cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.22m3xq
title: Occurrence Download

description: A dataset containing 132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-23.4668 24.25781,44.91211 24.25781,44.91211 62.92969,-23.4668 62.92969,-23.4668 24.25781))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Squatina squatina (Linnaeus, 1758)",
 "Year 1000-2021"
 ]
}

 The dataset includes 132 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043571-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ctv6s7
title: Occurrence Download

description: A dataset containing 20070 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chromolaena odorata (L.) R.M.King & H.Rob."
 ]
}

 The dataset includes 20070 records from 400 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0284255-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ea4ds5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helianthus annuus"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039573-210914110416597/datasets/export for details.
DOI: 10.15468/dl.ujxssu
title: Occurrence Download

description: A dataset containing 1376 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cystoseira compressa (Esper) Gerloff & Nizamuddin, 1975"
 ]
}

 The dataset includes 1376 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0081765-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.db88bh
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Guyalna glaucus (Goding, 1925)"
 ]
}

 The dataset includes 46 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0295396-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.grf3m6
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (United States of America)",
 "BasisOfRecord is one of (Specimen)",
 "Year is greater than or equal to 1990",
 "TaxonKey is Halyomorpha halys (Stål, 1855)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 51 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013202-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.umdy86
title: Occurrence Download

description: A dataset containing 272 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gamblea ciliata C.B.Clarke",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 272 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0322382-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qprznw
title: Occurrence Download

description: A dataset containing 324540 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ophrys L."
 ]
}

 The dataset includes 324540 records from 512 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0081770-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc25bqs1
title: CSD 2006313: Experimental Crystal Structure Determination

description: Related Article: Julia-Maria Hübner, Walter Jung, Marcus Schmidt, Matej Bobnar, Primož Koželj, Bodo Böhme, Michael Baitinger, Martin Etter, Yuri Grin, Ulrich Schwarz|2020|Inorg.Chem.|60|2160|doi:10.1021/acs.inorgchem.0c02357
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.6967421
title: OCR model for Pracalit for Sanskrit and Newar MSS 16th to 19th C., Ground Truth

description: Ground truth data (png and xml files) for a an OCR model. Will be continually updated. Originally trained on Transkribus with a PyLaia model created from ground truth data based on transcripts into Pracalit Unicode of four Nepalese manuscripts. The manuscripts used to create this model are Staatsbibliothek zu Berlin's Hitopadeśa (MIK I 4851) (mixed Newar and Sanskrit dating to 1561) and Vetālapañcaviṃśati (HS. Or. 6414) (Newar dating to 1675) as well as Cambridge Digital Library's Avalokiteśvaraguṇakāraṇḍavyūha (MS Add. 1322) (Sanskrit, 18th century) and the Royal Asiatic Society Online Collection's Madhyamasvayaṃbhūpurāṇa (RAS Hodgson MS 23) (Newar and Sanskrit dating to c. 1800). The training was done on 441 pages and validation on 242 pages. This model does not recognise spacing, except for large gaps (i.e. for pictures or string holes). Newar word divider markers may not be represented or may be transcribed as virama. In general, the model is made for MSS with scriptio continua and will transcribe into scriptio continua into Pracalit Unicode. Transcription was performed by Dr Alexander O'Neill (SOAS University of London). Transcription of the Vetālapañcaviṃśati (HS. Or. 6414) and Madhyamasvayaṃbhūpurāṇa (RAS Hodgson MS 23) was aided by unpublished materials provided by Dr Felix Otter (Philipps-Universität Marburg), as well as the published transcription in Shakya, Min Bahadur, and Shanta Harsha Bajracharya, eds. "Svayambhū Purāṇa." Lalitpur: Nagarjuna Institute of Exact Methods, 2001. The transcription of Avalokiteśvaraguṇakāraṇḍavyūha (MS Add. 1322) was aided by the transcription provided by the Digital Sanskrit Buddhist Canon Project based on Lokesh Chandra, "Guṇakāraṇḍavyūhasūtram," New Delhi: International Academy of Indian Culture, 1999.
DOI: 10.5281/zenodo.6967420
title: OCR model for Pracalit for Sanskrit and Newar MSS 16th to 19th C., Ground Truth

description: Ground truth data (png and xml files) for a an OCR model. Will be continually updated. Originally trained on Transkribus with a PyLaia model created from ground truth data based on transcripts into Pracalit Unicode of four Nepalese manuscripts. The manuscripts used to create this model are Staatsbibliothek zu Berlin's Hitopadeśa (MIK I 4851) (mixed Newar and Sanskrit dating to 1561) and Vetālapañcaviṃśati (HS. Or. 6414) (Newar dating to 1675) as well as Cambridge Digital Library's Avalokiteśvaraguṇakāraṇḍavyūha (MS Add. 1322) (Sanskrit, 18th century) and the Royal Asiatic Society Online Collection's Madhyamasvayaṃbhūpurāṇa (RAS Hodgson MS 23) (Newar and Sanskrit dating to c. 1800). The training was done on 441 pages and validation on 242 pages. This model does not recognise spacing, except for large gaps (i.e. for pictures or string holes). Newar word divider markers may not be represented or may be transcribed as virama. In general, the model is made for MSS with scriptio continua and will transcribe into scriptio continua into Pracalit Unicode. Transcription was performed by Dr Alexander O'Neill (SOAS University of London). Transcription of the Vetālapañcaviṃśati (HS. Or. 6414) and Madhyamasvayaṃbhūpurāṇa (RAS Hodgson MS 23) was aided by unpublished materials provided by Dr Felix Otter (Philipps-Universität Marburg), as well as the published transcription in Shakya, Min Bahadur, and Shanta Harsha Bajracharya, eds. "Svayambhū Purāṇa." Lalitpur: Nagarjuna Institute of Exact Methods, 2001. The transcription of Avalokiteśvaraguṇakāraṇḍavyūha (MS Add. 1322) was aided by the transcription provided by the Digital Sanskrit Buddhist Canon Project based on Lokesh Chandra, "Guṇakāraṇḍavyūhasūtram," New Delhi: International Academy of Indian Culture, 1999.
DOI: 10.6084/m9.figshare.19514269
title: A practical technique for estimating deer appearance frequency and cedar sapling damage in young plantations protected by tree shelters in western Japan

description: We developed simple practical methods to estimate deer appearance frequency and damage risk for cedar saplings protected by tree shelters, by using field signs such as browsed understory plants, debarked trees, and animal trails. The appearance frequency of the sika deer was recorded using camera traps at 29 clear-logged and young plantation sites in the Shikoku Island of western Japan. Field signs such as fecal pellets, footprints, animal trails, and browsed plants were recorded in three transects that were 2 m × 50 m each, located at the margins of the sites. Cubic regression analysis showed that the frequency of deer appearance could be predicted from the number of browsed plant species categorized into three ranks, that is, 0, 1, and ≥2 species. To use this method, plant species are not required for identification, as the user can simply judge whether browsed plants found in 5-m sections are all the same species or not. The damage of sheltered cedar saplings was assessed at 36 sites in the Kyushu and Shikoku Islands of western Japan, and surveys of deer field signs were also conducted. The proportion of heavily damaged saplings could be determined from the indices of binary summarized data of bark stripping and animal trails using a logistic regression model. The indices derived from the field signs will help forest managers to detect relatively low frequency of deer appearances and high risk of cedar sapling damage at a sheltered plantation in the western Japan.
DOI: 10.6084/m9.figshare.19514269.v1
title: A practical technique for estimating deer appearance frequency and cedar sapling damage in young plantations protected by tree shelters in western Japan

description: We developed simple practical methods to estimate deer appearance frequency and damage risk for cedar saplings protected by tree shelters, by using field signs such as browsed understory plants, debarked trees, and animal trails. The appearance frequency of the sika deer was recorded using camera traps at 29 clear-logged and young plantation sites in the Shikoku Island of western Japan. Field signs such as fecal pellets, footprints, animal trails, and browsed plants were recorded in three transects that were 2 m × 50 m each, located at the margins of the sites. Cubic regression analysis showed that the frequency of deer appearance could be predicted from the number of browsed plant species categorized into three ranks, that is, 0, 1, and ≥2 species. To use this method, plant species are not required for identification, as the user can simply judge whether browsed plants found in 5-m sections are all the same species or not. The damage of sheltered cedar saplings was assessed at 36 sites in the Kyushu and Shikoku Islands of western Japan, and surveys of deer field signs were also conducted. The proportion of heavily damaged saplings could be determined from the indices of binary summarized data of bark stripping and animal trails using a logistic regression model. The indices derived from the field signs will help forest managers to detect relatively low frequency of deer appearances and high risk of cedar sapling damage at a sheltered plantation in the western Japan.
DOI: 10.6084/m9.figshare.16917566
title: Effects of treeshelter on seedling performance: a meta-analysis

description: Treeshelters are used in a variety of environments for forestry and forest restoration purposes. Although their use is often effective, in some cases treeshelters are ineffective. To clarify the effects of treeshelters on seedling performance, a systematic literature review and meta-analysis was conducted. Of the 296 studies related to treeshelters, 139 studies were suitable for extraction of data on mortality rate, browsing damage rate, height growth, or diameter growth. The quality of the literature did not affect the results of the meta-analysis. Mortality, browsing damage, and height growth were positively affected by treeshelters in many subgroup analyses, but diameter growth did not conform with the perceived inhibitory effect of treeshelters. Regarding conifer species, treeshelters had no effect on mortality rate and non-ventilated treeshelters promoted diameter growth. However, many subgroup analyses showed publication bias as indicated by the significantly fewer negative-effect studies. Therefore, the effects of treeshelters may be overestimated although the effects revealed by the meta-analysis were reasonable from the viewpoint of plant physiological reactions. Heterogeneity was high in most of the subgroups, suggesting that factors other than the analyzed subgroups may contribute to the variance in treeshelter effects. Studies on treeshelters are concentrated under specific conditions, such as on species of the genus <i>Quercus</i> and a temperate climate. Thus, other under-represented conditions are considered to constitute research gaps. Further studies in these research gap areas are required to perform a meta-analysis with low heterogeneity.
DOI: 10.6084/m9.figshare.16917566.v1
title: Effects of treeshelter on seedling performance: a meta-analysis

description: Treeshelters are used in a variety of environments for forestry and forest restoration purposes. Although their use is often effective, in some cases treeshelters are ineffective. To clarify the effects of treeshelters on seedling performance, a systematic literature review and meta-analysis was conducted. Of the 296 studies related to treeshelters, 139 studies were suitable for extraction of data on mortality rate, browsing damage rate, height growth, or diameter growth. The quality of the literature did not affect the results of the meta-analysis. Mortality, browsing damage, and height growth were positively affected by treeshelters in many subgroup analyses, but diameter growth did not conform with the perceived inhibitory effect of treeshelters. Regarding conifer species, treeshelters had no effect on mortality rate and non-ventilated treeshelters promoted diameter growth. However, many subgroup analyses showed publication bias as indicated by the significantly fewer negative-effect studies. Therefore, the effects of treeshelters may be overestimated although the effects revealed by the meta-analysis were reasonable from the viewpoint of plant physiological reactions. Heterogeneity was high in most of the subgroups, suggesting that factors other than the analyzed subgroups may contribute to the variance in treeshelter effects. Studies on treeshelters are concentrated under specific conditions, such as on species of the genus <i>Quercus</i> and a temperate climate. Thus, other under-represented conditions are considered to constitute research gaps. Further studies in these research gap areas are required to perform a meta-analysis with low heterogeneity.
DOI: 10.5281/zenodo.6967641
title: HOT MAGs

description: MAGs of giant viruses at Station ALOHA
DOI: 10.5281/zenodo.6967640
title: HOT MAGs

description: MAGs of giant viruses at Station ALOHA
DOI: 10.6084/m9.figshare.14215797.v1
title: Landscape assessment of a 100-year-old sacred forest within a shrine using geotagged visitor employed photography

description: The forest of Meiji-Jingu shrine was afforested 100 years ago with the aim of creating a sublime forest one century later. In this study, we conducted a visual landscape assessment to explore whether the forest had reached sublime forest status. Specifically, the spatial condition of the forest associated with sublimity and landscape types that made visitors feel sublime were assessed using a combination of data collected from geotagged visitor employed photography and questionnaires. We performed a hotspot analysis with Getis-Ord Gi* statistics and the average nearest neighbor method to identify the landscape types and their characteristics that provided a sense of sublimity, and a content analysis and semantic differential method were employed to determine how current visitors perceived the forest of Meiji-Jingu. The main findings were as follows: (1) current visitors evaluated the forest as sublime; (2) tree height and a large trunk were the most important features contributing to sublimity; (3) the vicinity of the worship hall, the torii at Harajuku gate, and the bridge were identified as hotspots; and (4) while the forest was identified as a sublime landscape type, the worship hall and torii were rated as the most sublime by visitors. This framework for landscape assessments should be useful for the future creation and conservation of high quality forested landscapes.
DOI: 10.6084/m9.figshare.14215797
title: Landscape assessment of a 100-year-old sacred forest within a shrine using geotagged visitor employed photography

description: The forest of Meiji-Jingu shrine was afforested 100 years ago with the aim of creating a sublime forest one century later. In this study, we conducted a visual landscape assessment to explore whether the forest had reached sublime forest status. Specifically, the spatial condition of the forest associated with sublimity and landscape types that made visitors feel sublime were assessed using a combination of data collected from geotagged visitor employed photography and questionnaires. We performed a hotspot analysis with Getis-Ord Gi* statistics and the average nearest neighbor method to identify the landscape types and their characteristics that provided a sense of sublimity, and a content analysis and semantic differential method were employed to determine how current visitors perceived the forest of Meiji-Jingu. The main findings were as follows: (1) current visitors evaluated the forest as sublime; (2) tree height and a large trunk were the most important features contributing to sublimity; (3) the vicinity of the worship hall, the torii at Harajuku gate, and the bridge were identified as hotspots; and (4) while the forest was identified as a sublime landscape type, the worship hall and torii were rated as the most sublime by visitors. This framework for landscape assessments should be useful for the future creation and conservation of high quality forested landscapes.
DOI: 10.6084/m9.figshare.19076213
title: Niche adaptation of <i>Frankia</i> do not drastically influence their metabolic profiling

description: Metabolic-profiling (metabolomics/metabonomics) is a measurement strategy among biological systems for low-molecular-weight metabolites and their corresponding intermediates acting as dynamic physiological, pathophysiological and developmental stimuli. Information regarding the metabolomics of <i>Frankia</i> is elusive. In this study, we analyzed 48 <i>Frankia</i> whole-genome sequences. Kyoto Encyclopedia of Genes and Genomes (KEGG) database and KEGG Automatic Annotation Server (KAAS) were used for the prediction and functional annotation of genes associated with diverse metabolic pathways. Comprehensive codon and amino-acid usage analyses along with tRNA adaptation index and dN/dS-based evolutionary inquest were performed. We have used the Database-of-Essential-Genes (DEG) server to predict the essentiality of the metabolic pathway-related-genes. We found a strong effect of compositional constraints on the metabolic pathway genes of Frankia. The evolutionary analysis revealed the conserved nature of the studied genes. Since the metabolic pathway-related genes were found to be housekeeping genes, they are conserved and less evolved. This was further validated with a dN/dS value of less than 1. Moreover, the number of synonymous changes was more than non-synonymous changes so that the amino acid sequence remains identical. The cluster of orthologs (COG) analysis revealed “metabolism” as the main functional category of the studied gene set. The core metabolic pathway-related genes among considered <i>Frankia</i> strains accumulated 115 genes. This study for the first time reveals the genomic characteristics of the metabolic pathway-related genes among <i>Frankia</i>. From all the analysis, we could hypothesize that in spite of their host specificity and differential taxonomical distribution, <i>Frankia</i> maintain a core metabolic proficiency among them.
DOI: 10.6084/m9.figshare.19076213.v2
title: Niche adaptation of <i>Frankia</i> do not drastically influence their metabolic profiling

description: Metabolic-profiling (metabolomics/metabonomics) is a measurement strategy among biological systems for low-molecular-weight metabolites and their corresponding intermediates acting as dynamic physiological, pathophysiological and developmental stimuli. Information regarding the metabolomics of <i>Frankia</i> is elusive. In this study, we analyzed 48 <i>Frankia</i> whole-genome sequences. Kyoto Encyclopedia of Genes and Genomes (KEGG) database and KEGG Automatic Annotation Server (KAAS) were used for the prediction and functional annotation of genes associated with diverse metabolic pathways. Comprehensive codon and amino-acid usage analyses along with tRNA adaptation index and dN/dS-based evolutionary inquest were performed. We have used the Database-of-Essential-Genes (DEG) server to predict the essentiality of the metabolic pathway-related-genes. We found a strong effect of compositional constraints on the metabolic pathway genes of Frankia. The evolutionary analysis revealed the conserved nature of the studied genes. Since the metabolic pathway-related genes were found to be housekeeping genes, they are conserved and less evolved. This was further validated with a dN/dS value of less than 1. Moreover, the number of synonymous changes was more than non-synonymous changes so that the amino acid sequence remains identical. The cluster of orthologs (COG) analysis revealed “metabolism” as the main functional category of the studied gene set. The core metabolic pathway-related genes among considered <i>Frankia</i> strains accumulated 115 genes. This study for the first time reveals the genomic characteristics of the metabolic pathway-related genes among <i>Frankia</i>. From all the analysis, we could hypothesize that in spite of their host specificity and differential taxonomical distribution, <i>Frankia</i> maintain a core metabolic proficiency among them.