cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22714900
title: Systemic infection of <i>Bryoria</i> (Lecanoromycetes, Ascomycota) by <i>Athelia</i> (Agaricomycetes, Basidiomycota) in western North America

description: <i>Bryoria</i> (Parmeliaceae, Ascomycota) is one of the dominant genera of hair lichens in western North America and is characteristic of high-elevation conifer forest ecosystems. In areas where <i>Bryoria</i> is abundant, it is common to find thalli in which the thalline filaments become conglutinated, forming brittle dead zones. After sampling <i>Bryoria</i> thalli across western Canada and the northwestern United States at different times of the year, we found that this dieback phenomenon is associated with the winter growth of a mold-forming basidiomycete. We report that this fungus belongs to <i>Athelia</i> (Atheliaceae, Basidiomycota), a genus known to contain lichen pathogens, most notably <i>A. arachnoidea</i>. By sequencing a combination of genetic markers—nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), partial nuc 28S rDNA (28S), and partial translation elongation factor 1-α (<i>TEF1</i>)—paired with morphometric analyses, we reveal the involvement of at least three additional lineages of lichen-associated <i>Athelia</i> and describe one as a new species, <i>A. abscondita. Athelia abscondita</i> is morphologically distinguished from other <i>Athelia</i> species by its basidia and basidiospores, was found to frequently infect members of <i>Bryoria</i> sect. <i>Implexae</i>, and was occasionally on other foliose and fruticose species within Parmeliaceae.
DOI: 10.6084/m9.figshare.22568543
title: <i>Tuber rugosum</i>, a new species from northeastern North America: Slug mycophagy aides in electron microscopy of ascospores

description: Species in the genus <i>Tuber</i> are ascomycetous fungi that produce hypogeous fruiting bodies commonly called truffles. These fungi are ecologically relevant owing to the ectomycorrhizal symbiosis they establish with plants. One of the most speciose lineages within <i>Tuber</i> is the Rufum clade, which is widely distributed throughout Asia, Europe, and North America and is estimated to include more than 43 species. Most species in this clade have spiny spores, and many still have not been formally described. Here, we describe <i>T. rugosum</i> based on multigene phylogenetic analysis and its unique morphological characters. <i>Tuber rugosum</i> (previously designated in literature as <i>Tuber</i> sp. 69) has been collected throughout the Midwest, USA, and Quebec, Canada, and is an ectomycorrhizal symbiont of <i>Quercus</i> trees, as confirmed through morphological and molecular analyses of root tips presented here. We also present a novel method for preparing <i>Tuber</i> ascospores for scanning electron microscope imaging that includes feeding, digestion, and spore excretion by the slug <i>Arion subfuscus</i>. Following this method, spores become free from ascus and other mycelial debris that could obscure morphological traits during their passage through the snail gut while maintaining ornamentation. Finally, we report the fatty acid analysis, a fungicolous species association, and we provide an updated taxonomic key of the Rufum clade.
DOI: 10.6084/m9.figshare.22568543.v1
title: <i>Tuber rugosum</i>, a new species from northeastern North America: Slug mycophagy aides in electron microscopy of ascospores

description: Species in the genus <i>Tuber</i> are ascomycetous fungi that produce hypogeous fruiting bodies commonly called truffles. These fungi are ecologically relevant owing to the ectomycorrhizal symbiosis they establish with plants. One of the most speciose lineages within <i>Tuber</i> is the Rufum clade, which is widely distributed throughout Asia, Europe, and North America and is estimated to include more than 43 species. Most species in this clade have spiny spores, and many still have not been formally described. Here, we describe <i>T. rugosum</i> based on multigene phylogenetic analysis and its unique morphological characters. <i>Tuber rugosum</i> (previously designated in literature as <i>Tuber</i> sp. 69) has been collected throughout the Midwest, USA, and Quebec, Canada, and is an ectomycorrhizal symbiont of <i>Quercus</i> trees, as confirmed through morphological and molecular analyses of root tips presented here. We also present a novel method for preparing <i>Tuber</i> ascospores for scanning electron microscope imaging that includes feeding, digestion, and spore excretion by the slug <i>Arion subfuscus</i>. Following this method, spores become free from ascus and other mycelial debris that could obscure morphological traits during their passage through the snail gut while maintaining ornamentation. Finally, we report the fatty acid analysis, a fungicolous species association, and we provide an updated taxonomic key of the Rufum clade.
DOI: 10.6084/m9.figshare.22467363
title: Five new <i>Graphium</i> species from hardwood trees in Poland

description: <i>Graphium</i> species form a well-supported monophyletic lineage within the Microascales (Ascomycota). Members of this genus can be found in association with bark beetles, as well as on tree wounds and in soils. During surveys of bark and ambrosia beetle–associated fungi and cavities made by woodpeckers on hardwood trees in Poland, many isolates with an affinity to <i>Graphium</i> were recovered. They were identified based on their morphological characters and sequence data for the internal transcribed spacer (ITS), 28S rDNA, β-tubulin (<i>TUB2</i>), and translation elongation factor 1-α (<i>TEF1</i>) gene regions. The results revealed five new species, described here as <i>G. brachiatum, G. longistipitatum, G. polonicum, G. radicatum</i>, and <i>G. trypophloei</i>.
DOI: 10.6084/m9.figshare.22467363.v1
title: Five new <i>Graphium</i> species from hardwood trees in Poland

description: <i>Graphium</i> species form a well-supported monophyletic lineage within the Microascales (Ascomycota). Members of this genus can be found in association with bark beetles, as well as on tree wounds and in soils. During surveys of bark and ambrosia beetle–associated fungi and cavities made by woodpeckers on hardwood trees in Poland, many isolates with an affinity to <i>Graphium</i> were recovered. They were identified based on their morphological characters and sequence data for the internal transcribed spacer (ITS), 28S rDNA, β-tubulin (<i>TUB2</i>), and translation elongation factor 1-α (<i>TEF1</i>) gene regions. The results revealed five new species, described here as <i>G. brachiatum, G. longistipitatum, G. polonicum, G. radicatum</i>, and <i>G. trypophloei</i>.
DOI: 10.6073/pasta/3086f4fa60f1e0ec807c269490d47ed3
title: Monthly precipitation data from a network of standard gauges at the Jornada Experimental Range (Jornada Basin LTER) in southern New Mexico, January 1916 - ongoing

description: This ongoing dataset contains monthly precipitation measurements from a network of standard can rain gauges at the Jornada Experimental Range in Dona Ana County, New Mexico, USA. Precipitation physically collects within gauges during the month and is manually measured with a graduated cylinder at the end of each month. This network is maintained by USDA Agricultural Research Service personnel. This dataset includes 39 different locations but only 29 of them are current. Other precipitation data exist for this area, including event-based tipping bucket data with timestamps, but do not go as far back in time as this dataset.
DOI: 10.6073/pasta/cf3c45e5480551453f1f9041d664a28f
title: Gap-filled daily precipitation at the 15 long-term NPP sites at Jornada Basin LTER, 1980-ongoing

description: This package contains gap-filled daily precipitation values for the 15 NPP sites at Jornada Basin LTER in southern New Mexico, USA. Sites were selected to represent the 5 major ecosystem types in the Chihuahuan Desert (upland grasslands, playa grasslands, mesquite-dominated shrublands, creosotebush-dominated shrublands, tarbush-dominated shrublands). For each ecosystem type, three sites were selected to represent the range in variability in production and plant diversity; thus the locations are not replicates. Gap-filled daily precipitation was calculated for the period from 1980 to 2019 at each site using the closest rain gauges that provided a minimum resolution of daily precipitation data. The Methods section and attached documents describe this in detail. The rain gauges used are described, with respect to their relationship to NPP sites, in the attached "daily_gapfill_ppt_gauge_usage.csv" file. Although automated weather stations became operational at all NPP sites in 2013 (except P-SMAL, in 2017), updates to this data package are ongoing and are intended to gap-fill any missing or invalid data from the weather stations.
DOI: 10.5281/zenodo.7963545
title: micropsitta_geelvinkiana_zanfona_01.fasta.gz

description: .
DOI: 10.5281/zenodo.7963544
title: micropsitta_geelvinkiana_zanfona_01.fasta.gz

description: .
DOI: 10.6073/pasta/0c2c3eae0f6ba1fceb7ff16913c83712
title: Ice Storm Mycorrhizal Fungi data for Yancey et al. in press

description: Extreme weather events, such as ice storms, are increasing and have potentially large impacts on forests, including belowground structures such as fine roots and mycorrhizal fungi. Many forest trees rely on the mutualistic relationship between mycorrhizal fungi and plants; a relationship that when disrupted can negatively impact tree net primary productivity. We took advantage of a large-scale ice storm manipulation in the northeastern United States (US) to test the hypothesis that increasing ice storm intensity and frequency would reduce ectomycorrhizal fungal root tips per unit root length and arbuscular mycorrhizal fungal structures per unit root length, hereafter colonization. We found that ice storm intensity reduced spring ectomycorrhizal fungal and arbuscular mycorrhizal fungal colonization. However, these patterns changed in the fall where ice storm intensity still reduced ectomycorrhizal fungal root tips, but arbuscular mycorrhizal fungal colonization was higher in ice storm treatments than controls. The amount of ectomycorrhizal fungal root tips and arbuscular mycorrhizal fungal colonization differed seasonally: ectomycorrhizal fungal root tips were 1.7× higher in the spring than in the fall, while arbuscular mycorrhizal fungal colonization was 3× higher in the fall than in the spring. Our results indicate that mycorrhizal fungal colonization responses to ice storm severity vary temporally and by mycorrhizal fungal type. Further, arbuscular mycorrhizal fungi may recover from ice storms relatively quickly, potentially aiding forests in their recovery, whereas ice storms may have a longer lasting impact on ectomycorrhizal fungi.
DOI: 10.6084/m9.figshare.22362955
title: Accelerating Atmospheric Gravity Wave Simulations using Machine Learning

description: Gravity waves (GWs) and their associated multi-scale dynamics are known to play fundamental roles in energy and momentum transport and deposition processes throughout the atmosphere. We describe an initial machine learning model - the Compressible Atmosphere Model Network (CAM-Net). CAM-Net is trained on high-resolution simulations by the state-of-the-art model Complex Geometry Compressible Atmosphere Model (CGCAM). Two initial applications to a Kelvin-Helmholtz instability source and mountain wave generation, propagation, breaking, and Secondary GW (SGW) generation in two wind environments are described here. Results show that CAM-Net can capture the key 2-D dynamics modeled by CGCAM with high precision. Spectral characteristics of primary and SGWs estimated by CAM-Net agree well with those from CGCAM. Our results show that CAM-Net can achieve a several order-of-magnitude acceleration relative to CGCAM without sacrificing accuracy and suggests a potential for machine learning to enable efficient and accurate descriptions of primary and secondary GWs in global atmospheric models.
DOI: 10.18739/a26t0gx7k
title: Sulfur isotopes of sulfate measurements from a Greenland ice core (1850-2006)

description: Anthropogenic sulfate aerosols are estimated to have offset sixty percent of greenhouse-gas-induced warming in the Arctic, a region warming four times faster than the rest of the world. However, sulfate radiative forcing estimates remain uncertain because the relative contributions from anthropogenic versus natural sources to total sulfate aerosols are unknown. Here we measure sulfur isotopes of sulfate in a Summit, Greenland ice core from 1850 to 2006 CE to quantify the contribution of anthropogenic sulfur emissions to ice core sulfate. We use a Keeling Plot to determine the anthropogenic sulfur isotopic signature (δ34Santhro = +2.9  0.3 ‰), and compare this result to a compilation of sulfur isotope measurements of oil and coal. Using δ34Santhro, we quantify anthropogenic sulfate concentration separated from natural sulfate. Anthropogenic sulfate concentration increases to 68 ± 7% of non-sea-salt sulfate (65.1 ± 20.2 µg kg-1) during peak anthropogenic emissions from 1960 to 1990 and decreases to 45 ± 11% of non-sea-salt sulfate (25.4 ± 12.8 µg kg-1) from 1996 to 2006. These observations provide the first long-term record of anthropogenic sulfate distinguished from natural sources (e.g., volcanoes, dimethyl sulfide), and can be used to evaluate model characterization of anthropogenic sulfate aerosol fraction and radiative forcing over the industrial era. These data include sulfur isotopes of sulfate measurements from a Greenland ice core from 1850-2006. The preindustrial dataset (1200-1850) is uploaded to the Arctic data center here: doi:10.18739/A2N873162
DOI: 10.6073/pasta/8efff666c23b1a6a5396894398d049e7
title: Long-term monitoring of herpetofauna along the Salt and Gila Rivers in and near the greater Phoenix metropolitan area, ongoing since 2012 (Reformatted to a Darwin Core Archive)

description: This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/192/5, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-cap/627/5. The abstract below was extracted from the Level 0 data package and is included for context:
DOI: 10.6073/pasta/4e7028078c760696e16e54d1bae6a8a0
title: Bird surveys along the Salt River in and near the greater Phoenix metropolitan area: 2012-2013

description: Waterways are often the focus of restoration efforts in urban areas. In arid regions, passive discharge of urban water sources may stimulate the recovery or growth of wetland and riparian features in dewatered or ephemeral aquatic systems. In the greater Phoenix metropolitan area (GPMA), sections of the Salt and Gila Rivers have been the targets of active restoration through seeding, planting, and irrigation. At the same time, revegetation has occurred in some sections of the rivers in response to runoff from urban water sources (e.g., storm drains). This dataset catalogs the results of bird surveys conducted at several locations along the Salt River in and around the GPMA from March 2012 through October 2013. Survey locations include riparian areas in urban and non-urban locations that have been (actively) restored or have revegetated in response to urban runoff, and that feature ephemeral or perennial sources of water.
DOI: 10.6073/pasta/98dd5b92117e9d728b09e582fb4d1b17
title: Phoenix Area Social Survey (PASS): 2017

description: The Phoenix Area Social Survey (PASS) was established in 2001 as part of the Central Arizona–Phoenix Long-Term Ecological Research (CAP LTER) project’s long-term monitoring program. Every five years, the PASS team surveys households in select neighborhoods in metropolitan Phoenix in order to better understand people’s perceptions, attitudes, and behaviors on environmental issues such heat stress and climate change, water scarcity and policy, landscape choices and management, and urban wildlife and biodiversity. In 2001, the first PASS was piloted in 8 neighborhoods (n= 302) in the City of Phoenix, Arizona. Aiming for about 20 respondents per neighborhood, the 2006 (n= 808) and 2011 (n= 806) samples were expanded to cover a broader range of neighborhoods (40-45) that better represent the geography of the greater metropolitan area, both in terms of location and demographics. In order to characterize and examine residents’ views and practices in particular Phoenix-area neighborhoods, the 2017 survey was redesigned to target a larger number of people (~65) in fewer (12) neighborhoods across the region. The new sampling design allows for intensive neighborhood analyses that link residents’ perceptions, attitudes, and decisions to the local ecology (e.g., urban infrastructure, landscape attributes, species composition). The 2017 PASS neighborhoods were distributed across CAP LTER ecological monitoring sites at green/blue infrastructure such as the Salt River, Tempe Town Lake, and Indian Bend Wash, in addition to desert preserves such as South Mountain Park and McDowell Sonoran Preserve. Ecological data also collected at these sites included climate and temperature data, nutrient fluxes, and wildlife community measurements. In each neighborhood, for example, the local bird community was measured at three point-count stations so that we can link biodiversity metrics to people’s views and actions that affect them. Overall, the 2017 PASS survey explores major themes integral for understanding social-ecological system dynamics including urban ecosystem services, environmental satisfaction and perceptions, and vulnerability and adaptation to various urban ecological risks.
DOI: 10.3886/qcap-9n46
title: Moldova Compact - Transition to High Value Agriculture: Final Data Set
DOI: 10.5281/zenodo.7963500
title: Vps60 initiates alternative ESCRT-III filaments

description: Source data for :"Vps60 initiates alternative ESCRT-III filaments"
DOI: 10.5281/zenodo.7963499
title: Vps60 initiates alternative ESCRT-III filaments

description: Source data for :"Vps60 initiates alternative ESCRT-III filaments"
DOI: 10.6084/m9.figshare.12295922.v3
title: SomaticHaplotype recreate plots

description: Recreate figures from SomaticHaplotype manuscript (2022).
DOI: 10.3886/6vc6-cn49
title: Moldova Compact - Transition to High Value Agriculture: Final Data Set
DOI: 10.3886/hxv1-wq60
title: Moldova Compact - Transition to High Value Agriculture: Final Data Set
DOI: 10.5517/ccdc.csd.cc2brd4n
title: CCDC 2167431: Experimental Crystal Structure Determination

description: Related Article: Kena Zhang, Qiushuang Wang, Yuanyuan Gong, Nairong Wang, Xia Li|2023|CrystEngComm|25|3033|doi:10.1039/D3CE00179B
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: 10.5517/ccdc.csd.cc2d9rcv
title: CCDC 2213907: Experimental Crystal Structure Determination

description: Related Article: Jiayue Hao, Ran An, Yao Li, Ke Wang, Shuyan Song, Jing Feng, Xinyu Wang, Hongjie Zhang|2023|Dalton Trans.|52|6799|doi:10.1039/D3DT00673E
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: 10.5517/ccdc.csd.cc2dfxnf
title: CCDC 2217915: Experimental Crystal Structure Determination

description: Related Article: Ming-Kun Li, Yi-Han Lu, Ting Wang, Peng-Xun Li, Ning-Ning Zhang, Qing-Shun Fan, Fan Shang, Guang-Ning Liu, Cuncheng Li|2023|Inorg.Chem.|62|7324|doi:10.1021/acs.inorgchem.3c00410
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: 10.5517/ccdc.csd.cc2f9qgy
title: CCDC 2243670: Experimental Crystal Structure Determination

description: Related Article: Ming-Kun Li, Yi-Han Lu, Ting Wang, Peng-Xun Li, Ning-Ning Zhang, Qing-Shun Fan, Fan Shang, Guang-Ning Liu, Cuncheng Li|2023|Inorg.Chem.|62|7324|doi:10.1021/acs.inorgchem.3c00410
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: 10.5517/ccdc.csd.cc2f9qfx
title: CCDC 2243669: Experimental Crystal Structure Determination

description: Related Article: Ming-Kun Li, Yi-Han Lu, Ting Wang, Peng-Xun Li, Ning-Ning Zhang, Qing-Shun Fan, Fan Shang, Guang-Ning Liu, Cuncheng Li|2023|Inorg.Chem.|62|7324|doi:10.1021/acs.inorgchem.3c00410
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.7961764
title: CornWeed Dataset: A dataset for training maize and weed object detectors for agricultural machines

description: There are many datasets available for training object detectors in non agricultural domains such as Autonomous Driving but these datasets fail to generalize well enough to an agricultural use-case. This dataset contains 3574 hand labelled images with bounding boxes provided in both YOLO and COCO dataset format. Additionally there are 4981 unlabelled images for testing purposes. All the images are hand labelled with bounding boxes with several labellers and reviewed. The dataset contains two class IDs namely maize and weeds. The dataset also contains a crop-row instance but has not been used in the accompanying paper but could be interesting for other future work. The images have been recorded in two resolutions i.e. 720 x 1280 and 480 x 640 covering two crop rows and single crop row respectively.
DOI: 10.5281/zenodo.7961763
title: CornWeed Dataset: A dataset for training maize and weed object detectors for agricultural machines

description: There are many datasets available for training object detectors in non agricultural domains such as Autonomous Driving but these datasets fail to generalize well enough to an agricultural use-case. This dataset contains 3574 hand labelled images with bounding boxes provided in both YOLO and COCO dataset format. Additionally there are 4981 unlabelled images for testing purposes. All the images are hand labelled with bounding boxes with several labellers and reviewed. The dataset contains two class IDs namely maize and weeds. The dataset also contains a crop-row instance but has not been used in the accompanying paper but could be interesting for other future work. The images have been recorded in two resolutions i.e. 720 x 1280 and 480 x 640 covering two crop rows and single crop row respectively.
DOI: 10.5281/zenodo.7963848
title: Claude Debussy – Children's Corner

description: This dataset originates from the DCML corpus initiative and contains musicological research data. For more information, please refer to its documentation page https://dcmlab.github.io/debussy_childrens_corner