategies in mycorrhizal plants is shaped by the interplay between phylogeny and climate.
DOI: 10.5281/zenodo.7909656
title: rCRUX Generated ITS2 Plants Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: ITS2 Plants<br> Gene: ITS2<br> Length of Target: 450-550<br> get_seeds_local() minimum length: 315<br> get_seeds_local() maximum length: 600<br> blast_seeds() minimum length: 270<br> blast_seeds() maximum length: 560<br> max_to_blast: 100<br> Forward Sequence (5'-3'): ATGCGATACTTGGTGTGAAT<br> Reverse Sequence (5'-3'): GACGCTTCTCCAGACTACAAT<br> Reference: Gu, W., Song, J., Cao, Y., Sun, Q., Yao, H., Wu, Q., ... & Duan, J. (2013). Application of the ITS2 region for barcoding medicinal plants of Selaginellaceae in Pteridophyta. PloS one, 8(6), e67818. https://doi.org/10.1371/journal.pone.0067818 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909649
title: rCRUX Generated Fungal ITS Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Fungal_ITS gITS7/ITS4<br> Gene: FITS<br> Length of Target: 150-330<br> get_seeds_local() minimum length: 105<br> get_seeds_local() maximum length: 500<br> blast_seeds() minimum length: 65<br> blast_seeds() maximum length: 461<br> max_to_blast: 100<br> Forward Sequence (5'-3'): GTGARTCATCGARTCTTTG<br> Reverse Sequence (5'-3'): TCCTCCGCTTATTGATATGC<br> Reference: White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications, 18(1), 315–322.<br> Ihrmark, K., Bödeker, I., Cruz-Martinez, K., Friberg, H., Kubartova, A., Schenck, J., Strid, Y., Stenlid, J., Brandström-Durling, M., & Clemmensen, K. E. (2012). New primers to amplify the fungal ITS2 region–evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiology Ecology, 82(3), 666–677. https://doi.org/10.1111/j.1574-6941.2012.01437.x We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909643
title: rCRUX Generated Ford Fish 16S Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Ford Fish 16S<br> Gene: 16S<br> Length of Target: 330<br> get_seeds_local() minimum length: 279<br> get_seeds_local() maximum length: 477<br> blast_seeds() minimum length: 231<br> blast_seeds() maximum length: 429<br> max_to_blast: 1000<br> Forward Sequence (5'-3'): GCAATCACTTGTCTTTTAAATGAAGACC, GTAATCACTTGTCTTTTAAATGAAGACC<br> Reverse Sequence (5'-3'): GGATTGCGCTGTTATCCCTA<br> Reference: Ford MJ, Hempelmann J, Hanson MB, Ayres KL, Baird RW, et al. (2016) Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces. PLOS ONE 11(1): e0144956. https://doi.org/10.1371/journal.pone.0144956 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909640
title: rCRUX Generated Cephalpod 18S Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Ceph18S<br> Gene: 18S<br> Length of Target: 150–190<br> get_seeds_local() minimum length: 105<br> get_seeds_local() maximum length: 235<br> blast_seeds() minimum length: 65<br> blast_seeds() maximum length: 195<br> max_to_blast: 100<br> Forward Sequence (5'-3'): CGCGGCGCTACATATTAGAC<br> Reverse Sequence (5'-3'): GCACTTAACCGACCGTCGAC<br> Reference: D. S. W. de Jonge, V. Merten, T. Bayer, O. Puebla, T. B. H. Reusch, H.-J. T. Hoving, A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region. R. Soc. Open Sci. 8, 201388 (2021) https://doi.org/10.1098/rsos.201388 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7908865
title: rCRUX Generated MiFish Universal 12S Expanded Reference Database

description: rCRUX generated reference database using NCBI nt blast database and an additional custom blast database comprised of all Actinopterygii mitogenomes. Both blast databases were downloaded in December 2022. Primer Name: MiFish Universal<br> Gene: 12S<br> Length of Target: 163–185<br> get_seeds_local() minimum length: 170<br> get_seeds_local() maximum length: 250<br> blast_seeds() minimum length: 140<br> blast_seeds() maximum length: 250<br> max_to_blast: 1000<br> Forward Sequence (5'-3'): GTGTCGGTAAAACTCGTGCCAGC<br> Reverse Sequence (5'-3'): CATAGTGGGGTATCTAATCCCAGTTTG<br> Reference: Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., ... & Kondoh, M. (2015). MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society open science, 2(7), 150088. https://doi.org/10.1098/rsos.150088 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.15151/esrf-es-1307695441
title: Danish crystallography BAG

description: Despite PI changes, the BAG will continue to work on diverse areas of structural biology, ranging from fundamental of enzyme mechanisms, structure-based engineering of enzymes for industrial applications, particularly involving degradation and transformation of plant biomass, and viral, microbial and mammalian proteins involved in different aspects of health and disease. Among the specific targets are glycosyltransferases, fluorinases, sterol and sugar transporters, NS5B, Keap1, lytic polysaccharide monooxygenases, glucuronylesterases, phage repressor peptidase, alginate degrading polysaccharide lyases, mucin degrading glycosylhydrolases, type V autotransporters.
DOI: 10.15151/esrf-es-1313930306
title: Histatins: Saliva proteins with important functions for our innate immune system

description: This study focuses on Histatins, a family of saliva proteins that act as a first line of defence of our innate immune system and possess antiviral/antimicrobial/antifungal properties. Of specific interest are Histatin 1 (Hst1), Histatin 3 (Hst3), and Histatin 5 (Hst5), which contain 38, 32, and 24 amino acids, respectively, of which the 22 first amino acids in the primary sequence are identical. This study aims to understand why Hst5 has a greater killing efficacy for fungi and microbes and less for Influenza Virus A, while the opposite relationship prevails for Hst1 and Hst3. We will learn about the distribution of oligomers/complexes, their structure, size, and shape, and the intra-complex/oligomers' distances. We aim to understand what differs in the interaction between Hst1/Hst3/Hst5 and how their structure relates to their function. Computer simulations will give us atomistic insight, which is impossible through experiments.
DOI: 10.15151/esrf-es-1312446196
title: Structural studies of redox Nickel enzymes and nickel proteins

description: We are interested in the study of structure/function relationships of nickel enzymes, nickel proteins and nickel protein-based artificial metalloenzymes. Our objectives are the structural characterization of our artificial metalloenzymes as well as the trapping of reaction intermediates. We are alos interested in the biosynthesis of carbon monoxide dehydrogenase (CODH), a nickel enzyme with a complex multimetallic active site. We aim at the determination of the crystal structure of CODH and its nickel chaperones CooJ, CooT and CooC, involved in nickel insertion into CODH.
DOI: 10.15151/esrf-es-1347146703
title: XMCD on Nd3Fe3Sb7

description: XMCD on Nd3Fe3Sb7
DOI: 10.15151/esrf-es-1335370596
title: Hybrid Luminescent Materials of Nano-Sized Metal Halide Clusters in Metal-Organic and Covalent Organic Reticular Templates

description: We explore various reticular porous materials, such as metal-organic and covalent organic frameworks and polyhedra as molecular templates for formation of confined atomically defined nano-sized solid-state structures within the pores by incorporation of main group metal halide (MH) compounds. MH materials are known to exhibit exceptional luminescence and other optoelectronic properties. Single crystals of the porous materials can be employed as molecular templates for crystallizing MHs within the cavities. In this way, geometry, functionality, electric charge and topology of the pores determines the structure of resulting MH nano-sized units, what might enable rational synthesis of desired solids and gives access to structures which are not known to form otherwise, and thus further tailoring optoelectronic properties. Our current work focuses on explorations of various frameworks and polyhedra and MHs as hosts and guests, respectively, offering vast compositional and structural space.
DOI: 10.15151/esrf-es-1336088858
title: XMCD studies of TiPtCoFeB)AlOx, MgOFeTa, and Ni50Pt50AlOx

description: Magnetic moment determination of this multilayer structures
DOI: 10.15151/esrf-es-1337567222
title: Temperature dependent phase transition XAFS study of Fe-triazole complexes for bioimaging applications

description: We propose the study of silica covered Fe2+ triazole nanoparticles (with a diameter of 10-50 nm), which have potential applications as thermally responsive agents in Magnetic Resonance Imaging (MRI), by means of temperature dependent XAFS measurements. In the samples under study, Fe forms polynuclear coordination complexes with triazole ligands in a chain-like fashion. It is expected that the magnetic and structural properties of the Fe-triazole nanoparticles will be affected by the synthesis route, the nanoparticle size, and doping with lanthanide elements. Spectra acquisition at temperatures ranging from 300 K to around 470 K is requested, because various types of temperature-induced transitions take place. At intermediate temperatures order-disorder transition of the chain arrangement may be detectable while in the temperature range 300-350 K, spin-crossover happens.
DOI: 10.5281/zenodo.8409190
title: Dataset: Tautomeric Mixture Coordination Enables Efficient Lead-Free Perovskite LEDs

description: Molecular dynamics trajectories showing the adsorption, clustering and tautomerization of Cyanuric acids molecules on 2D TEA<sub>2</sub>SnI<sub>4 </sub>and 3D CsSnI<sub>3</sub> Perovskites Typical input file for running these simulations on CP2k
DOI: 10.5281/zenodo.8409189
title: Dataset: Tautomeric Mixture Coordination Enables Efficient Lead-Free Perovskite LEDs

description: Molecular dynamics trajectories showing the adsorption, clustering and tautomerization of Cyanuric acids molecules on 2D TEA<sub>2</sub>SnI<sub>4 </sub>and 3D CsSnI<sub>3</sub> Perovskites Typical input file for running these simulations on CP2k
DOI: 10.4121/772f102d-6d41-428b-b3fb-65ea6ea1ee9e.v1
title: Data underlying the PhD thesis: The Climate Impact of Hypersonic Aircraft

description: The datasets contain data to plot figures part of the related dissertation. Results are based on simulations of the atmosphere with the Earth system models EMAC and LMDZ-INCA. The research objective was to evaluate the climate impact of civil hypersonic aircraft. The first step is to calculate middle atmospheric changes caused by hypersonic emission of water vapour, hydrogen and nitrogen oxides. The second step is to calculate the radiative forcing and mean surface temperature change following the change in atmospheric composition.
DOI: 10.5281/zenodo.8409239
title: rCRUX Generated MiFish Universal 12S Expanded +FishCARD Reference Database

description: rCRUX generated reference database using NCBI nt blast database and an additional custom blast database comprised of all Actinopterygii mitogenomes. Both blast databases were downloaded in December 2022 and supplemented with the FishCARD sequences from https://doi.org/10.5281/zenodo.4315277 . Primer Name: MiFish Universal<br> Gene: 12S<br> Length of Target: 163–185<br> get_seeds_local() minimum length: 170<br> get_seeds_local() maximum length: 250<br> blast_seeds() minimum length: 140<br> blast_seeds() maximum length: 250<br> max_to_blast: 1000<br> Forward Sequence (5'-3'): GTGTCGGTAAAACTCGTGCCAGC<br> Reverse Sequence (5'-3'): CATAGTGGGGTATCTAATCCCAGTTTG<br> Reference: Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., ... & Kondoh, M. (2015). MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society open science, 2(7), 150088. https://doi.org/10.1098/rsos.150088 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8409238
title: rCRUX Generated MiFish Universal 12S Expanded +FishCARD Reference Database

description: rCRUX generated reference database using NCBI nt blast database and an additional custom blast database comprised of all Actinopterygii mitogenomes. Both blast databases were downloaded in December 2022 and supplemented with the FishCARD sequences from https://doi.org/10.5281/zenodo.4315277 . Primer Name: MiFish Universal<br> Gene: 12S<br> Length of Target: 163–185<br> get_seeds_local() minimum length: 170<br> get_seeds_local() maximum length: 250<br> blast_seeds() minimum length: 140<br> blast_seeds() maximum length: 250<br> max_to_blast: 1000<br> Forward Sequence (5'-3'): GTGTCGGTAAAACTCGTGCCAGC<br> Reverse Sequence (5'-3'): CATAGTGGGGTATCTAATCCCAGTTTG<br> Reference: Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., ... & Kondoh, M. (2015). MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society open science, 2(7), 150088. https://doi.org/10.1098/rsos.150088 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.25781/kaust-7q5mv
title: Fine and Coarse Dust Effects on Radiative Forcing, Mass Deposition, and Solar Devices over the Middle East

description: The dataset which is used in the preparation of the manuscript on "Fine and Coarse Dust Effects on Radiative Forcing, Mass Deposition, and Solar Devices over the Middle-East"
DOI: 10.5281/zenodo.8339969
title: Boron-, carbon-, and silicon-bridged 1,12-dihydroxy-perylene bisimides with tuned structural and optical properties

description: Additional data to report https://doi.org/10.1039/D3QO01389H Establishing suitable design strategies to tailor the functional properties of perylene bisimide (PBI) dyes are critical for their successful application in various devices. Herein, we report a new synthetic strategy to tune their structural and fluorescence properties by employing 1,12-bay-substitution pattern that has been seldomly investigated in the past. Central to the strategy is the use of 1,12-dihydroxy-PBI as a starting compound and the subsequent bridging of these hydroxy bay-functional groups with either a boron, carbon or silicon atom resulting in derivatives with rigidified perylene core. This is followed by a detailed exploration of synthetic possibilities to functionalize the unsubstituted 6,7-positions at the opposite bay area to achieve novel perylene dyes with excellent structural and optical properties. The fluorescence color could be tuned from green to dark-orange while retaining the almost unity fluorescence quantum yield in solution. Moreover, a strong fluorescence with quantum yields as high as 40% has been observed for powders, which clearly illustrates the potential of the presented structural design to obtain new solid-state emitters.
description: Additional data to report: https://doi.org/10.1039/D3QO01389H
DOI: 10.5281/zenodo.8339968
title: Boron-, carbon-, and silicon-bridged 1,12-dihydroxy-perylene bisimides with tuned structural and optical properties

description: Additional data to report https://doi.org/10.1039/D3QO01389H Establishing suitable design strategies to tailor the functional properties of perylene bisimide (PBI) dyes are critical for their successful application in various devices. Herein, we report a new synthetic strategy to tune their structural and fluorescence properties by employing 1,12-bay-substitution pattern that has been seldomly investigated in the past. Central to the strategy is the use of 1,12-dihydroxy-PBI as a starting compound and the subsequent bridging of these hydroxy bay-functional groups with either a boron, carbon or silicon atom resulting in derivatives with rigidified perylene core. This is followed by a detailed exploration of synthetic possibilities to functionalize the unsubstituted 6,7-positions at the opposite bay area to achieve novel perylene dyes with excellent structural and optical properties. The fluorescence color could be tuned from green to dark-orange while retaining the almost unity fluorescence quantum yield in solution. Moreover, a strong fluorescence with quantum yields as high as 40% has been observed for powders, which clearly illustrates the potential of the presented structural design to obtain new solid-state emitters.
description: Additional data to report: https://doi.org/10.1039/D3QO01389H
DOI: 10.5281/zenodo.8409262
title: OI 630 nm Airglow Images during 1530-1930 UT on 06 March 2013

description: Processed OI 630 nm Airglow Images during 1530-1930 UT on 06 March 2013
DOI: 10.5281/zenodo.8409261
title: OI 630 nm Airglow Images during 1530-1930 UT on 06 March 2013

description: Processed OI 630 nm Airglow Images during 1530-1930 UT on 06 March 2013