cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10535451
title: Phylogenetic relationships and evolution of the major groups of Siluriformes

description: In the book chapter we offer a reappraisal of the phylogenetic relationships of the order Siluriformes. Results are based on an original supermatrix ML analysis of sequence data in combination with previously published hypotheses based on both morphology and molecular data. Relationships proposed are summarized in a revised classification of the Siluriformes to family level. The position of Diplomystidae is corroborated as the sister group to all other catfishes, with Loricarioidei as the next sister group to the rest of the order. Other results include a monophyletic group composed of Pangasiidae, Ictaluridae and Cranoglanididae and another including Austroglanididae, Ariidae and Anchariidae. Previously proposed large clades in Africa and Asia are mostly corroborated. A possible narrative biogeographic scenario is described where siluriform continental diversification occurred in tandem with the separation of Gondwana, in close association with the expanding coastal waterways and their occupation of lowland and estuarine environments. All datasets used to generate the trees, including a spreadsheet with GenBank accession numbers, independent alignments of nuclear and mitochondrial genomic markers, concatenated matrices and best-fit partitioning schemes, RAxML log files, and the best ML trees, are available for download at the Zenodo repository (10.5281/zenodo.10535451).





Prelim chapter citation:

de Pinna, M.C.C.  L. Peixoto, V. Tagliacollo and M. Britto. 2024. Phylogenetic relationships of the major groups of Siluriformes. pp. xx–xx. In: G. Arratia and R.E. Reis [eds.]. Catfishes, a Highly Diversified Group. Science Publishers, Inc., Enfield, Jersey, Plymouth.
DOI: 10.5281/zenodo.13830593
title: Phylogenetic relationships and evolution of the major groups of Siluriformes

description: In the book chapter we offer a reappraisal of the phylogenetic relationships of the order Siluriformes. Results are based on an original supermatrix ML analysis of sequence data in combination with previously published hypotheses based on both morphology and molecular data. Relationships proposed are summarized in a revised classification of the Siluriformes to family level. The position of Diplomystidae is corroborated as the sister group to all other catfishes, with Loricarioidei as the next sister group to the rest of the order. Other results include a monophyletic group composed of Pangasiidae, Ictaluridae and Cranoglanididae and another including Austroglanididae, Ariidae and Anchariidae. Previously proposed large clades in Africa and Asia are mostly corroborated. A possible narrative biogeographic scenario is described where siluriform continental diversification occurred in tandem with the separation of Gondwana, in close association with the expanding coastal waterways and their occupation of lowland and estuarine environments. All datasets used to generate the trees, including a spreadsheet with GenBank accession numbers, independent alignments of nuclear and mitochondrial genomic markers, concatenated matrices and best-fit partitioning schemes, RAxML log files, and the best ML trees, are available for download at the Zenodo repository (10.5281/zenodo.10535451).





Prelim chapter citation:

de Pinna, M.C.C.  L. Peixoto, V. Tagliacollo and M. Britto. 2024. Phylogenetic relationships of the major groups of Siluriformes. pp. xx–xx. In: G. Arratia and R.E. Reis [eds.]. Catfishes, a Highly Diversified Group. Science Publishers, Inc., Enfield, Jersey, Plymouth.
DOI: 10.25376/hra.27091732
title: Mixed nuts and microbiome - J Med Food-2023.pdf

description: This is a published paper in J Med Food, 2023
DOI: 10.25376/hra.27091732.v1
title: Mixed nuts and microbiome - J Med Food-2023.pdf

description: This is a published paper in J Med Food, 2023
DOI: 10.25345/c5j38kv94
title: MassIVE MSV000095933 - Genetic architecture of the red blood cell proteome.
title: Red blood cells (RBCs) represent a simplified and highly specialized cellular system for oxygen transport. Furthermore, RBC function and quality are highly clinically relevant given the ubiquity and life-saving role of blood transfusions. RBC oxygen carrying capacity and its reduction during storage at blood bank due to the accumulation of metabolic damage ( storage lesion), varies across individuals, and genetics plays a role. We profiled the proteomes of both fresh and post-storage RBCs from a genetically diverse mouse population and integrated with previously collected metabolomics and lipidomics data from these same mice. Cumulatively, we mapped 6,000 quantitative trait loci (QTLs) for proteins, peptides, and post-translational modifications (PTMs). We observed reduced cis and increased trans genetic effects compared to other tissues, potentially reflecting RBCs lack of a nucleus and lack of de novo protein synthesis. The trans signal was concentrated to QTL hotspots at hemoglobin beta (Hbb), Mon1a, and hemoglobin alpha (Hba), in both fresh and stored RBCs. A storage-specific QTL hotspot at the ferrireductase Steap3 locus was also observed, which was further supported by a cis protein QTL for STEAP3. The hemoglobin components were the primary sites of ptmQTLs, consistent with having many interactions with other proteins and their integral role in oxygen metabolism. These results were mirrored in a follow-up humanized mouse study in which the reactive cysteine residue of Hbb was removed, resulting in widespread changes in metabolites, proteins, and glutathionylation.
DOI: 10.6084/m9.figshare.27091738
title: Escherichia coli tRNA sequences, non-redundant

description: The following is a list of non-redundant Escherichia coli tRNA sequences used an a negative control for bisulfite sequencing analysis.
DOI: 10.6084/m9.figshare.27091738.v1
title: Escherichia coli tRNA sequences, non-redundant

description: The following is a list of non-redundant Escherichia coli tRNA sequences used an a negative control for bisulfite sequencing analysis.
DOI: 10.6073/pasta/cb5734d20d8be6a8060b6bd62f179b2a
title: Florida Bay Stable Isotope Data Everglades National Park (FCE LTER), Florida, USA, September 2000 - ongoing

description: 13C and 15N stable isotope data from seagrasses collected during visits to FCE LTER core research sites TS/Ph7a, TS/Ph8, TS/Ph9, TS/Ph10 and TS/Ph11.
DOI: 10.15468/dl.3hrh66
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "Geometry POLYGON((-3.33467 51.36243,-3.18743 51.36433,-3.10167 51.46297,-3.03972 51.54673,-3.11349 51.58805,-3.15473 51.58686,-3.22636 51.60128,-3.44363 51.56288,-3.4284 51.3627,-3.33467 51.36243))",
 "HasCoordinate is true",
 "TaxonKey is Geoglossaceae",
 "Year 2014-2024"
 ]
}

 The dataset includes 54 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027252-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7mk6mn
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "StateProvince is Kansas",
 "TaxonKey is Catocala delilah Strecker, 1874"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027253-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nq7ruw
title: Occurrence Download

description: A dataset listing the 4073 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "GadmGid is one of (BRA.13.664_2, BRA.13.167_2, BRA.13.460_2)",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 4073 records were derived from 150 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027243-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vyz6nj
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Depth 2870.0-4250.0m",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cyclamminidae"
 ]
}

 The dataset includes 103 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027255-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qkt2jk
title: Occurrence Download

description: A dataset containing 123 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Infundibulicybe gibba (Pers.) Harmaja",
 "Year 2000-2024"
 ]
}

 The dataset includes 123 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027256-240906103802322/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.27091753
title: Trypanosoma brucei tRNA sequences, non-redundant

description: The following is a list of non-redundant Trypanosoma brucei tRNA sequences for mapping of bisulfite sequencing experiments.
DOI: 10.6084/m9.figshare.27091753.v1
title: Trypanosoma brucei tRNA sequences, non-redundant

description: The following is a list of non-redundant Trypanosoma brucei tRNA sequences for mapping of bisulfite sequencing experiments.
DOI: 10.15468/dl.gdh2ww
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Jacaranda heterophylla M.M.Silva"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027257-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e209285v1
title: Replication Material for COEP The Causal Effect of Economic Freedom on Female Employment & Education

description: While there are decades of evidence that economically free economies grow faster and are more productive than less free ones, there is less knowledge about the effect of economic freedom on groups that have traditionally been disadvantaged. I study the causal effects of large and sustained jumps in economic freedom on women’s labor force participation and primary school enrollment. I find that these jumps have a positive and statistically significant effect in both cases--economic freedom is good for women’s labor force opportunities and female education.
DOI: 10.15468/dl.zw3z6u
title: Occurrence Download

description: A dataset listing the 11 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sialia sialis (Linnaeus, 1758)"
 ]
}

 The dataset's 11 records were derived from 181 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027247-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7ryqkr
title: Occurrence Download

description: A dataset listing the 66 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((37.79713 55.26632,37.85768 55.26632,37.85768 55.29422,37.79713 55.29422,37.79713 55.26632))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 66 records were derived from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027238-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dy4kny
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is January",
 "OccurrenceStatus is Present",
 "TaxonKey is Carcharias taurus Rafinesque, 1810",
 "Year is 2016"
 ]
}

 The dataset includes 35 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027259-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cktcpe
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 },
 "TaxonKey is Diplocladiella G.Arnaud ex M.B.Ellis",
 "Year is greater than or equal to 1991"
 ]
}

 The dataset includes 41 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027258-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fbwyea
title: Occurrence Download

description: A dataset containing 3942 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 },
 "TaxonKey is Dothideaceae",
 "Year is greater than or equal to 1991"
 ]
}

 The dataset includes 3942 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027260-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4t6khk
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Oceania",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is February",
 "TaxonKey is Carcharias taurus Rafinesque, 1810",
 "Year 2016-2016"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027261-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48577/jpl.xfsmsx
title: The EnMAP spaceborne imaging spectroscopy mission: Initial scientific results after one year into operation

description: Imaging spectroscopy has been a recognized and established technology since the 1980s from mainly airborne and field based platforms for the identification and quantification of key bio- and geo-chemical surface and atmospheric compounds based on characteristic spectral reflectance features in the visible-near infrared (VNIR) and short-wave infrared (SWIR). Meanwhile, spaceborne missions, a leap in technology, were sparse, starting with the CHRIS/PROBA and EO1/Hyperion missions in the early 2000s providing spectroscopy data with limited spectral coverage or lesser data quality in the SWIR. Since 2019, several countries and agencies have successfully launched several spaceborne imaging spectroscopy systems in orbit or on the ISS such as DESIS, PRISMA, HISUI, GF-5, EnMAP and EMIT. As part of these recent missions, the German Environmental Mapping and Analysis Program (EnMAP) stands for its long-term development, sophisticated design with on-board calibration, high data quality requirements, and strong science accompanying program. EnMAP was launched in April 2022 and, following a successful commissioning phase, started its operational activities in November 2022. The EnMAP mission encompasses global coverage from 74° N to 74° S through on-demand data acquisitions. Data are characterized by open free access, 30 m spatial resolution, high spectral resolution with a spectral sampling distance of 6.5 nm and 10 nm in the VNIR and SWIR regions respectively, and high signal-to-noise ratio. In this paper, we aim to present the current status of the mission, coverage, science capabilities and performances after one year into operation. We use EnMAP to show the potential of space-based imaging spectroscopy to operate in various environments, including high and low light levels, dense forests, Antarctica glaciers, and arid agricultural areas, which can and which enable application field areas, including agriculture and forest, soil compositional mapping, raw materials, methane mapping, water, snow and ice. These results show that the performance of EnMAP is beyond the mission requirements, and the high potential of EnMAP for contribution to scientific exploitation in various geo- and bio-fields. EnMAP also represents a key tool for the development an testing of data processing algorithms for upcoming global operational missions.
DOI: 10.48577/jpl.jjj6je
title: A First Assessment of Airborne HyTES-based Land Surface Temperature and Evapotranspiration

description: The Hyperspectral Thermal Emission Spectrometer (HyTES) offers high spatial and spectral resolution thermal infrared (TIR) airborne measurements, which are crucial for deriving land surface temperature and emissivity (LST&E). These measurements have wide-ranging applications, particularly in understanding water stress and plant water use. One critical application of TIR satellite-sensor systems is the estimation of evapotranspiration (ET), which can be derived from LST. ET is essential for modeling water fluxes from the land surface, and various algorithms leverage LST as a key boundary condition for this purpose. In this study, we apply an ET algorithm to HyTES LST data for the first time, using an analytical surface energy balance model, the Surface Temperature Initiated Closure (STIC) version 1.3. We provide an overview of the STIC model, detailing its application to HyTES data, including the integration of ancillary datasets. We demonstrate the practicality of this approach by presenting ET and LST calculations for 35 HyTES flightlines from field campaigns conducted in 2019, 2021, and 2023. To validate our results, we compare the derived ET and LST against available in situ measurements, including eddy covariance-derived latent heat flux and radiometer-derived LST. While this study focuses on HyTES data, the same methodology is applicable to any instantaneous LST dataset. Advancing TIR mapping of ET is crucial for applications in agriculture, water management and for understanding the evolving water cycle.
DOI: 10.48577/jpl.4hvytu
title: Dual Sources of S2 Observed in Comet 67P: Insights from Comparing ROSINA Measurements and Laboratory Simulations

description: Hydrogen sulfide (H2S) is the fifth most abundant molecule found in the coma of comet 67P/Churyumov-Gerasimenko (67P). Prior to its incorporation into cometary materials, H2S likely underwent ultraviolet (UV) radiation exposure, which is thought to initiate a complex sulfur chemistry. In this study, we present a comprehensive investigation into the UV photochemistry of H2S ice films using IR, Raman, and mass spectrometry techniques. Our study reveals the production of complex sulfur allotropes ranging from S2 to S6, alongside polysulfanes (H2Sn, n=2-3). Temperature Programmed Desorption (TPD) measurements post-irradiation exhibit two peaks for S2 molecules: a broad peak between 80 K and 140 K and a distinct peak at ~ 245 K. Notably, larger allotropes S3-S5 exclusively display the 245 K peak. Furthermore, ROSINA measurements of the S2/H2S ratio during dust impact events and previously reported S2/H2S ratios in the undisturbed coma are compared to our laboratory determined S2/H2S values. This analysis identifies two distinct sources of S2: a volatile S2 potentially sublimated directly from the comet's surface, and a secondary source likely resulting from fragmentation of larger sulfur chains during dust impacts. We determined the ratio of produced S2 to the initial H2S for both the volatile component, denoted as (S2/H2S)volatile, and the refractory component at 245 K, labeled as (S2/H2S)refractory, with both measurements conducted at an irradiation fluence of 2.25 1017 photons.cm-2. Remarkably, these laboratory-derived S2/H2S ratios exhibit concordance with ROSINA measurements. When extrapolated to irradiation fluences anticipated in molecular clouds, this photo-processing mechanism offers a plausible explanation for the measured S2/H2S ratio in comet 67P.
DOI: 10.15468/dl.gf9yag
title: Occurrence Download

description: A dataset containing 1180 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Material citation, Material sample)",
 "DatasetKey is one of (CAS Herpetology (HERP), Museum of Comparative Zoology, Harvard University, NMNH Extant Specimen Records (USNM, US), University of Florida Herpetology, Northern Territory Museum and Art Gallery provider for OZCAM, Australian Museum provider for OZCAM, Vertebrate Zoology Division - Herpetology, Yale Peabody Museum, MVZ Herp Collection (Arctos), KUBI Herpetology Collection, International Barcode of Life project (iBOL))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "PublishingOrg is one of (66522820-055c-11d8-b84e-b8a03c50a862, b4640710-8e03-11d8-b956-b8a03c50a862, bc092ff0-02e4-11dc-991f-b8a03c50a862, 8483a1f0-1032-11db-ae00-b8a03c50a862, 8cdd9232-84eb-4bad-9d9b-a36910cd524b, 770c30d2-c2a8-4bb2-8056-6167297cddae, 2e167bb0-4441-11db-9ba2-b8a03c50a862, 8edbbde0-055e-11d8-b850-b8a03c50a862, b554c320-0560-11d8-b851-b8a03c50a862, b3bf3a83-1f68-4541-a03f-330d30d567f5)",
 "TaxonKey is Indotyphlops braminus (Daudin, 1803)",
 "Year 1950-2024"
 ]
}

 The dataset includes 1180 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027263-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5873gx
title: Occurrence Download

description: A dataset containing 197 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Fossil)",
 "TaxonKey is Pelecanus crispus Bruch, 1832"
 ]
}

 The dataset includes 197 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027262-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18112/openneuro.ds005121.v1.0.0
title: Siefert2024
DOI: 10.15468/dl.fas4zd
title: Occurrence Download

description: A dataset containing 15541 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Museo Nacional de Ciencias Naturales, Madrid: MNCN_Herpeto",
 "TaxonKey is Squamata"
 ]
}

 The dataset includes 15541 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0093607-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.py49sq
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Peru",
 "OccurrenceStatus is Present",
 "TaxonKey is Ipomoea pauciflora M.Martens & Galeotti"
 ]
}

 The dataset includes 26 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0430284-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.