cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12827453
title: Supplementary Tables 1-8 from Multi-omic detection of <i>Mycobacterium leprae</i> in archaeological human dental calculus

description: Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here, we present a <i>Mycobacterium leprae</i> genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. <i>Mycobacterium leprae</i> can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of <i>M. leprae</i> from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing <i>M. leprae</i> in individuals from the archaeological record.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12827453.v1
title: Supplementary Tables 1-8 from Multi-omic detection of <i>Mycobacterium leprae</i> in archaeological human dental calculus

description: Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here, we present a <i>Mycobacterium leprae</i> genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. <i>Mycobacterium leprae</i> can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of <i>M. leprae</i> from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing <i>M. leprae</i> in individuals from the archaeological record.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12291638.v1
title: Additional file 1 of Adaptive strategy of allohexaploid wheat to long-term salinity stress

description: Additional file 1: Figure S1. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of differentially expressed genes in allohexaploid wheat leaf. Top 20 KEGG pathways with adjusted P value&lt;0.05 are displayed. Figure S2. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of differentially expressed genes in allohexaploid wheat root. KEGG pathways with adjusted P value&lt;0.05 are displayed. Figure S3. Effects of long-term salinity stress on gene expression involved in wax biosynthesis. (a) Gene expression change was marked on the pathway of wax biosynthesis, and the red box indicates up-regulated expression under long-term salinity stress. The wax biosynthesis pathway diagram was adapted from the diagram of KEGG website. (b) Gene expression data involved in wax metabolism in wheat leaf under long-term salinity stress. FAR, alcohol-forming fatty acyl-CoA reductase. MAH1, midchain alkane hydroxylase; CYP96A15; WSD1, wax-ester synthase/diacylglycerol O-acyltransferase. Fold change = stress/control, Q value is the adjusted P value using the Benjamini-Hochberg method. Figure S4. Effects of long-term salinity stress on expression of two ferredoxin-NADP+ reductase (petH) genes in wheat leaves. Figure S5. Relationships among A, B and D homeologs in terms of expression fold change (stress/control) for all salinity-tolerant triads. Figure S6. Expression fold change (stress/control) of A, B and D homeologs of 15 typical salinity-tolerant triads. * indicates significant difference (adjusted P value &lt; 0.05 and |log2fold change| ≥ 1).
DOI: 10.6084/m9.figshare.12291647
title: Additional file 2 of Adaptive strategy of allohexaploid wheat to long-term salinity stress

description: Additional file 2: Table S1. Fold change and percent contribution to total molarity of each compatible solute. Fold change is ratio of stress /control. Percent contribution is calculated with following equation: Percent contribution of a given solute = its molarity content (μmol g-1 DW) × 100/total molarity content, where total molarity content is sum of molarity contents of all 37 solutes. The wheat seeds were treated with 100 mM NaCl for 30 days. CL, control leaf; SL, stress leaf; CR, control root; SR, stress root. Table S2. Expression data of salinity-tolerant genes involved in osmotic adjustment, ion homeostasis and tissue tolerance. Table S3. Percentage of the triad showing stress-induced significant change in relative expression of homeolog. Significant change was defined as ≥20% difference between stress and control in relative expression of homeologs. Table S4. Number of triads showing differential homeolog expression bias categories between control and stress treatments. Table S5. Expression data and homeolog expression bias categories of salinity-tolerant triads involved in osmotic adjustment, ion homeostasis and tissue tolerance. A-S, A suppressed; A-D, A dominant; B-S, B suppressed; B-D, B dominant; D-S, D suppressed; D-D, D dominant. Table S6: Results of qRT-PCR of wheat leaves. Each treatment had three biological replicates.
DOI: 10.6084/m9.figshare.12291647.v1
title: Additional file 2 of Adaptive strategy of allohexaploid wheat to long-term salinity stress

description: Additional file 2: Table S1. Fold change and percent contribution to total molarity of each compatible solute. Fold change is ratio of stress /control. Percent contribution is calculated with following equation: Percent contribution of a given solute = its molarity content (μmol g-1 DW) × 100/total molarity content, where total molarity content is sum of molarity contents of all 37 solutes. The wheat seeds were treated with 100 mM NaCl for 30 days. CL, control leaf; SL, stress leaf; CR, control root; SR, stress root. Table S2. Expression data of salinity-tolerant genes involved in osmotic adjustment, ion homeostasis and tissue tolerance. Table S3. Percentage of the triad showing stress-induced significant change in relative expression of homeolog. Significant change was defined as ≥20% difference between stress and control in relative expression of homeologs. Table S4. Number of triads showing differential homeolog expression bias categories between control and stress treatments. Table S5. Expression data and homeolog expression bias categories of salinity-tolerant triads involved in osmotic adjustment, ion homeostasis and tissue tolerance. A-S, A suppressed; A-D, A dominant; B-S, B suppressed; B-D, B dominant; D-S, D suppressed; D-D, D dominant. Table S6: Results of qRT-PCR of wheat leaves. Each treatment had three biological replicates.
DOI: 10.6084/m9.figshare.12827742
title: PredictionExcSigns.R from A multivariate geostatistical framework for combining multiple indices of abundance for disease vectors and reservoirs: a case study of <i>rattiness</i> in a low-income urban Brazilian community

description: A key requirement in studies of endemic vector-borne or zoonotic disease is an estimate of the spatial variation in vector or reservoir host abundance. For many vector species, multiple indices of abundance are available, but current approaches to choosing between or combining these indices do not fully exploit the potential inferential benefits that might accrue from modelling their joint spatial distribution. Here, we develop a class of multivariate generalized linear geostatistical models for multiple indices of abundance. We illustrate this novel methodology with a case study on Norway rats in a low-income urban Brazilian community, where rat abundance is likely risk factor for human leptospirosis. We combine three indices of rat abundance to draw predictive inferences on a spatially continuous latent process, <i>rattiness</i>, that acts as a proxy for abundance. We show how to explore the association between <i>rattiness</i> and spatially varying environmental factors, evaluate the relative importance of each of the three contributing indices and assess the presence of residual, unexplained spatial variation, and identify <i>rattiness</i> hotspots. The proposed methodology is applicable more generally as a tool for understanding the role of vector or reservoir host abundance in predicting spatial variation in the risk of human disease.
DOI: 10.6084/m9.figshare.12827745.v1
title: 2-PdLPredictionGrid.csv from A multivariate geostatistical framework for combining multiple indices of abundance for disease vectors and reservoirs: a case study of <i>rattiness</i> in a low-income urban Brazilian community

description: A key requirement in studies of endemic vector-borne or zoonotic disease is an estimate of the spatial variation in vector or reservoir host abundance. For many vector species, multiple indices of abundance are available, but current approaches to choosing between or combining these indices do not fully exploit the potential inferential benefits that might accrue from modelling their joint spatial distribution. Here, we develop a class of multivariate generalized linear geostatistical models for multiple indices of abundance. We illustrate this novel methodology with a case study on Norway rats in a low-income urban Brazilian community, where rat abundance is likely risk factor for human leptospirosis. We combine three indices of rat abundance to draw predictive inferences on a spatially continuous latent process, <i>rattiness</i>, that acts as a proxy for abundance. We show how to explore the association between <i>rattiness</i> and spatially varying environmental factors, evaluate the relative importance of each of the three contributing indices and assess the presence of residual, unexplained spatial variation, and identify <i>rattiness</i> hotspots. The proposed methodology is applicable more generally as a tool for understanding the role of vector or reservoir host abundance in predicting spatial variation in the risk of human disease.
DOI: 10.6084/m9.figshare.17010232
title: Additional file 10 of A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit

description: Additional file 10. The reported distant eQTL for genes in stone cell modules.
DOI: 10.6084/m9.figshare.12291611
title: Additional file 2 of APEC: an accesson-based method for single-cell chromatin accessibility analysis

description: Additional file 2. Table S1.
DOI: 10.15468/dl.krmn3j
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Sinosenecio bodinieri (Vaniot) B.Nord."
 ]
}

 The dataset includes 44 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0323092-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qagr77
title: Occurrence Download

description: A dataset containing 2314 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2024",
 "Geometry POLYGON ((-130.7383528944533 -59.46314024951374, -130.7383528944533 32.71876227804215, -26.26729810228821 32.71876227804215, -26.26729810228821 -59.46314024951374, -130.7383528944533 -59.46314024951374))",
 "OccurrenceStatus is Present",
 "TaxonKey is Myiophobus phoenicomitra (Taczanowski & Berlepsch, 1885)"
 ]
}

 The dataset includes 2314 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052031-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.phma6q
title: Occurrence Download

description: A dataset containing 16054 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Quintinia A.DC."
 ]
}

 The dataset includes 16054 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0304639-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b9mmtq
title: Occurrence Download

description: A dataset containing 186 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Colpoda inflata (Stokes, 1884) Kahl, 1931"
 ]
}

 The dataset includes 186 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015518-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mkhsck
title: Occurrence Download

description: A dataset containing 407 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Varecia variegata (Kerr, 1792)"
 ]
}

 The dataset includes 407 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000477-150407101314760/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f89whg
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Saussurea polycolea Hand.-Mazz.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 51 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0321299-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7wawzr
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyrtanthus rotundilobus N.E.Br."
 ]
}

 The dataset includes 11 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016672-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/8569779
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.15468/dl.44sd07
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eucnide xylinea C.H.Mull.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000477-150811131857512/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hsrf2x
title: Occurrence Download

description: A dataset containing 4977 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Croatia",
 "TaxonKey is Reptilia"
 ]
}

 The dataset includes 4977 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016648-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mf678c
title: Occurrence Download

description: A dataset containing 11476 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-4989.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is Geodetic datum assumed WGS84",
 "TaxonKey is Chelonia mydas (Linnaeus, 1758)"
 ]
}

 The dataset includes 11476 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0317541-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.67ioi3
title: Occurrence Download

description: A dataset containing 2225 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Argentina",
 "Country is Bolivia (Plurinational State of)",
 "Country is Peru",
 "Country is Venezuela (Bolivarian Republic of)",
 "Country is Paraguay",
 "Country is Colombia",
 "Country is Brazil",
 "Country is Uruguay",
 "Country is Ecuador",
 "Country is Guyana"
 ]
 },
 "Year 1998-2019",
 "HasCoordinate is true",
 "TaxonKey is Odontophorus capueira (Spix, 1825)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2225 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007921-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lgdfcp
title: Occurrence Download

description: A dataset containing 595 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Pseudoleskeella tectorum (Funck ex Brid.) Kindb. ex Broth.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 595 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000477-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4bruph
title: Occurrence Download

description: A dataset containing 5510 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lynx rufus (Schreber, 1777)"
 ]
}

 The dataset includes 5510 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0246008-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3qnyv6
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Greece",
 "TaxonKey is Nyctalus Bowditch, 1825"
 ]
}

 The dataset includes 43 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005451-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mzhyja
title: Occurrence Download

description: A dataset containing 6375 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sceloporus variabilis Wiegmann, 1834",
 "HasCoordinate is TRUE",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 6375 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007921-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ouakjm
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Penelope jacucaca Spix, 1825",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000478-150523225239109/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.awn8w9
title: Occurrence Download

description: A dataset containing 5758 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Système d'Information sur la Nature et les Paysages d'Ile de France - Données de la structure CERF (Centre d'Etude de Rambouillet et de sa Forêt) provenant de la base de donnée du SINP Île-de-France CETTIA"
 ]
}

 The dataset includes 5758 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0231989-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7uyzsa
title: Occurrence Download

description: A dataset containing 238 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Beilschmiedia volckii B.Hyland"
 ]
}

 The dataset includes 238 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0317550-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4rqm87
title: Occurrence Download

description: A dataset containing 31057 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Setophaga ruticilla (Linnaeus, 1758)"
 ]
}

 The dataset includes 31057 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052741-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w3w44x
title: Occurrence Download

description: A dataset containing 937 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Erioneuron avenaceum (Kunth) Tateoka"
 ]
}

 The dataset includes 937 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0323086-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5g66gt
title: Occurrence Download

description: A dataset containing 7970 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cyanocitta cristata (Linnaeus, 1758)",
 "Year 2011-2018"
 ]
}

 The dataset includes 7970 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0246004-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ft6b69
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Cyprus",
 "TaxonKey is Miniopterus Bonaparte, 1837"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005413-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.