cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19554823.v1
title: Systematic revision of <i>Hydnum</i> species in Japan

description: <i>Hydnum</i> (Hydnaceae, Basidiomycota) exhibits endemic species diversity in East Asia; however, few comprehensive systematic studies have been conducted to date. Here, we performed morphological, ecological, phylogenetic, and biological evaluations of the taxonomy of <i>Hydnum</i> species in Japan. In total, 186 Japanese <i>Hydnum</i> specimens were used for morphological observations. Phylogenetic trees were constructed using sequence data of nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) region and a portion of translation elongation factor 1-α (<i>tef1</i>). Intra- and interspecific mating tests using 78 monokaryotic strains of 13 species did not conflict with species delimitation inferred from their ITS and <i>tef1</i> phylogenetic relationships. This study provides detailed morphological descriptions of 15 rigorously identified species from Japan, nine of which are described as new: <i>H. alboluteum, H. albopallidum, H. pinicola, H. itachiharitake, H. minospororufescens, H. orientalbidum, H. subberkeleyanum, H. tomaense</i>, and <i>H. tottoriense</i>. Three species documented in this work are new to Japan: <i>H. boreorepandum, H. mulsicolor</i>, and <i>H. umbilicatum</i>. The remaining three species (<i>H. cremeoalbum, H. minus</i>, and <i>H. repando-orientale</i>), previously reported from Japan, are redescribed using data from newly collected materials. We also transferred two old species (<i>Hericium fimbrillatum</i> and <i>Sarcodon nauseofoetidus</i>) from East Asian <i>Hydnum</i> into other genera.
DOI: 10.6084/m9.figshare.19554823
title: Systematic revision of <i>Hydnum</i> species in Japan

description: <i>Hydnum</i> (Hydnaceae, Basidiomycota) exhibits endemic species diversity in East Asia; however, few comprehensive systematic studies have been conducted to date. Here, we performed morphological, ecological, phylogenetic, and biological evaluations of the taxonomy of <i>Hydnum</i> species in Japan. In total, 186 Japanese <i>Hydnum</i> specimens were used for morphological observations. Phylogenetic trees were constructed using sequence data of nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) region and a portion of translation elongation factor 1-α (<i>tef1</i>). Intra- and interspecific mating tests using 78 monokaryotic strains of 13 species did not conflict with species delimitation inferred from their ITS and <i>tef1</i> phylogenetic relationships. This study provides detailed morphological descriptions of 15 rigorously identified species from Japan, nine of which are described as new: <i>H. alboluteum, H. albopallidum, H. pinicola, H. itachiharitake, H. minospororufescens, H. orientalbidum, H. subberkeleyanum, H. tomaense</i>, and <i>H. tottoriense</i>. Three species documented in this work are new to Japan: <i>H. boreorepandum, H. mulsicolor</i>, and <i>H. umbilicatum</i>. The remaining three species (<i>H. cremeoalbum, H. minus</i>, and <i>H. repando-orientale</i>), previously reported from Japan, are redescribed using data from newly collected materials. We also transferred two old species (<i>Hericium fimbrillatum</i> and <i>Sarcodon nauseofoetidus</i>) from East Asian <i>Hydnum</i> into other genera.
DOI: 10.6084/m9.figshare.19400729
title: New species of <i>Tulasnella</i> associated with Australian terrestrial orchids in the subtribes Megastylidinae and Thelymitrinae

description: <i>Tulasnella</i> (Tulasnellaceae) is a genus of fungus that can form mycorrhizal associations with orchids (Orchidaceae). Here we used molecular phylogenetic analyses and morphological characteristics of pure cultures across four different media to support the description of five new <i>Tulasnella</i> species associated with commonly occurring and endangered Australian orchids. <i>Tulasnella nerrigaensis</i> associates with <i>Calochilus; T. subasymmetrica and T. kiataensis with Thelymitra; and T. korungensis and T. multinucleata</i> with <i>Pyrorchis</i> and <i>Rimacola</i> respectively. The newly described species were primarily delimited by analyses of five loci: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), <i>C14436</i> (adenosine triphosphate [ATP] synthase), <i>C4102</i> (glutamate synthase), <i>C3304</i> (ATP helicase), and mt large subunit 16S rDNA (mtLSU). <i>Tulasnella subasymmetrica</i> is introduced for some isolates previously identified as <i>T. asymmetrica</i>, and this latter species is characterized from multilocus sequencing of a new isolate that matches ITS sequences from the ex-type culture. Morphological differences between the new species are slight. <i>Tulasnella multinucleata</i> has 6–12 nuclei per hyphal compartment which is the first instance of multinucleate rather than binucleate or trinucleate hyphal compartments in <i>Tulasnella</i>. The formal description of these species of <i>Tulasnella</i> will aid in future evolutionary and ecological studies of orchid-fungal interactions.
DOI: 10.6084/m9.figshare.19400729.v1
title: New species of <i>Tulasnella</i> associated with Australian terrestrial orchids in the subtribes Megastylidinae and Thelymitrinae

description: <i>Tulasnella</i> (Tulasnellaceae) is a genus of fungus that can form mycorrhizal associations with orchids (Orchidaceae). Here we used molecular phylogenetic analyses and morphological characteristics of pure cultures across four different media to support the description of five new <i>Tulasnella</i> species associated with commonly occurring and endangered Australian orchids. <i>Tulasnella nerrigaensis</i> associates with <i>Calochilus; T. subasymmetrica and T. kiataensis with Thelymitra; and T. korungensis and T. multinucleata</i> with <i>Pyrorchis</i> and <i>Rimacola</i> respectively. The newly described species were primarily delimited by analyses of five loci: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), <i>C14436</i> (adenosine triphosphate [ATP] synthase), <i>C4102</i> (glutamate synthase), <i>C3304</i> (ATP helicase), and mt large subunit 16S rDNA (mtLSU). <i>Tulasnella subasymmetrica</i> is introduced for some isolates previously identified as <i>T. asymmetrica</i>, and this latter species is characterized from multilocus sequencing of a new isolate that matches ITS sequences from the ex-type culture. Morphological differences between the new species are slight. <i>Tulasnella multinucleata</i> has 6–12 nuclei per hyphal compartment which is the first instance of multinucleate rather than binucleate or trinucleate hyphal compartments in <i>Tulasnella</i>. The formal description of these species of <i>Tulasnella</i> will aid in future evolutionary and ecological studies of orchid-fungal interactions.
DOI: 10.6084/m9.figshare.19436655
title: Fire as a driver of fungal diversity — A synthesis of current knowledge

description: Fires occur in most terrestrial ecosystems where they drive changes in the traits, composition, and diversity of fungal communities. Fires range from rare, stand-replacing wildfires to frequent, prescribed fires used to mimic natural fire regimes. Fire regime factors, including burn severity, fire intensity, and timing, vary widely and likely determine how fungi respond to fires. Despite the importance of fungi to post-fire plant communities and ecosystem functioning, attempts to identify common fungal responses and their major drivers are lacking. This synthesis addresses this knowledge gap and ranges from fire adaptations of specific fungi to succession and assembly fungal communities as they respond to spatially heterogenous burning within the landscape. Fires impact fungi directly and indirectly through their effects on fungal survival, substrate and habitat modifications, changes in environmental conditions, and/or physiological responses of the hosts with which fungi interact. Some specific pyrophilous, or “fire-loving,” fungi often appear after fire. Our synthesis explores whether such taxa can be considered cosmopolitan, and whether they are truly fire-adapted or simply opportunists adapted to rapidly occupy substrates and habitats made available by fires. We also discuss the possible inoculum sources of post-fire fungi and explore existing conceptual models and ecological frameworks that may be useful in generalizing fungal fire responses. We conclude with identifying research gaps and areas that may best transform the current knowledge and understanding of fungal responses to fire.
DOI: 10.6084/m9.figshare.19554820.v1
title: Systematic revision of the Roseinae clade of <i>Russula</i>, with a focus on eastern North American taxa

description: The Roseinae clade is a lineage of the genus <i>Russula</i> primarily composed of species of <i>Russula</i> subsect. <i>Roseinae</i>. Species in this morphologically distinct clade possess a white to pale cream spore print, mild taste, positive reaction to sulfovanillin, and primordial hyphae with acid-resistant crystals in the pileipellis. Here, we present a morphological and phylogenetic assessment that distinguishes seven eastern North American species of the core Roseinae lineage and a new subsection, Russula subsection <i>Albidinae</i>, to accommodate members of the Albida clade. We assign the previously described species <i>R. peckii, R. rubellipes</i>, and <i>R. pseudopeckii</i> to three species-level clades, and three other species, <i>R. cardinalis, R. cordata</i>, and <i>R. rheubarbarina</i>, are described as new. Comparative morphological analyses reveal differences in the conformation of terminal elements in the pileipellis, spore size, hymenial cystidia contents, and pigmentation on the stipe surface as key features to recognize species in the group. Based on the analysis of publicly available data, we recognize a potential total of nine temperate North American species within <i>R.</i> subsect. <i>Roseinae</i>, in addition to four from Central America, two from Europe, and 14 from Asia.
DOI: 10.6084/m9.figshare.19554820
title: Systematic revision of the Roseinae clade of <i>Russula</i>, with a focus on eastern North American taxa

description: The Roseinae clade is a lineage of the genus <i>Russula</i> primarily composed of species of <i>Russula</i> subsect. <i>Roseinae</i>. Species in this morphologically distinct clade possess a white to pale cream spore print, mild taste, positive reaction to sulfovanillin, and primordial hyphae with acid-resistant crystals in the pileipellis. Here, we present a morphological and phylogenetic assessment that distinguishes seven eastern North American species of the core Roseinae lineage and a new subsection, Russula subsection <i>Albidinae</i>, to accommodate members of the Albida clade. We assign the previously described species <i>R. peckii, R. rubellipes</i>, and <i>R. pseudopeckii</i> to three species-level clades, and three other species, <i>R. cardinalis, R. cordata</i>, and <i>R. rheubarbarina</i>, are described as new. Comparative morphological analyses reveal differences in the conformation of terminal elements in the pileipellis, spore size, hymenial cystidia contents, and pigmentation on the stipe surface as key features to recognize species in the group. Based on the analysis of publicly available data, we recognize a potential total of nine temperate North American species within <i>R.</i> subsect. <i>Roseinae</i>, in addition to four from Central America, two from Europe, and 14 from Asia.
DOI: 10.6084/m9.figshare.17086412
title: VASP calculations

description: All input files (INCAR, POSCAR, KPOINTS) needed to reproduce the MD results, trajectories (XDATCAR), and Movie from two-phase simulations are deposited here.
DOI: 10.6084/m9.figshare.17086412.v2
title: VASP calculations

description: All input files (INCAR, POSCAR, KPOINTS) needed to reproduce the MD results, and the trajectories (XDATCAR) from two-phase simulations are deposited here.
DOI: 10.6084/m9.figshare.19436655.v1
title: Fire as a driver of fungal diversity — A synthesis of current knowledge

description: Fires occur in most terrestrial ecosystems where they drive changes in the traits, composition, and diversity of fungal communities. Fires range from rare, stand-replacing wildfires to frequent, prescribed fires used to mimic natural fire regimes. Fire regime factors, including burn severity, fire intensity, and timing, vary widely and likely determine how fungi respond to fires. Despite the importance of fungi to post-fire plant communities and ecosystem functioning, attempts to identify common fungal responses and their major drivers are lacking. This synthesis addresses this knowledge gap and ranges from fire adaptations of specific fungi to succession and assembly fungal communities as they respond to spatially heterogenous burning within the landscape. Fires impact fungi directly and indirectly through their effects on fungal survival, substrate and habitat modifications, changes in environmental conditions, and/or physiological responses of the hosts with which fungi interact. Some specific pyrophilous, or “fire-loving,” fungi often appear after fire. Our synthesis explores whether such taxa can be considered cosmopolitan, and whether they are truly fire-adapted or simply opportunists adapted to rapidly occupy substrates and habitats made available by fires. We also discuss the possible inoculum sources of post-fire fungi and explore existing conceptual models and ecological frameworks that may be useful in generalizing fungal fire responses. We conclude with identifying research gaps and areas that may best transform the current knowledge and understanding of fungal responses to fire.
DOI: 10.6073/pasta/0b9edfbf9856e89b1ab525ec5e356941
title: Jornada Basin LTER: Wireless meteorological station at NPP G-SUMM site: 30-minute soil volumetric water content data: 2013 - ongoing

description: 30-minute Soil Moisture data at NPP G-SUMM met station. Collection of soil volumetric water content data at Jornada LTER NPP sites, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are measured every 30 minutes at an automated meteorological station installed at Jornada LTER NPP G-SUMM site. Measurements are made every 30 minutes at 10 cm, 20 cm, and 30 cm soil depths. This is an ONGOING dataset.
DOI: 10.6073/pasta/1539b0025735545984bd2863a1ef32b6
title: Jornada Basin LTER: Wireless meteorological station at NPP G-SUMM site: Daily average soil volumetric water content data: 2013 - ongoing

description: Daily average of 30-minute Volumetric Water Content at NPP G-SUMM met station. Collection of soil volumetric water content data at Jornada LTER NPP sites, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are measured and calculated at an automated meteorological station installed at Jornada LTER NPP G-SUMM site. The daily average at 3 soil depths is calculated from measurements made every 30 minutes at 10 cm, 20 cm, and 30 cm. This is an ONGOING dataset.
DOI: 10.34740/kaggle/dsv/3576789
title: Covid-19 in Singapore : Latest Detailed Data
DOI: 10.6073/pasta/9ec9725cbee8a3a6f0eb5b7df1e9b6a5
title: Jornada Basin LTER: Wireless meteorological station at NPP M-NORT site: 5-minute summary air temperature data: 2013 - ongoing

description: 5-minute summary data at NPP M-NORT met station. Average air temperature measured and calculated based on 1-second scan rate of all sensors located at an automated meteorological station installed at Jornada LTER NPP M-NORT site. Air temperature is measured at approximate 2.5m. This climate station is operated by the Jornada LTER Program. This is an ONGOING dataset.
DOI: 10.6073/pasta/532212a4263d0c3f5c7d7d4e83b1d2fd
title: Jornada Basin LTER: Wireless meteorological station at NPP M-NORT site: 1-hour summary data: 2013 - ongoing

description: Hourly summary data at NPP M-NORT met station. Average/maximum/minimum air temperature; average relative humidity. 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 M-NORT site. Air temperature and relative humidity are measured at approximately 2.5m. This climate station is operated by the Jornada LTER Program. This is an ONGOING dataset.
DOI: 10.6073/pasta/e2f5c2ab38924ba351a716005abae27a
title: Jornada Basin LTER: Wireless meteorological station at NPP M-NORT site: 30-minute summary data: 2013 - ongoing

description: 30-minute summary data at NPP M-NORT met station. Average air temperature and relative humidity are measured and calculated based on 1-second scan rate of all sensors located at an automated meteorological station installed at Jornada LTER NPP G-SUMM site. Air temperature and relative humidity are measured at approximate 2.5m. This climate station is operated by the Jornada LTER Program. This is an ONGOING dataset.
DOI: 10.6073/pasta/9fa019f9f22187a5e26fd1bf319f6ead
title: Jornada Basin LTER: Wireless meteorological station at NPP M-NORT site: Daily summary data: 2013 - ongoing

description: Daily summary data at NPP M-NORT met station. Average/maximum/minimum air temperature; average/maximum relative humidity. 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 M-NORT site. Air temperature and relative humidity are measured at approximately 2.5m. This climate station is operated by the Jornada LTER Program. This is an ONGOING dataset.
DOI: 10.6073/pasta/5a2f0a02530c0b2dad515a99507cacae
title: Jornada Basin LTER: Wireless meteorological station at NPP M-NORT site: 30-minute soil volumetric water content data: 2013 - ongoing

description: 30-minute Soil Moisture data at NPP M-NORT met station. Collection of soil volumetric water content data at Jornada LTER NPP sites, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are measured every 30 minutes at an automated meteorological station installed at Jornada LTER NPP M-NORT site. Measurements are made every 30 minutes at 10 cm, 20 cm, and 30 cm soil depths. This is an ONGOING dataset.
DOI: 10.6073/pasta/372e59d26118e77788ff9f13e0a1dff1
title: Jornada Basin LTER: Wireless meteorological station at NPP M-NORT site: Daily average soil volumetric water content data: 2013 - ongoing

description: Daily average of 30-minute Volumetric Water Content at NPP M-NORT met station. Collection of soil volumetric water content data at Jornada LTER NPP sites, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are measured and calculated at an automated meteorological station installed at Jornada LTER NPP M-NORT site. The daily average at 3 soil depths is calculated from measurements made every 30 minutes at 10 cm, 20 cm, and 30 cm. This is an ONGOING dataset.
DOI: 10.5281/zenodo.6510358
title: FlowNet-PET Training Set

description: The training set used for FlowNet-PET found in https://github.com/teaghan/FlowNet_PET A dataset of 300 phantoms generated using the 4D extended cardiac-torso (XCAT) anthropomorphic digital phantom (2x4x4) mm<sup>3</sup> voxels. The dataset is split into training (270) and validation (30) sets. For each phantom, ten frames spaced across a single breath cycle were created, each frame having (108x152x152) pixels resembling the activity distribution throughout the phantom. To emulate a simple representation of PET data acquisition, these distributions were used to sample a random number (between 1x10<sup>6</sup> and 9x10<sup>6</sup>) of counts per frame.<br> <br> The parameters for each XCAT phantom were varied randomly. This included the gender, axial section included, transaxial shifts, scaling factors in each direction, size and location of the lung lesion, extent of the diaphragm motion, extent of the chest expansion, and the activity of each organ.
DOI: 10.5281/zenodo.6510357
title: FlowNet-PET Training Set

description: The training set used for FlowNet-PET found in https://github.com/teaghan/FlowNet_PET A dataset of 300 phantoms generated using the 4D extended cardiac-torso (XCAT) anthropomorphic digital phantom (2x4x4) mm<sup>3</sup> voxels. The dataset is split into training (270) and validation (30) sets. For each phantom, ten frames spaced across a single breath cycle were created, each frame having (108x152x152) pixels resembling the activity distribution throughout the phantom. To emulate a simple representation of PET data acquisition, these distributions were used to sample a random number (between 1x10<sup>6</sup> and 9x10<sup>6</sup>) of counts per frame.<br> <br> The parameters for each XCAT phantom were varied randomly. This included the gender, axial section included, transaxial shifts, scaling factors in each direction, size and location of the lung lesion, extent of the diaphragm motion, extent of the chest expansion, and the activity of each organ.
DOI: 10.6084/m9.figshare.12498671
title: Data from: Variability in grazing on juvenile giant kelp throughout an upwelling season

description: Data generated from field experiments, surveys, and pH, temperature, and oxygen sensors.
DOI: 10.6084/m9.figshare.12498671.v3
title: Data from: Variability in grazing on juvenile giant kelp throughout an upwelling season

description: Data generated from field experiments, surveys, and pH, temperature, and oxygen sensors.
DOI: 10.6084/m9.figshare.12498671.v2
title: Data from: Variability in juvenile giant kelp survival throughout an upwelling season

description: Data generated from field experiments, surveys, and pH, temperature, and oxygen sensors. R code for data analysis is also included. Metadata is included within the Excel file.
DOI: 10.5517/ccdc.csd.cc28jv8y
title: CCDC 2101560: Experimental Crystal Structure Determination

description: Related Article: Tian Wang, Junan Duan, Hongliu Shi, Minmin Wang, Ping Lian, Guohai Xu|2022|Z.Anorg.Allg.Chem.|648|e202100315|doi:10.1002/zaac.202100315
DOI: 10.5517/ccdc.csd.cc28jv9z
title: CCDC 2101561: Experimental Crystal Structure Determination

description: Related Article: Tian Wang, Junan Duan, Hongliu Shi, Minmin Wang, Ping Lian, Guohai Xu|2022|Z.Anorg.Allg.Chem.|648|e202100315|doi:10.1002/zaac.202100315
DOI: 10.6073/pasta/7a31579db0dcf35b384bdd7b79b829f4
title: Jornada Basin LTER: Wireless meteorological station at NPP M-RABB site: 1-hour summary data: 2013 - ongoing

description: Hourly summary data at NPP M-RABB 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 M-RABB 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.19701484
title: Supplemental data_MT. Controls of SAR11 subclade abundance, diversity, and growth in two Mid-Atlantic estuaries

description: Supplemental data for metatranscriptome comparisons of SAR11 MAGs from the Delaware and Chesapeake Bays
DOI: 10.6084/m9.figshare.19701484.v1
title: Supplemental data_MT. Controls of SAR11 subclade abundance, diversity, and growth in two Mid-Atlantic estuaries

description: Supplemental data for metatranscriptome comparisons of SAR11 MAGs from the Delaware and Chesapeake Bays