cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/cy6a1s
title: True Fruit Flies (Diptera, Tephritidae) of the Afrotropical Region

description: This checklist covers all relevant information of the major dacine fruit fly genera of Africa.
Initially established under the ENBI project, it provides a list current taxonomic status of species involved, as well as synonymy.
Limitations of scope: the pilot study is focusing on a group of Afrotropical fruit flies only. Reason is that, over the last decade years several projects have focused on this group (cf. above) and that a mass of specimen related data are available. Afrotropical is used here in the biogeographical sense, hence the region below of the Sahara dessert. However, some additional records from northern Africa and the Middle East are included but not as exhaustive as those for the true Afrotropical region.
DOI: 10.6084/m9.figshare.25869418
title: <b><i>In vitro </i></b><b>transcription-based biosensing of glycolate for prototyping of a complex enzyme cascade</b>

description: Revised dataset of Barthel et al., 2024, '<i>In vitro</i> transcription-based biosensing of glycolate for prototyping of a complex enzyme cascade'. See abstract below.<br><i>In vitro</i> metabolic systems allow the reconstitution of natural and new-to-nature pathways outside of their cellular context and are of increasing interest in bottom-up synthetic biology, cell-free manufacturing and metabolic engineering. Yet, the prototyping of such <i>in vitro</i> networks is very often restricted by time- and cost-intensive analytical methods. To overcome these limitations, we sought to develop an <i>in vitro</i> transcription (IVT)-based biosensing workflow that is compatible with complex conditions. As proof-of-concept, we developed an IVT biosensor for the CETCH cycle, a 27-component <i>in vitro</i> metabolic system that converts CO<sub>2</sub> into glycolate. We constructed a sensor module that is based on the transcriptional repressor GlcR from <i>Paracoccus denitrificans</i>, and established an IVT biosensing workflow that allows to quantify glycolate from CETCH samples in the µM to mM range. We show that free Mg<sup>2+</sup> and phosphorylated compounds strongly influence IVT activity and are critical for robust signal output. Our optimized IVT biosensor correlates well with LC-MS-based glycolate quantification of CETCH samples with one enzyme varied (Pearson r = 0.9827) or multiple components varied (Pearson r = 0.9446), but notably at ~10-fold lowered cost and ~10 times faster turnover time. Our results demonstrate the potential of IVT-based biosensor systems to break current limitations in biological design-build-test cycles for the prototyping of individual enzymes, complex reaction cascades and <i>in vitro</i> metabolic networks.
DOI: 10.6084/m9.figshare.25869418.v1
title: All data (main text & supplementary) presented in '<i>In vitro </i> transcription-based biosensing of glycolate for prototyping of a complex enzyme cascade'

description: <i>This dataset contains all data published in the bioRxiv pre-print: </i><i>In vitro</i> transcription-based biosensing of glycolate for prototyping of a complex enzyme cascade (https://doi.org/10.1101/2024.04.26.591264). See the abstract as description below.<br><i>In vitro</i> metabolic systems allow the reconstitution of natural and new-to-nature pathways outside of their cellular context and are of increasing interest in bottom-up synthetic biology, cell-free manufacturing and metabolic engineering. Yet, the prototyping of such <i>in vitro</i> networks is very often restricted by time- and cost-intensive analytical methods. To overcome these limitations, we sought to develop an <i>in vitro</i> transcription (IVT)-based biosensing workflow that offers fast results at low-cost, minimal volumes and high-throughput. As a proof-of-concept, we present an IVT biosensor for the so-called CETCH cycle, a complex <i>in vitro</i> metabolic system that converts CO<sub>2</sub> into glycolate. To quantify glycolate production, we constructed a sensor module that is based on the glycolate repressor GlcR from <i>Paracoccus denitrificans</i>, and established an IVT biosensing off-line workflow that allows to measure glycolate from CETCH samples from the µM to mM range. We characterized the influence of different cofactors on IVT output and further optimized our IVT biosensor against varying sample conditions. We show that availability of free Mg<sup>2+</sup> is a critical factor in IVT biosensing and that IVT output is heavily influenced by ATP, NADPH and other phosphorylated metabolites frequently used in <i>in vitro</i> systems. Our final biosensor is highly robust and shows an excellent correlation between IVT output and classical LC-MS quantification, but notably at ~10-fold lowered cost and ~10 times faster turnover time. Our results demonstrate the potential of IVT-based biosensor systems to break current limitations in biological design-build-test cycles for the prototyping of individual enzymes, complex reaction cascades and <i>in vitro</i> metabolic networks.
DOI: 10.15468/dl.ueca8k
title: Occurrence Download

description: A dataset containing 11395 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vachellia karroo (Hayne) Banfi & Galasso",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 11395 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017598-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c5542jm3b
title: MassIVE MSV000095874 - NAD-supplementation enables late life dietary restriction to improve proteostasis, stem cells, and lifespan
title: : Dietary restriction (DR) has long been recognized as one of the most effective interventions for extending both healthspan and lifespan across various species. However, its efficacy diminishes significantly when initiated later in life, and the underlying mechanisms responsible for this reduction remain elusive. In this study, we demonstrate that supplementation with nicotinamide riboside (NR), a precursor to NAD+, can restore the benefits of late-life DR. Notably, this combination (NRDR) is required to enhance hematopoietic stem cell function and doubles the effect of late life DR on lifespan extension, reaching an increase of 14.3% in total lifespan. Our findings reveal that NRDR is essential to counteract the decline in proteostasis, a hallmark of aging. This is achieved by reducing protein synthesis and translation error rates, while simultaneously promoting the clearance of protein damage and aggregates through ribophagy. Overall, our results underscore NRDR as a potent dietary intervention capable of enhancing stem cell function and extending lifespan, even when initiated at an advanced age.
DOI: 10.15468/dl.vwz5dh
title: Occurrence Download

description: A dataset containing 4249 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hypodematiaceae"
 ]
}

 The dataset includes 4249 records from 157 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017599-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zz2krg
title: Occurrence Download

description: A dataset containing 724 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Machaerium scleroxylon Tul."
 ]
}

 The dataset includes 724 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017600-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hyf2sd
title: Occurrence Download

description: A dataset containing 56365 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Africa",
 "Country is Uganda",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2000-2024"
 ]
}

 The dataset includes 56365 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017601-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ytvqp4
title: Occurrence Download

description: A dataset containing 2249 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Metopium brownei (Jacq.) Urb."
 ]
}

 The dataset includes 2249 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017602-240906103802322/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.cc276y5l
title: CCDC 2062249: Experimental Crystal Structure Determination

description: Related Article: Marc Devillard, Nour Nour Eddine, Marie Cordier, Gilles Alcaraz|2021|Angew.Chem.,Int.Ed.|60|12356|doi:10.1002/anie.202102540
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: 10.15468/dl.mh6fzq
title: Occurrence Download

description: A dataset containing 307 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-64.35616 -15.03682,-64.35616 -15.03682,-65.1771 -29.67091,-52.9133 -30.35196,-49.71936 -15.03682,-64.35616 -15.03682))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Serrapinnus calliurus (Boulenger, 1900)"
 ]
}

 The dataset includes 307 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017603-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ycs6an
title: Occurrence Download

description: A dataset containing 214 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Microberlinia brazzavillensis A.Chev."
 ]
}

 The dataset includes 214 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017605-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7yqukm
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-64.35616 -15.03682,-64.35616 -15.03682,-65.1771 -29.67091,-52.9133 -30.35196,-49.71936 -15.03682,-64.35616 -15.03682))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Serrapinnus kriegi (Schindler, 1937)"
 ]
}

 The dataset includes 155 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017607-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ryn74u
title: Occurrence Download

description: A dataset containing 1091 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pterocarpus soyauxii Taub."
 ]
}

 The dataset includes 1091 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017611-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yapedk
title: Occurrence Download

description: A dataset containing 623882 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Anguilla, Aruba, Bonaire, Sint Eustatius and Saba, Virgin Islands (British), Cayman Islands, Curaçao, Guadeloupe, Martinique, Montserrat, Puerto Rico, Saint Barthélemy, Saint Martin (French part), Sint Maarten (Dutch part), Turks and Caicos Islands, Virgin Islands (U.S.))",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 623882 records from 524 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017571-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xhhqyh
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((120.17938 35.98036,120.84504 35.98036,120.84504 36.24663,120.17938 36.24663,120.17938 35.98036))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Circus Lacepede, 1799"
 ]
}

 The dataset includes 13 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017612-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.27024757.v1
title: RAW20240916

description: To investigate the changes in plasma metabolic characteristics. The experiment received approval from the Ethics Review Committee of Guangzhou Sports University, and all experimental subjects were informed of the relevant details regarding the study and provided informed consent.
DOI: 10.6084/m9.figshare.27037456
title: <b>Mapping the global end-of-life vehicles</b>

description: This dataset is the first to discribe the global ELV generation. Around 144 countries and regions are given for the ELV in a detail.
DOI: 10.15468/dl.56usm3
title: Occurrence Download

description: A dataset containing 774 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Roupala brasiliensis Klotzsch"
 ]
}

 The dataset includes 774 records from 97 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017613-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qnj7yz
title: Occurrence Download

description: A dataset containing 12142287 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Pl@ntNet automatically identified occurrences",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 12142287 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017587-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.24435034.v1
title: SmallMammalsCooccur

description: Corresponding publication:Costa, A. P. L., Winck, G. R., Teixeira, B. R., Gentile, R., Vieira, E. M., Pardini, R., Püttker, T., D’Andrea, P. S. and C. S. Andreazzi. 2023. Ecological interactions without co-occurrence are not evidence of spillover risk: Predicting the impact of landscape conversion on small mammal occurrence and the transmission of parasites in the Atlantic Forest. Under submissionData LocationsGeographic locations of data collection: Brazilian Atlantic Forest (see publication for more details)Methodological InformationMethods of data collection/generation: see manuscript for detailsThe authors respectfully request to be contacted by researchers interested in the raw data of small mammal occurrences.Contact InformationName: Ana Paula Lula CostaAffiliation: Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil.ORCID ID: https://orcid.org/0000-0003-4854-160XEmail: anapaulalula@gmail.comCode and Data overviewCodeAll analyses were made in R.Script for network analysesCosta.2023-Hmsc_CentralHosts.RScript for constructing Hmsc model and analyzing its parametersCosta.2023-Hmsc_Cooccur.RDataSmall mammal occurrence matrixcom.f_pa.csvcoordinates of each landscape used as sample sites for small mammal communitiesbuffer_id.csvLandscape metrics calculated for each sample siteland.feat.na.e.csvSmall mammal species traitsTrData2.csvSmall mammal phylogenetic treeSmallmammals_maxlike_nf.nwkModule clustering and categorization of small mammal species based on their centrality valuesNet_metrics.csv
DOI: 10.6084/m9.figshare.27037318
title: <b>Complete mitochondrial</b><b> </b><b>genome</b><b> </b><b>assembly of </b><b><i>Juglans regia</i></b>

description: The Persian walnut (<i>Juglans regia</i>), an economically vital species within the Juglandaceae family, has seen its mitochondrial genome sequenced and assembled in the current study using advanced Illumina and Nanopore sequencing technology.<b> </b>The 1,007,576 bp mitogenome of <i>J. regia</i> consisted of three circular chromosomes with a 44.52% GC content encoding 39 PCGs, 47 tRNA, and five rRNA genes. Extensive repetitive sequences, including 320 SSRs, 512 interspersed, and 83 tandem repeats, were identified, contributing to genomic complexity. The protein-coding sequences (PCGs) favored A/T-ending codons, and the codon usage bias was primarily shaped by selective pressure. Intracellular gene transfer occurred among the mitogenome, chloroplast, and nuclear genomes. Comparative genomic analysis unveiled abundant structure and sequence variation among <i>J. regia </i>and related species. The results of selective pressure analysis indicated that most PCGs underwent purifying selection, whereas the<i> atp4 </i>and<i> ccmB </i>genes had experienced positive selection between many species pairs. In addition, the phylogenetic examination, grounded in mitochondrial genome data, precisely delineated the evolutionary and taxonomic relationships of <i>J. regia</i> and its relatives. We identified a total of 539 RNA editing sites, among which 288 were corroborated by transcriptome sequencing data. Furthermore, expression profiling under temperature stress highlighted the complex regulation pattern of 28 differently expressed PCGs, wherein NADH dehydrogenase and ATP synthase genes might be critical in the mitochondria response to cold stress. Our results provided valuable molecular resources for understanding the genetic characteristics of <i>J. regia</i> and offered novel perspectives for population genetics and evolutionary studies in<i> Juglans</i> and related woody species.
DOI: 10.6084/m9.figshare.27037318.v1
title: <b>Complete mitochondrial</b><b> </b><b>genome</b><b> </b><b>assembly of </b><b><i>Juglans regia</i></b>

description: The Persian walnut (<i>Juglans regia</i>), an economically vital species within the Juglandaceae family, has seen its mitochondrial genome sequenced and assembled in the current study using advanced Illumina and Nanopore sequencing technology.<b> </b>The 1,007,576 bp mitogenome of <i>J. regia</i> consisted of three circular chromosomes with a 44.52% GC content encoding 39 PCGs, 47 tRNA, and five rRNA genes. Extensive repetitive sequences, including 320 SSRs, 512 interspersed, and 83 tandem repeats, were identified, contributing to genomic complexity. The protein-coding sequences (PCGs) favored A/T-ending codons, and the codon usage bias was primarily shaped by selective pressure. Intracellular gene transfer occurred among the mitogenome, chloroplast, and nuclear genomes. Comparative genomic analysis unveiled abundant structure and sequence variation among <i>J. regia </i>and related species. The results of selective pressure analysis indicated that most PCGs underwent purifying selection, whereas the<i> atp4 </i>and<i> ccmB </i>genes had experienced positive selection between many species pairs. In addition, the phylogenetic examination, grounded in mitochondrial genome data, precisely delineated the evolutionary and taxonomic relationships of <i>J. regia</i> and its relatives. We identified a total of 539 RNA editing sites, among which 288 were corroborated by transcriptome sequencing data. Furthermore, expression profiling under temperature stress highlighted the complex regulation pattern of 28 differently expressed PCGs, wherein NADH dehydrogenase and ATP synthase genes might be critical in the mitochondria response to cold stress. Our results provided valuable molecular resources for understanding the genetic characteristics of <i>J. regia</i> and offered novel perspectives for population genetics and evolutionary studies in<i> Juglans</i> and related woody species.
DOI: 10.15468/dl.kmasgp
title: Occurrence Download

description: A dataset containing 28816 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Orchidaceae",
 "Country is Colombia",
 "HasCoordinate is true",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 28816 records from 137 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017614-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k5qn97
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Asia",
 "Country is India",
 "DatasetKey is one of (iNaturalist Research-grade Observations, India Biodiversity Portal publication grade dataset)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Macaca arctoides (I.Geoffroy Saint-Hilaire, 1831)"
 ]
}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017616-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7equm3
title: Occurrence Download

description: A dataset containing 421351 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Abies Mill., Larix occidentalis Nutt., Pseudotsuga menziesii (Mirb.) Franco)",
 "Year 1970-2024"
 ]
}

 The dataset includes 421351 records from 1602 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017590-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qewwwp
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Elaeocarpus rutengii Weibel"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035983-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mpcta2
title: Occurrence Download

description: A dataset containing 1923 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Raphia P.Beauv.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1923 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054673-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a3f46h
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Saussurea involucrata (Kar. & Kir.) Sch.Bip."
 ]
}

 The dataset includes 42 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0141202-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.