cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25505/fiz.icsd.cc20jh24
title: CSD 1862885: Experimental Crystal Structure Determination

description: Related Article: Hillary E. Mitchell Warden, Paul M. Voyles, Daniel C. Fredrickson|2018|Inorg.Chem.|57|13880|doi:10.1021/acs.inorgchem.8b02353
DOI: 10.5517/ccdc.csd.cc20jc75
title: CCDC 1862766: Experimental Crystal Structure Determination

description: Related Article: Chen Yushuang|2018|CSD Communication|||
description: Related Article: Yushuang Chen, Shunxi Dong, Xi Xu, Xiaohua Liu, Xiaoming Feng|2018|Angew.Chem.,Int.Ed.|57|16554|doi:10.1002/anie.201810410
DOI: 10.5517/ccdc.csd.cc20jcwt
title: CCDC 1862786: Experimental Crystal Structure Determination

description: Related Article: Zhe Ji, Christopher A. Trickett, Xiaokun Pei, Omar M. Yaghi|2018|J.Am.Chem.Soc.|140|13618|doi:10.1021/jacs.8b09807
DOI: 10.5517/ccdc.csd.cc20jcxv
title: CCDC 1862787: Experimental Crystal Structure Determination

description: Related Article: Zhe Ji, Christopher A. Trickett, Xiaokun Pei, Omar M. Yaghi|2018|J.Am.Chem.Soc.|140|13618|doi:10.1021/jacs.8b09807
DOI: 10.6084/m9.figshare.4884365
title: Plasmid sequences from A CRISPR Cas9 high-throughput genome editing toolkit for kinetoplastids.

description: Plasmid sequences in GenBank format. For visualization we recommend SnapGene software (from GSL Biotech; free SnapGene Viewer available at snapgene.com).
DOI: 10.6084/m9.figshare.4884365.v1
title: Plasmid sequences from A CRISPR Cas9 high-throughput genome editing toolkit for kinetoplastids

description: Plasmid sequences in GenBank format. For visualization we recommend SnapGene software (from GSL Biotech; free SnapGene Viewer available at snapgene.com).
DOI: 10.6084/m9.figshare.12854604.v1
title: Experimental Analysis of Interactions Among Saprotrophic Fungi from A Phosphorous-Poor Desert Oasis in the Chihuahuan Desert

description: Fungal ecological interactions play a key role in structuring community assemblages. These associations may involve both antagonistic and synergistic relationships, which are commonly influenced by abiotic factors such as nutrient conditions. However, information for extreme, oligotrophic systems remain poor. Herein, interactions among key members of the aquatic transient fungal community (<i>Aspergillus niger</i>, <i>Cladosporium</i> sp., and <i>Coprinellus micaceus</i>) of a low-nutrient freshwater system in the Cuatro Ciénegas Basin, Mexico were studied. Pairwise interaction bioassays were explored <i>in vitro</i> under different nutrient conditions, including carbohydrates-rich, carbohydrates and amino peptides-rich, and low nutrients. Our results indicated that antagonistic patterns prevail among the studied taxa. However, nutrient-dependent changes were observed in <i>Cladosporium</i> sp. shifting to synergy under carbohydrates-rich conditions, suggesting changes in the fungal community composition as a result of nutrient enrichment. Remarkably, our findings contrast with previous work demonstrating mainly synergistic interactions between our tested fungal isolates and co-occurring autochthonous bacteria (<i>Aeromonas</i> spp. and <i>Vibrio</i> sp.) under low-nutrient conditions. This observation may indicate that bacteria and fungi exhibit distinct community-level responses, driven by nutrient conditions. This contributes to the knowledge of fungal community dynamics and interspecific interactions in an oligotrophic ecosystem, highlighting the relevance of nutrient-based shifts and antagonistic interactions in ecosystem dynamics.
DOI: 10.6084/m9.figshare.12962690
title: Characterization of Soil Microorganism from Humus and Indigenous Microorganism Amendments

description: This study was conducted to understand the dynamics of microbial communities of soil microorganisms, and their distribution and abundance in the indigenous microorganisms (IMOs) manipulated from humus collected from the forest near the crop field. The soil microorganisms originated from humus and artificially cultured microbial-based soil amendments were characterized by molecular and biochemical analyses. The bacterial population (2 × 10<sup>6</sup>∼13 × 10<sup>6</sup> CFU/g sample) was approximately 100-fold abundant than the fungal population (2 × 10<sup>4</sup>∼8 × 10<sup>4</sup> CFU/g sample). The 16S rDNA and ITS sequence analyses showed that the bacterial and fungal communities in humus and IMOs were mainly composed of <i>Bacillus</i> and <i>Pseudomonas</i>, and <i>Trichoderma</i> and <i>Aspergillus</i> species, respectively. Some of the bacterial isolates from the humus and IMOs showed strong inhibitory activity against soil-borne pathogenic fungi <i>Fusarium oxysporum</i> and <i>Sclerotinia sclerotiorum</i>. These bacteria also showed the siderophore production activity as well as phosphate solubilizing activity, which are requisite traits for biological control of plant pathogenic fungi. These results suggest that humus and IMOs could be a useful resource for sustainable agriculture.
DOI: 10.6084/m9.figshare.12962690.v1
title: Characterization of Soil Microorganism from Humus and Indigenous Microorganism Amendments

description: This study was conducted to understand the dynamics of microbial communities of soil microorganisms, and their distribution and abundance in the indigenous microorganisms (IMOs) manipulated from humus collected from the forest near the crop field. The soil microorganisms originated from humus and artificially cultured microbial-based soil amendments were characterized by molecular and biochemical analyses. The bacterial population (2 × 10<sup>6</sup>∼13 × 10<sup>6</sup> CFU/g sample) was approximately 100-fold abundant than the fungal population (2 × 10<sup>4</sup>∼8 × 10<sup>4</sup> CFU/g sample). The 16S rDNA and ITS sequence analyses showed that the bacterial and fungal communities in humus and IMOs were mainly composed of <i>Bacillus</i> and <i>Pseudomonas</i>, and <i>Trichoderma</i> and <i>Aspergillus</i> species, respectively. Some of the bacterial isolates from the humus and IMOs showed strong inhibitory activity against soil-borne pathogenic fungi <i>Fusarium oxysporum</i> and <i>Sclerotinia sclerotiorum</i>. These bacteria also showed the siderophore production activity as well as phosphate solubilizing activity, which are requisite traits for biological control of plant pathogenic fungi. These results suggest that humus and IMOs could be a useful resource for sustainable agriculture.
DOI: 10.6084/m9.figshare.12854604
title: Experimental Analysis of Interactions Among Saprotrophic Fungi from A Phosphorous-Poor Desert Oasis in the Chihuahuan Desert

description: Fungal ecological interactions play a key role in structuring community assemblages. These associations may involve both antagonistic and synergistic relationships, which are commonly influenced by abiotic factors such as nutrient conditions. However, information for extreme, oligotrophic systems remain poor. Herein, interactions among key members of the aquatic transient fungal community (<i>Aspergillus niger</i>, <i>Cladosporium</i> sp., and <i>Coprinellus micaceus</i>) of a low-nutrient freshwater system in the Cuatro Ciénegas Basin, Mexico were studied. Pairwise interaction bioassays were explored <i>in vitro</i> under different nutrient conditions, including carbohydrates-rich, carbohydrates and amino peptides-rich, and low nutrients. Our results indicated that antagonistic patterns prevail among the studied taxa. However, nutrient-dependent changes were observed in <i>Cladosporium</i> sp. shifting to synergy under carbohydrates-rich conditions, suggesting changes in the fungal community composition as a result of nutrient enrichment. Remarkably, our findings contrast with previous work demonstrating mainly synergistic interactions between our tested fungal isolates and co-occurring autochthonous bacteria (<i>Aeromonas</i> spp. and <i>Vibrio</i> sp.) under low-nutrient conditions. This observation may indicate that bacteria and fungi exhibit distinct community-level responses, driven by nutrient conditions. This contributes to the knowledge of fungal community dynamics and interspecific interactions in an oligotrophic ecosystem, highlighting the relevance of nutrient-based shifts and antagonistic interactions in ecosystem dynamics.
DOI: 10.6084/m9.figshare.12948408
title: Comparison of Soil Higher Fungal Communities between Dead and Living <i>Abies koreana</i> in Mt. Halla, the Republic of Korea

description: To improve our understanding of the relationship between soil higher fungi (belonging to Ascomycota and Basidiomycota) and <i>Abies koreana</i>, we surveyed <i>A. koreana</i> soil fungal communities in a forest in Mt. Halla, Jeju Island, Korea by next-generation sequencing (Illumina Miseq). To confirm the soil higher fungal communities, we collected two types of soils from a defined plot: soils with dead (AKDTs) and living <i>A. koreana</i> (AKLTs), respectively. Soil fungi were classified into 2 phyla, 19 classes, 64 orders, 133 families, 195 genera, and 229 OTUs (895,705 sequence reads). Nonmetric multidimensional scaling (NMDS) showed significantly different soil higher fungal communities between AKDTs and AKLTs (<i>p</i> A. koreana status (<i>p</i> Clavulina spp. was different between soils with AKDTs and AKLTs, suggesting that <i>Clavulina</i> spp. may be a crucial soil fungal species influencing <i>A. koreana</i>. This study will lead to a better understanding of the ecological status of <i>A. koreana</i> in Mt. Halla. In addition, this study could be useful for the conservation and management of <i>A. koreana</i> habitats.
DOI: 10.6084/m9.figshare.12948408.v1
title: Comparison of Soil Higher Fungal Communities between Dead and Living <i>Abies koreana</i> in Mt. Halla, the Republic of Korea

description: To improve our understanding of the relationship between soil higher fungi (belonging to Ascomycota and Basidiomycota) and <i>Abies koreana</i>, we surveyed <i>A. koreana</i> soil fungal communities in a forest in Mt. Halla, Jeju Island, Korea by next-generation sequencing (Illumina Miseq). To confirm the soil higher fungal communities, we collected two types of soils from a defined plot: soils with dead (AKDTs) and living <i>A. koreana</i> (AKLTs), respectively. Soil fungi were classified into 2 phyla, 19 classes, 64 orders, 133 families, 195 genera, and 229 OTUs (895,705 sequence reads). Nonmetric multidimensional scaling (NMDS) showed significantly different soil higher fungal communities between AKDTs and AKLTs (<i>p</i> A. koreana status (<i>p</i> Clavulina spp. was different between soils with AKDTs and AKLTs, suggesting that <i>Clavulina</i> spp. may be a crucial soil fungal species influencing <i>A. koreana</i>. This study will lead to a better understanding of the ecological status of <i>A. koreana</i> in Mt. Halla. In addition, this study could be useful for the conservation and management of <i>A. koreana</i> habitats.
DOI: 10.6084/m9.figshare.12879144
title: Alterations in Growth and Morphology of <i>Ganoderma lucidum</i> and <i>Volvariella volvaceae</i> in Response to Nanoparticle Supplementation

description: Use of nanoparticles (NPs) in several commercial products has led to emergence of novel contaminants of air, soil and water bodies. The NPs may exhibit greater ecotoxicity due to nano-scale dependent properties over their bulk counterparts. The present investigation explores the effect of <i>in vitro</i> supplementation of TiO<sub>2</sub>, silica and silver NPs on radial growth and ultrastructural changes in the hyphae and spores of two mushroom genera, <i>Ganoderma lucidum</i> and <i>Volvariella volvaceae.</i> A concentration dependent decrease in radial growth on NP amended potato dextrose agar medium was recorded. However, in comparison to control, there was decrease in radial diameter on supplementation with TiO<sub>2</sub> NPs while an increase was recorded for silica and silver NPs amendments as compared to their bulk salts at same concentrations after 48 h of incubation. Optical microscopy studies showed decrease in the number of spores while increase in spore diameter and thinning of hyphal diameter on NPs supplementation. Scanning electron microscopy analysis of fungal growth showed presence of deflated and oblong spores in two fruiting strains of <i>Ganoderma</i> while <i>Volvariella</i> exhibited decreased sporulation. Further, hyphal thinning and branching was recorded in response to NP amendments in both the test mushrooms. Enhancement of protein content was observed on NP compared to bulk supplementation for all cultures, concentrations and hours of incubation except for TiO<sub>2</sub> NPs. Likewise, bulk and NP supplementations (at 100 mg <i>L</i> <sup>−1</sup>) resulted in enhanced laccase activity with occurrence of laccase specific protein bands on SDS-PAGE analysis.
DOI: 10.6084/m9.figshare.12879144.v1
title: Alterations in Growth and Morphology of <i>Ganoderma lucidum</i> and <i>Volvariella volvaceae</i> in Response to Nanoparticle Supplementation

description: Use of nanoparticles (NPs) in several commercial products has led to emergence of novel contaminants of air, soil and water bodies. The NPs may exhibit greater ecotoxicity due to nano-scale dependent properties over their bulk counterparts. The present investigation explores the effect of <i>in vitro</i> supplementation of TiO<sub>2</sub>, silica and silver NPs on radial growth and ultrastructural changes in the hyphae and spores of two mushroom genera, <i>Ganoderma lucidum</i> and <i>Volvariella volvaceae.</i> A concentration dependent decrease in radial growth on NP amended potato dextrose agar medium was recorded. However, in comparison to control, there was decrease in radial diameter on supplementation with TiO<sub>2</sub> NPs while an increase was recorded for silica and silver NPs amendments as compared to their bulk salts at same concentrations after 48 h of incubation. Optical microscopy studies showed decrease in the number of spores while increase in spore diameter and thinning of hyphal diameter on NPs supplementation. Scanning electron microscopy analysis of fungal growth showed presence of deflated and oblong spores in two fruiting strains of <i>Ganoderma</i> while <i>Volvariella</i> exhibited decreased sporulation. Further, hyphal thinning and branching was recorded in response to NP amendments in both the test mushrooms. Enhancement of protein content was observed on NP compared to bulk supplementation for all cultures, concentrations and hours of incubation except for TiO<sub>2</sub> NPs. Likewise, bulk and NP supplementations (at 100 mg <i>L</i> <sup>−1</sup>) resulted in enhanced laccase activity with occurrence of laccase specific protein bands on SDS-PAGE analysis.
DOI: 10.6084/m9.figshare.13095519
title: Comparative Genomics Platform and Phylogenetic Analysis of Fungal Laccases and Multi-Copper Oxidases

description: Laccases (EC 1.10.3.2), a group of multi-copper oxidases (MCOs), play multiple biological functions and widely exist in many species. Fungal laccases have been extensively studied for their industrial applications, however, there was no database specially focused on fungal laccases. To provide a comparative genomics platform for fungal laccases, we have developed a comparative genomics platform for laccases and MCOs (http://laccase.riceblast.snu.ac.kr/). Based on protein domain profiles of characterized sequences, 3,571 laccases were predicted from 690 genomes including 253 fungi. The number of putative laccases and their properties exhibited dynamic distribution across the taxonomy. A total of 505 laccases from 68 genomes were selected and subjected to phylogenetic analysis. As a result, four clades comprised of nine subclades were phylogenetically grouped by their putative functions and analyzed at the sequence level. Our work would provide a workbench for putative laccases mainly focused on the fungal kingdom as well as a new perspective in the identification and classification of putative laccases and MCOs.
DOI: 10.6084/m9.figshare.13095519.v1
title: Comparative Genomics Platform and Phylogenetic Analysis of Fungal Laccases and Multi-Copper Oxidases

description: Laccases (EC 1.10.3.2), a group of multi-copper oxidases (MCOs), play multiple biological functions and widely exist in many species. Fungal laccases have been extensively studied for their industrial applications, however, there was no database specially focused on fungal laccases. To provide a comparative genomics platform for fungal laccases, we have developed a comparative genomics platform for laccases and MCOs (http://laccase.riceblast.snu.ac.kr/). Based on protein domain profiles of characterized sequences, 3,571 laccases were predicted from 690 genomes including 253 fungi. The number of putative laccases and their properties exhibited dynamic distribution across the taxonomy. A total of 505 laccases from 68 genomes were selected and subjected to phylogenetic analysis. As a result, four clades comprised of nine subclades were phylogenetically grouped by their putative functions and analyzed at the sequence level. Our work would provide a workbench for putative laccases mainly focused on the fungal kingdom as well as a new perspective in the identification and classification of putative laccases and MCOs.
DOI: 10.5285/b1282b1e-7852-5d16-e053-6c86abc04c61
title: X-ray fluorescence spectroscopy analysis for major and minor trace elements in sediment samples from the west Antarctic Peninsula Shelf from JR15003.

description: This dataset contains concentrations of major and minor elements from upper sediment samples, collected at three Collaborative Gearing Scheme (CGS) stations along the West Antarctic Peninsula (WAP) during cruise JR15003. Samples were collected by box coring, at the beginning of the ice-free season, between 25th and 28th December 2015. Sub-cores were taken from the box core for core sectioning, with the core sliced every 2 cm for sediment analysis. Sediment fractions were dried and prepared for major and minor element analysis by X-ray fluorescence spectroscopy at the School of Geosciences, University of Edinburgh. Instrument performance was evaluated by measuring major and minor element composition of 20 internationally recognised standard materials BHVO-1, sTD-bEN, sTD-BCR for majors, and Cody Shale, Ohio Shale, Shale for minors according to Govindaraju (1994). Data were generated by Sian Henley and Nicholas Odling at the School of Geosciences, University of Edinburgh. Data collection was funded by the NERC Independent Research Fellowship NE/K010034/1 entitled "Isotopic characterisation of nutrient dynamics and UCDW behaviour in the west Antarctic Peninsula sea ice environment". Additional analyses were funded by the School of Geosciences, University of Edinburgh.
DOI: 10.5281/zenodo.4084857
title: Keys from the Sky: A First Exploration of Physical-Layer Security Using Satellite Links

description: Datasets containing the UBX files used for the evaluation in arXiv:2010.07194. The .ubx files stem from a ublox ZED-F9P and can be converted to the RINEX .obs format with the open source software rtklib.<br> These contain the used carrier phase observables in an easily parseable format. <br> The binary .ubx files contain additional signal information (lock time, satellite ephemeris, etc.) and can be viewed with u_center.
DOI: 10.5281/zenodo.4084856
title: Keys from the Sky: A First Exploration of Physical-Layer Security Using Satellite Links

description: Datasets containing the UBX files used for the evaluation in arXiv:2010.07194. The .ubx files stem from a ublox ZED-F9P and can be converted to the RINEX .obs format with the open source software rtklib.<br> These contain the used carrier phase observables in an easily parseable format. <br> The binary .ubx files contain additional signal information (lock time, satellite ephemeris, etc.) and can be viewed with u_center.
DOI: 10.6084/m9.figshare.4924547
title: Table S2 from Concerted and mosaic evolution of functional modules in songbird brains.

description: Raw data
DOI: 10.6084/m9.figshare.4924547.v2
title: Table S2 from Concerted and mosaic evolution of functional modules in songbird brains.

description: Raw data
DOI: 10.6084/m9.figshare.4924547.v1
title: Table S2 from Concerted and mosaic evolution of functional modules in songbird brains

description: Raw data
DOI: 10.6084/m9.figshare.4990457
title: Data from Social bet-hedging in vampire bats.

description: Data used in analysis and Figure 1
DOI: 10.6084/m9.figshare.4990457.v2
title: Data from Social bet-hedging in vampire bats.

description: Data used in analysis and Figure 1
DOI: 10.6084/m9.figshare.4990457.v1
title: Data from Social bet-hedging in vampire bats

description: Data used in analysis and Figure 1
DOI: 10.6084/m9.figshare.13095545
title: Focus Groups on Technical Excellence

description: Two focus groups on technical excellence.
DOI: 10.6073/pasta/b44fcfb4f641d586ce9796b817a5f65c
title: Jornada Basin LTER: Wireless meteorological station at NPP P-TOBO site: 1-hour summary data: 2013 - ongoing

description: Hourly summary data at NPP P-TOBO met station. Average/maximum/minimum air temperature; average relative humidity and wind direction; average/maximum wind speed; solar radiation; albedo. These are measured and calculated based on 1-second scan rate of all sensors located at an automated meteorological station installed at Jornada LTER NPP P-TOBO site. Wind speed is measured at 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Solar radiation is measured at 3m. This climate station is operated by the Jornada LTER Program. This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.5008460
title: Average log2ratios for all conditions tested by Bar-seq from Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress.

description: For Bar-Seq data generated for each deletion collection and drug or environmental experimental condition relative to its control, average log2ratios for condition replicates are given.
DOI: 10.6084/m9.figshare.5008460.v2
title: Average log2ratios for all conditions tested by Bar-seq from Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress.

description: For Bar-Seq data generated for each deletion collection and drug or environmental experimental condition relative to its control, average log2ratios for condition replicates are given.
DOI: 10.6084/m9.figshare.5008460.v1
title: Average log2ratios for all conditions tested by Bar-seq from Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress

description: For Bar-Seq data generated for each deletion collection and drug or environmental experimental condition relative to its control, average log2ratios for condition replicates are given.
DOI: 10.6084/m9.figshare.5008442
title: GO enrichment of deletion strains present in the HLU signature from Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress.

description: GO biological process enrichment for the 73 deletion strains present in the HLU deletion signature.
DOI: 10.5517/ccdc.csd.cc2f67qm
title: CCDC 2240330: Experimental Crystal Structure Determination

description: Related Article: Jun Guo, Qi Xia, Wing Yi Tang, Zekun Li, Xia Wu, Li-Juan Liu, Wai-Pong To, Hui-Xing Shu, Kam-Hung Low, Philip C. Y. Chow, Tsz Woon Benedict Lo, Jian He|2024|Nat. Catal.|7|307|doi:10.1038/s41929-024-01112-9
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.