cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12545234
title: Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota
title: Dataset

description: Background: Gut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) and whole shotgun metagenomic sequencing to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) colorectal lesion patients (HRL), and CRC cases, with each sample sequenced using both 16S and shotgun methods. We thoroughly compared both sequencing technologies at the species, genus, and family annotation levels, the abundance differences in these taxa, sparsity, alpha and beta diversities, ability to train prediction models, and the similarity of the microbial signature derived from these models. 




Results: As expected, the results showed that 16S detects only part of the gut microbiota community revealed by shotgun, although some genera were only profiled by 16S. The 16S abundance data was sparser and exhibited lower alpha diversity. In lower taxonomic ranks, shotgun and 16S highly differed, partially due to a disagreement in reference databases. When considering only shared taxa, the abundance was positively correlated between the two strategies. We also found a moderate correlation between the shotgun and 16S alpha-diversity measures, as well as their PCoAs. Regarding the machine learning models, only some of the shotgun models showed some degree of predictive power in an independent test set, but we could not demonstrate a clear superiority of one technology over the other. Microbial signatures from both sequencing techniques revealed taxa previously associated with CRC development, e.g., Parvimonas micra. 




Conclusions: Shotgun and 16S sequencing provide two different lenses to examine microbial communities. While we have demonstrated that they can unravel common patterns (including microbial signatures), shotgun often gives a more detailed snapshot than 16S, both in depth and breadth. Instead, 16S will tend to show only part of the picture, giving greater weight to dominant bacteria in a sample. Therefore, we recommend choosing one or another sequencing technique before launching a study. Specifically, shotgun sequencing is preferred for stool microbiome samples and in-depth analyses, while 16S is more suitable for tissue samples and studies with targeted aims.
DOI: 10.5281/zenodo.12545235
title: Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota
title: Dataset

description: Background: Gut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) and whole shotgun metagenomic sequencing to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) colorectal lesion patients (HRL), and CRC cases, with each sample sequenced using both 16S and shotgun methods. We thoroughly compared both sequencing technologies at the species, genus, and family annotation levels, the abundance differences in these taxa, sparsity, alpha and beta diversities, ability to train prediction models, and the similarity of the microbial signature derived from these models. 




Results: As expected, the results showed that 16S detects only part of the gut microbiota community revealed by shotgun, although some genera were only profiled by 16S. The 16S abundance data was sparser and exhibited lower alpha diversity. In lower taxonomic ranks, shotgun and 16S highly differed, partially due to a disagreement in reference databases. When considering only shared taxa, the abundance was positively correlated between the two strategies. We also found a moderate correlation between the shotgun and 16S alpha-diversity measures, as well as their PCoAs. Regarding the machine learning models, only some of the shotgun models showed some degree of predictive power in an independent test set, but we could not demonstrate a clear superiority of one technology over the other. Microbial signatures from both sequencing techniques revealed taxa previously associated with CRC development, e.g., Parvimonas micra. 




Conclusions: Shotgun and 16S sequencing provide two different lenses to examine microbial communities. While we have demonstrated that they can unravel common patterns (including microbial signatures), shotgun often gives a more detailed snapshot than 16S, both in depth and breadth. Instead, 16S will tend to show only part of the picture, giving greater weight to dominant bacteria in a sample. Therefore, we recommend choosing one or another sequencing technique before launching a study. Specifically, shotgun sequencing is preferred for stool microbiome samples and in-depth analyses, while 16S is more suitable for tissue samples and studies with targeted aims.
DOI: 10.5066/p1hrgtqz
title: Estimated crop irrigation water use withdrawals in McMullen Valley Groundwater Basin, Arizona for 2023

description: Observations of irrigated agricultural land within the McMullen Valley Groundwater Basin in Arizona. Crops were verified in situ three times in 2023, first on May 10th, then on Aug 24th, and finally on Sep 27th; based on digitized field boundaries. Field boundaries were digitized from U.S. Department of Agriculture, National Agriculture Imagery Program County Mosaic 2023 imagery for Arizona and supplemented with the Sentinel2 imagery collection accessed via the European Space Agency, Copernicus Browser (https://browser.dataspace.copernicus.eu/). Satellite images were also used to identify the length of the growing season and crop condition. Water withdrawals were calculated using the modified Blaney-Criddle model of calculating consumptive use (U.S. Bureau of Reclamation, 1992 appendix A) using crop coefficients from Doorenbos and Pruitt (1975), the number of acres with active crops, crop condition, and irrigation system efficiency. The withdrawal equation was modified from "Water withdrawals for irrigation, municipal, mining, thermoelectric-power, and drainage uses in Arizona outside of active management areas, 1991-2000" (Tadayon, 2005) to account for variations in water application.


Data are available as a shapefile for visualization or as a stand-alone csv table for attributes only.


Bureau of Reclamation, 1992, Plan of study and methods manual for Colorado River system consumptive uses and losses report 1985–1990: Bureau of Reclamation, Appendix A, 23 p.

Doorenbos, J. and Pruitt, W.O.,1975, Guidelines for predicting crop water requirements: Irrigation and drainage paper FAO No. 24, p195, https://www.nrc.gov/docs/ML1821/ML18215A282.pdf.

Tadayon, Saeid, 2005, Water withdrawals for irrigation, municipal, mining, thermoelectric-power, and drainage uses in Arizona outside of Active Management Areas, 1991–2000: U.S. Geological Survey Scientific Investigations Report 2004-5293, 28 p, https://doi.org/10.3133/sir20045293.
DOI: 10.15468/dl.yhntpz
title: Occurrence Download

description: A dataset containing 89945455 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is iNaturalist Research-grade Observations"
 ]
}

 The dataset includes 89945455 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010156-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fzhspr
title: Occurrence Download

description: A dataset containing 7717 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Calophyllum brasiliense Cambess., Calophyllum angulare A.C.Sm., Calophyllum lucidum Benth.)"
 ]
}

 The dataset includes 7717 records from 378 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010169-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12635755
title: EVENTS ACCEL BBD66 (28-06-24 to 02-07-24)

description: Sampling frequency: 80 Hz

Resolution: 0.125/4096
DOI: 10.5281/zenodo.12635756
title: EVENTS ACCEL BBD66 (28-06-24 to 02-07-24)

description: Sampling frequency: 80 Hz

Resolution: 0.125/4096
DOI: 10.5281/zenodo.12635783
title: Sexual fantasies in Spain

description: We used an exploratory approach over a large sample of the general population interpreting the frequencies of those contents by taking into account whether participants thought of, desired to realize or have effectively done them, as well as their gender.
DOI: 10.5281/zenodo.12635784
title: Sexual fantasies in Spain

description: We used an exploratory approach over a large sample of the general population interpreting the frequencies of those contents by taking into account whether participants thought of, desired to realize or have effectively done them, as well as their gender.
DOI: 10.5281/zenodo.12635791
title: EVENTS ACCEL BBDF3 (28-06-24 to 02-07-24)

description: Sampling frequency: 80 Hz

Resolution: 0.125/4096
DOI: 10.5281/zenodo.12635792
title: EVENTS ACCEL BBDF3 (28-06-24 to 02-07-24)

description: Sampling frequency: 80 Hz

Resolution: 0.125/4096
DOI: 10.5281/zenodo.12635811
title: EVENTS ACCEL BBE27 (28-06-24 to 02-07-24)

description: Sampling frequency: 80 Hz

Resolution: 0.125/4096
DOI: 10.5281/zenodo.12635812
title: EVENTS ACCEL BBE27 (28-06-24 to 02-07-24)

description: Sampling frequency: 80 Hz

Resolution: 0.125/4096
DOI: 10.15468/dl.vck4cc
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Chaetomys subspinosus (Olfers, 1818)",
 "Year 1974-2024"
 ]
}

 The dataset includes 13 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010172-240626123714530/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.26166898
title: Raw data associated with manuscript titled: <b>TKI Type Switching Overcomes ROS1 L2086F in ROS1 Fusion-Positive Cancers</b>

description: The graphs in the manuscript are based on these raw data collected with experimentation.
DOI: 10.6084/m9.figshare.26166898.v1
title: Raw data associated with manuscript titled: <b>TKI Type Switching Overcomes ROS1 L2086F in ROS1 Fusion-Positive Cancers</b>

description: The graphs in the manuscript are based on these raw data collected with experimentation.
DOI: 10.15468/dl.bk6syv
title: Occurrence Download

description: A dataset containing 134 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Microglanis parahybae (Steindachner, 1880)"
 ]
}

 The dataset includes 134 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010173-240626123714530/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.26166892
title: Data from Stryker et al (2024) "Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria."

description: Data from Stryker et al (2024) "Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria."For analyses refer to code from Stryker et al (2024) "Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria."
DOI: 10.15468/dl.dq2xk6
title: Occurrence Download

description: A dataset containing 2898 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Garcinia gardneriana (Planch. & Triana) Zappi, Rheedia gardneriana Planch. & Triana, Rheedia gardneriana var. parvifolia Engl., Rheedia calyptrata (Schltdl.) Planch. & Triana, Rheedia gardneriana var. glaziovii Engl., Rheedia spruceana Engl., Rheedia tenuifolia Engl., Tovomita calyptrata Schltdl., Rheedia spruceana var. cuneata Engl.)"
 ]
}

 The dataset includes 2898 records from 175 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010174-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qsvupx
title: Occurrence Download

description: A dataset containing 282 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-96.69986 17.0101,-96.66547 17.0101,-96.66547 17.03189,-96.69986 17.03189,-96.69986 17.0101))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 282 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010176-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z3uxmn
title: Occurrence Download

description: A dataset containing 19085 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Información florística del Proyecto Mapa de Vegetación para la Clasificación de Ecosistemas del Ecuador Continental",
 "Geometry POLYGON((-96.64723 -8.75579,-60.35277 -8.75579,-60.35277 5.75579,-96.64723 5.75579,-96.64723 -8.75579))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 19085 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010175-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kbj6nj
title: Occurrence Download

description: A dataset containing 13191 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Registro de avistamientos de fauna durante recorridos de control y vigilancia en el Parque Nacional Yasuní",
 "Geometry POLYGON((-94.64723 -8.25579,-58.35277 -8.25579,-58.35277 6.25579,-94.64723 6.25579,-94.64723 -8.25579))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 13191 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010178-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a6m9us
title: Occurrence Download

description: A dataset containing 3608 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Birds of Cerro Blanco: new records and richness update"
 ]
}

 The dataset includes 3608 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010179-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qhpv24
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Monitoreo de anidación de la tortuga verde (Chelonia mydas) en las Islas Galápagos"
 ]
}

 The dataset's 1 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010168-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.483ufc
title: Occurrence Download

description: A dataset containing 2196 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Kielmeyera rubriflora Cambess.)"
 ]
}

 The dataset includes 2196 records from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010180-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5725kd
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hydromedusa maximiliani (Mikan, 1825)",
 "Year 1974-2024"
 ]
}

 The dataset includes 55 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010182-240626123714530/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.26166946
title: Code from Stryker et al (2024) "Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria." For info or help with what is here, contact Brad Oberle: brad.oberle@gmail.com

description: R Code from Stryker et al (2024) "Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria."For data refer to Data from Stryker et al (2024) "Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria."
DOI: 10.6084/m9.figshare.26166946.v1
title: Code from Stryker et al (2024) "Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria." For info or help with what is here, contact Brad Oberle: brad.oberle@gmail.com

description: R Code from Stryker et al (2024) "Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria."For data refer to Data from Stryker et al (2024) "Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria."
DOI: 10.6084/m9.figshare.26166988
title: ReadMe.txt

description: Figshare repository including data and code from Stryker et al (2024) "Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria." For info or help with what is here, contact Brad Oberle: brad.oberle@gmail.com
DOI: 10.6084/m9.figshare.26166988.v1
title: ReadMe.txt

description: Figshare repository including data and code from Stryker et al (2024) "Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria." For info or help with what is here, contact Brad Oberle: brad.oberle@gmail.com
DOI: 10.15468/dl.esfqq5
title: Occurrence Download

description: A dataset containing 7847 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tectona grandis L.f."
 ]
}

 The dataset includes 7847 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010183-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zqszhd
title: Occurrence Download

description: A dataset containing 1220564 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Ireland, United Kingdom of Great Britain and Northern Ireland, Portugal, Spain, Italy, Greece, Svalbard and Jan Mayen, Denmark, Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Belgium, Netherlands, France, Germany, Switzerland, Austria, Türkiye, Russian Federation, Belarus, Ukraine, Romania, Bulgaria, North Macedonia, Albania, Montenegro, Serbia, Kosovo, Slovenia, Bosnia and Herzegovina, Poland, Czechia, Slovakia, Hungary)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Quercus robur L."
 ]
}

 The dataset includes 1220564 records from 3394 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010181-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.869f4j
title: Occurrence Download

description: A dataset containing 660 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alouatta belzebul (Linnaeus, 1766)"
 ]
}

 The dataset includes 660 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0145490-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t3mrp2
title: Occurrence Download

description: A dataset containing 2671 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((35.32496433333334 48.58410666666667, 69.37031999999999 48.58410666666667, 69.37031999999999 65.67073733333334, 35.32496433333334 65.67073733333334, 35.32496433333334 48.58410666666667))",
 "EventDate is 2016-02-01,2016-02-29"
 ]
}

 The dataset includes 2671 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028267-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jpcf3j
title: Occurrence Download

description: A dataset containing 9540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Aphelocoma californica (Vigors, 1839)"
 ]
}

 The dataset includes 9540 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0187910-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z7g3g9
title: Occurrence Download

description: A dataset containing 16630 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puma concolor (Linnaeus, 1771)"
 ]
}

 The dataset includes 16630 records from 287 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0354903-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t6rr6m
title: Occurrence Download

description: A dataset containing 280 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Commelinaceae)",
 "Country is United States of America",
 "StateProvince is Utah"
 ]
}

 The dataset includes 280 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028226-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gqd6qi
title: Occurrence Download

description: A dataset containing 1457 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spodoptera frugiperda J.E.Smith, 1797"
 ]
}

 The dataset includes 1457 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030396-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.