cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/r3t9jm798y.1
title: Metatranscriptomics Uncover Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects

description: This dataset contains code and processed data used to perform analysis and generate figures for our manuscript "Diurnal Characterization of Metatranscriptomics Yields Bacterial Transgenes with Pronounced Metabolic Effects" . The main folder are "code", "data", and "figures". Within each folder, it is organized as follows:

- diversity_analysis: contains the code, data, or figures for the diversity analysis comparing 16S, metagenomics genes, and metatranscriptomic transcripts. Related to Figure 1.
- DE_analysis: contains the code, data, or figures for the differential abundance analysis for the metagenomics genes and metatranscriptomic transcripts. Related to Figure 2.
- cycling_analysis: contains the code, data, or figures for the cycling analysis for the metagenomics genes and metatranscriptomic transcripts. Related to Figure 3.
- bsh_analysis: contains the code, data, or figures for the bsh differential expression analysis using the targeted and untargeted search for bsh in the metatranscriptomics. Related to Figure 4.
- ENB_invitro_metab: contains the code, data, or figures the bile acid quantification from the cultures of ENBs. Related to Figure 5.
- ENB_invivo_metab: contains the code, data, or figures for the phenotypic measurements of mice gavaged with ENBs. Also contains the fecal bile acid quantification of these mice. Related to Figure 6.
- replotting_AZ2014_CD2022: contains the code, data, or figures for weight and glucose measurements from Zarrinpar 2014 and ileum bile acid quantification from Dantas Machado, 2022 we replotted in Figure S1 and S4, respectively.

Under "code" we also include:
- processing_metaG: contains the code used to process the metagenomic data from fastq to counts table.
- processing_metaT: contains the code used to process the metatranscriptomics data from fastq to counts table.

Under "data" we also include:
- m16s: contains the processed 16s counts data from Zarrinpar 2014
- genome_metaG: contains woltka processed metagenomic counts data at the genome level
- genome_metaT: contains woltka processed metatranscriptomics counts data at the genome level
- pfam_metaG: contains woltka processed metagenomic counts data collapsed to pfam functions
- pfam_metaT: contains woltka processed metatranscriptomics counts data collapsed to pfam functions
DOI: 10.17632/gkg3tfrp6z
title: M6P and GDP-mannose measure

description: We measured the levels of M6P and GDP-mannose in frozen HCC tumor and adjacent normal tissues from patients (n=42 pairs). Notably, both metabolites were elevated in tumor tissues compared to their matched normal counterparts. All metabolite levels were normalized to the average levels observed in adjacent normal tissues.
DOI: 10.17632/gkg3tfrp6z.1
title: M6P and GDP-mannose measure

description: We measured the levels of M6P and GDP-mannose in frozen HCC tumor and adjacent normal tissues from patients (n=42 pairs). Notably, both metabolites were elevated in tumor tissues compared to their matched normal counterparts. All metabolite levels were normalized to the average levels observed in adjacent normal tissues.
DOI: 10.17632/72b3hyjgdh.1
title: Datasets for the article “Smallholder cropping systems contribute limited greenhouse gas fluxes in upper Eastern Kenya”

description: The datasets were collected from two smallholder farms in Upper Eastern Kenya over a year (April 2019–April 2020). The study aimed to quantify greenhouse gas (GHG) emissions from different smallholder cropping systems. The cropping systems investigated included i) sole maize, ii) maize-beans intercrop, iii) agroforestry, iv) banana, and v) coffee. The GHG data (carbon dioxide [CO₂], methane [CH₄], and nitrous oxide [N₂O]) were collected using static chamber methods, and gas samples were analyzed using gas chromatography. Soil samples were collected at 0 –20 cm depth and analyzed for bulk density, pH, organic carbon, and total nitrogen. Daily precipitation and soil moisture content were recorded throughout the study. Biomass measurements (grain, leaves, stems, and roots) were measured for the two cropping seasons. To determine GHG emissions, cumulative fluxes were calculated. Statistical analysis, including analysis of variance (ANOVA), was conducted to evaluate differences in GHG emissions across cropping systems. This dataset is supplementary to the research article Lemarpe, S.E., Musafiri, C.M., Kiboi, M.N., Ng'etich, O.K., Macharia, J.M., Shisanya, C.A., Kibet, E., Zeila, A., Mutuo, P. and Ngetich, F.K., (2023). Smallholder cropping systems contribute limited greenhouse gas fluxes in upper Eastern Kenya. Nature-Based Solutions, 4, p.100098. https://doi.org/10.1016/j.nbsj.2023.100098
DOI: 10.17632/72b3hyjgdh.2
title: Datasets for the article “Smallholder cropping systems contribute limited greenhouse gas fluxes in upper Eastern Kenya”

description: The datasets were collected from two smallholder farms in Upper Eastern Kenya over a year (April 2019–April 2020). The study aimed to quantify greenhouse gas (GHG) emissions from different smallholder cropping systems. The cropping systems investigated included i) sole maize, ii) maize-beans intercrop, iii) agroforestry, iv) banana, and v) coffee. The GHG data (carbon dioxide [CO₂], methane [CH₄], and nitrous oxide [N₂O]) were collected using static chamber methods, and gas samples were analyzed using gas chromatography. Soil samples were collected at 0 –20 cm depth and analyzed for bulk density, pH, organic carbon, and total nitrogen. Daily precipitation and soil moisture content were recorded throughout the study. Biomass measurements (grain, leaves, stems, and roots) were measured for the two cropping seasons. To determine GHG emissions, cumulative fluxes were calculated. Statistical analysis, including analysis of variance (ANOVA), was conducted to evaluate differences in GHG emissions across cropping systems. This dataset is supplementary to the research article Lemarpe, S.E., Musafiri, C.M., Kiboi, M.N., Ng'etich, O.K., Macharia, J.M., Shisanya, C.A., Kibet, E., Zeila, A., Mutuo, P. and Ngetich, F.K., (2023). Smallholder cropping systems contribute limited greenhouse gas fluxes in upper Eastern Kenya. Nature-Based Solutions, 4, p.100098. https://doi.org/10.1016/j.nbsj.2023.100098
DOI: 10.3886/e207982
title: Data and Code for: An American Macroeconomic Picture: Supply and Demand Shocks in the Frequency Domain

description: We provide a few new empirical facts that theoretical models should feature
in order to be consistent with US data. 1) There are two classes of
shocks: demand and supply. Supply shocks have long-run effects on economic
activity, demand shocks do not. 2) Both supply and demand shocks
are important sources of business cycles fluctuations. 3) Supply shocks are
the primary driver for consumption fluctuations, demand shocks for investment.
4) The demand shock is closely related to the credit spread, while
the supply shock is essentially a news shock. The results are obtained
using a novel approach which combines frequency domain identification
and Dynamic Factor Model analysis.
DOI: 10.3886/e207982v1
title: Data and Code for: An American Macroeconomic Picture: Supply and Demand Shocks in the Frequency Domain

description: We provide a few new empirical facts that theoretical models should feature
in order to be consistent with US data. 1) There are two classes of
shocks: demand and supply. Supply shocks have long-run effects on economic
activity, demand shocks do not. 2) Both supply and demand shocks
are important sources of business cycles fluctuations. 3) Supply shocks are
the primary driver for consumption fluctuations, demand shocks for investment.
4) The demand shock is closely related to the credit spread, while
the supply shock is essentially a news shock. The results are obtained
using a novel approach which combines frequency domain identification
and Dynamic Factor Model analysis.
DOI: 10.15468/dl.q4xkmc
title: Occurrence Download

description: A dataset containing 1097755 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cabomba caroliniana A.Gray, Cipangopaludina chinensis (J.E.Gray, 1833), Salvinia ×molesta D.S.Mitch., Xenopus laevis (Daudin, 1802), Apalone ferox (Schneider, 1783), Muntiacus reevesi (Ogilby, 1839), Myriophyllum aquaticum (Vell.) Verdc., Alternanthera philoxeroides (Mart.) Griseb., Mustela vison Schreber, 1777, Procyon lotor (Linnaeus, 1758), Faxonius virilis (Hagen, 1870), Procambarus clarkii (Girard, 1852), Pacifastacus leniusculus (Dana, 1852), Neogobius melanostomus (Pallas, 1814), Pseudorasbora parva (Temminck & Schlegel, 1846), Elaphe taeniura (Cope, 1861), Heracleum mantegazzianum Sommier & Levier, Ambrosia artemisiifolia L., Misgurnus mohoity (Dybowski, 1869))",
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Specimen, Unknown evidence, Machine Observation, Occurrence evidence)",
 "Year is greater than or equal to 1971",
 "Year is less than or equal to 2024",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1097755 records from 3024 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025237-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/examiner-c44-4213
title: Fiesta of Stars, 1951

description: 30 images. Fiesta of Stars, April 29, 1951. Loretta Young; Van Johnson; Father Patrick Peyton; Margaret O'Brien; Clare Boothe Luce; Irene Dunn; Louella Parsons; George Jesel; John Lombardi; Harry Crocker.; More descriptive information with originals.
DOI: 10.15468/dl.6vybmn
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Pristimantis tayrona (Lynch & Ruiz-Carranza, 1985)"
 ]
}

 The dataset includes 151 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025696-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nkgsq8
title: Occurrence Download

description: A dataset containing 561 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paspalum denticulatum Trin.",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 561 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046806-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jdzh8f
title: Occurrence Download

description: A dataset containing 5913 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pentameris P.Beauv., Pentameris E.Mey., Pentamerismus McGregor, 1949, Pentamerista Maguire)",
 "HasCoordinate is true",
 "Country is South Africa"
 ]
}

 The dataset includes 5913 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025707-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xwbvuq
title: Occurrence Download

description: A dataset containing 309 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Abies flinckii Rushforth"
 ]
}

 The dataset includes 309 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002229-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.teoztu
title: Occurrence Download

description: A dataset containing 11519 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paspalum distichum L.",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 11519 records from 172 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046809-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/examiner-ouc11690966
title: Emelita Street Elementary School opens, 1953

description: 7 images. Emelita Street Elementary School opens, 13 February 1953. Miss Rosalie Hill (Kindergarten teacher); Miss Maxine Mitchell (Principal of new school); Mrs. Edith K. Stafford (member of Board of Education); Mrs. Ruth C. Cole (member of Board of Education). ; Caption slip reads: "Photographer: Glickman. Date: 1953-02-13. Assignment: Emelita Street Elementary School opens. G111-112: Mothers and kids heading for new school. G117: Kids lined up waiting to get into classrooms. 118-121: Miss Rasalie Hill conducts class of kindergarten students who are attending school for first time. 120-122, l to r: Miss Maxine Mitchell, principal of new school; Mrs. Edith K. Stafford and Mrs. Ruth C. Cole, members of Board of Education."
DOI: 10.15468/dl.7vjef6
title: Occurrence Download

description: A dataset containing 1946 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Grus grus (Linnaeus, 1758)"
 ]
}

 The dataset includes 1946 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024492-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u68zmj
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Plectrohyla chrysopleura Wilson, McCranie & Cruz-Díaz, 1994"
 ]
}

 The dataset includes 37 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025730-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zuh8rw
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paspalum falcatum Nees ex Steud.",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 57 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046816-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n8u6na
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aeridostachya propinqua (Ames) W.Suarez & Cootes"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0199538-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6samwm
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium ortholepium Omang"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021136-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2wphbf
title: Occurrence Download

description: A dataset containing 2642 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Columba oenas Linnaeus, 1758",
 "DatasetKey is Observation.org, Nature data from around the World",
 "Country is one of (Germany, France, Spain, Portugal, Denmark, Austria, Italy, Switzerland, Greece, Poland, Hungary, Slovenia, Sweden, Norway, Slovakia, Montenegro, Croatia, North Macedonia, Serbia, Iceland, Ireland, United Kingdom of Great Britain and Northern Ireland, Albania, Bosnia and Herzegovina, Bulgaria, Finland)"
 ]
}

 The dataset includes 2642 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006082-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6cw4x2
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paspalum flavum J.Presl",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 10 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046820-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wxdpfe
title: Occurrence Download

description: A dataset containing 14513 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tockus deckeni (Cabanis, 1868)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 14513 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025716-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bowh4t
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paspalum foliiforme S.Denham",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 69 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046822-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vbpjxt
title: Occurrence Download

description: A dataset containing 553721 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((7.45929 47.45474,7.73965 47.45474,7.73965 47.67194,7.45929 47.67194,7.45929 47.45474))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 553721 records from 305 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0199531-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wuyxck
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Centrolene acanthidiocephalum (Ruiz-Carranza & Lynch, 1989)"
 ]
}

 The dataset includes 62 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025708-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ya2wnf
title: Occurrence Download

description: A dataset containing 385 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Muhlenbergia arenicola Buckley",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 385 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046823-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8kpkv9
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Ectopoglossus atopoglossus (Grant, Humphrey & Myers, 1997)"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025793-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.brszhf
title: Occurrence Download

description: A dataset containing 147231 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2023-11-13",
 "EventDate is less than or equal to 2023-12-13",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 147231 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023524-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qfnksq
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paspalum glabrinode (Hack.) Morrone & Zuloaga",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 14 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046824-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.78bhz6
title: Occurrence Download

description: A dataset containing 3776550 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pelecanidae",
 "Continent is one of (North America, South America)"
 ]
}

 The dataset includes 3776550 records from 276 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061618-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u66ndh
title: Occurrence Download

description: A dataset containing 14204 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Heliodoxa leadbeateri (Bourcier, 1843)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 14204 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025739-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.