cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10373031
title: Intermediate data for TE calculation

description: This dataset includes intermediate data from RiboBase that generates translation efficiency (TE). The code to generate the files can be found at https://github.com/CenikLab/TE_model.

We uploaded demo HeLa .ribo files, but due to the large storage requirements of the full dataset, I recommend contacting Dr. Can Cenik directly to request access to the complete version of RiboBase if you need the original data.

The detailed explanation for each file:

human_flatten_ribo_clr.rda: ribosome profiling clr normalized data with GEO GSM ids in columns and genes in rows in human.

human_flatten_rna_clr.rda: matched RNA-seq clr normalized data with GEO GSM ids in columns and genes in rows in human.

human_flatten_te_clr.rda: TE clr data with GEO GSM ids in columns and genes in rows in human.

human_TE_cellline_all_plain.csv: TE clr data with genes in rows and cell lines in rows in human.

human_RNA_rho_new.rda: matched RNA-seq proportional similarity data as genes by genes matrix in human.

human_TE_rho.rda: TE proportional similarity data as genes by genes matrix in human.

mouse_flatten_ribo_clr.rda: ribosome profiling clr normalized data with GEO GSM ids in columns and genes in rows in mouse.

mouse_flatten_rna_clr.rda: matched RNA-seq clr normalized data with GEO GSM ids in columns and genes in rows in mouse.

mouse_flatten_te_clr.rda: TE clr data with GEO GSM ids in columns and genes in rows in mouse.

mouse_TE_cellline_all_plain.csv: TE clr data with genes in rows and cell lines in rows in mouse.

mouse_RNA_rho_new.rda: matched RNA-seq proportional similarity data as genes by genes matrix in mouse.

mouse_TE_rho.rda: TE proportional similarity data as genes by genes matrix in mouse.

All the data was passed quality control. There are 1054 mouse samples and 835 mouse samples: * coverage > 0.1 X * CDS percentage > 70% * R2 between RNA and RIBO >= 0.188 (remove outliers)

All ribosome profiling data here is non-dedup winsorizing data paired with RNA-seq dedup data without winsorizing (even though it names as flatten, it just the same format of the naming)

####codeIf you need to read rda data please use load("rdaname.rda") with R

If you need to calculate proportional similarity from clr data:library(propr)human_TE_homo_rho <- propr:::lr2rho(as.matrix(clr_data))rownames(human_TE_homo_rho) <- colnames(human_TE_homo_rho) <- rownames(clr_data)
DOI: 10.5281/zenodo.10373032
title: Intermediate data for TE calculation

description: This dataset includes intermediate data from RiboBase that generates translation efficiency (TE). The code to generate the files can be found at https://github.com/CenikLab/TE_model.

We uploaded demo HeLa .ribo files, but due to the large storage requirements of the full dataset, I recommend contacting Dr. Can Cenik directly to request access to the complete version of RiboBase if you need the original data.

The detailed explanation for each file:

human_flatten_ribo_clr.rda: ribosome profiling clr normalized data with GEO GSM ids in columns and genes in rows in human.

human_flatten_rna_clr.rda: matched RNA-seq clr normalized data with GEO GSM ids in columns and genes in rows in human.

human_flatten_te_clr.rda: TE clr data with GEO GSM ids in columns and genes in rows in human.

human_TE_cellline_all_plain.csv: TE clr data with genes in rows and cell lines in rows in human.

human_RNA_rho_new.rda: matched RNA-seq proportional similarity data as genes by genes matrix in human.

human_TE_rho.rda: TE proportional similarity data as genes by genes matrix in human.

mouse_flatten_ribo_clr.rda: ribosome profiling clr normalized data with GEO GSM ids in columns and genes in rows in mouse.

mouse_flatten_rna_clr.rda: matched RNA-seq clr normalized data with GEO GSM ids in columns and genes in rows in mouse.

mouse_flatten_te_clr.rda: TE clr data with GEO GSM ids in columns and genes in rows in mouse.

mouse_TE_cellline_all_plain.csv: TE clr data with genes in rows and cell lines in rows in mouse.

mouse_RNA_rho_new.rda: matched RNA-seq proportional similarity data as genes by genes matrix in mouse.

mouse_TE_rho.rda: TE proportional similarity data as genes by genes matrix in mouse.

All the data was passed quality control. There are 1054 mouse samples and 835 mouse samples: * coverage > 0.1 X * CDS percentage > 70% * R2 between RNA and RIBO >= 0.188 (remove outliers)

All ribosome profiling data here is non-dedup winsorizing data paired with RNA-seq dedup data without winsorizing (even though it names as flatten, it just the same format of the naming)

####codeIf you need to read rda data please use load("rdaname.rda") with R

If you need to calculate proportional similarity from clr data:library(propr)human_TE_homo_rho <- propr:::lr2rho(as.matrix(clr_data))rownames(human_TE_homo_rho) <- colnames(human_TE_homo_rho) <- rownames(clr_data)
DOI: 10.21233/ev57-kf67
title: Trout L. (Ed.) diatom dataset

description: Raw data for the Trout L. (Ed.) diatom dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/hjq1-e776
title: Manic testate amoebae surface sample dataset

description: Raw data for the Manic testate amoebae surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/j97k-ds95
title: Lake Voulkaria pollen dataset

description: Raw data for the Lake Voulkaria pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.v2gw36
title: Occurrence Download

description: A dataset listing the 2819 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "TaxonKey is one of (Rhodophyta, Chlorophyta, Phaeophyceae)"
 ]
}

 The dataset's 2819 records were derived from 166 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023620-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/ya5f-n675
title: Bancos Village [LA 4380] vertebrate fauna dataset

description: Raw data for the Bancos Village [LA 4380] vertebrate fauna dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/92b2-mt37
title: Cheng et al. 2020 Site 133 pollen surface sample dataset

description: Raw data for the Cheng et al. 2020 Site 133 pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/n578-0d50
title: Qizimeishan testate amoebae surface sample dataset

description: Raw data for the Qizimeishan testate amoebae surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.zer6qc
title: Occurrence Download

description: A dataset containing 215 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Armenia, Georgia, Azerbaijan)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Psittaciformes",
 "Year 2005-2025"
 ]
}

 The dataset includes 215 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023625-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/6zqg-nx03
title: Agar Refuge N. Farm ostracode surface sample dataset

description: Raw data for the Agar Refuge N. Farm ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/vty1-9f50
title: Pickeral River ostracode surface sample dataset

description: Raw data for the Pickeral River ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/vrhv-en09
title: Čejčské jezero pollen dataset

description: Raw data for the Čejčské jezero pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/ajgx-q485
title: Bailey's Hot Spring ostracode surface sample dataset

description: Raw data for the Bailey's Hot Spring ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.57982/vemk-7927
title: ATN 143: Comparison of Men's Prevention Apps to Research Efficacy

description: COMPARE was part of the iTech NIH U19, which had an overall goal to develop innovative technology-focused interventions addressing the HIV prevention and care continuum for youth. In years 1-2 of the grant, the investigators optimized and pilot tested using a similar study design and identical study outcomes, two distinct mobile apps called LYNX and MyChoices. Each app was designed to increase HIV testing and PrEP uptake among YMSM. In this study, the individual apps were tested in a follow-on research study and evaluated for efficacy. YMSM were randomized to receive either MyChoices, LYNX, or SOC. It included three major functions that were designed to promote self-efficacy, self-regulation, goal-setting and environmental influences to impact behavior change. Compared to standard of care (59%), participants randomized to MyChoices (74%; p=.010) were more likely to have received at least one HIV test over 6 months of follow up; those randomized to LYNX also had higher proportion of testing (70%) but it was marginally statistically different (p=.078). While participants in both MyChoices (21%) and LYNX (20%) arms had higher rates of starting PrEP compared to SOC (16%), these differences were not significant (p=.516). Given the ubiquity of mobile app use and modest resources required to scale this intervention, a 25% relative increase in HIV testing among YSMM, as seen in this study, could facilitate curtailment of the epidemic in the U.S. and even globally.
DOI: 10.21233/mzmm-hp70
title: Roma testate amoebae surface sample dataset

description: Raw data for the Roma testate amoebae surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/q8qx-e336
title: PRCO7 pollen surface sample dataset

description: Raw data for the PRCO7 pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.n5tcvt
title: Occurrence Download

description: A dataset containing 69437 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thelypteris palustris Schott",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2010",
 "HasCoordinate is true"
 ]
}

 The dataset includes 69437 records from 464 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023615-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/pwvx-9569
title: Lac Long diatom surface sample dataset

description: Raw data for the Lac Long diatom surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/rrdf-7s51
title: Kesaji River ostracode surface sample dataset

description: Raw data for the Kesaji River ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.5281/zenodo.15375662
title: TABLE 1. Sampling stations during the 31 in Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records

description: TABLE 1. Sampling stations during the 31 st Soviet Antarctic expedition in 1986/87 where molluscs were found.
StationAreaSouthWestDepth (m)Date1Fildes Strait62.233259.00125018 January 19862Fildes Strait62.233258.99857031 January 19863Ardley Cove62.202558.918710028 February 19864Krestianka Point62.198258.95040.58 times from 12/1986 to 03/19875Ardley Cove62.201658.94861506 January 19876Ardley Cove62.201958.916710006 January 19877Ardley Cove62.200058.94725009 January 19878Ardley Cove62.203258.94103513 January 19879Lapidary Point62.196958.93570.53 times from 1/1987 to 2/198710Ardley Cove62.201958.9393602 times from 1/1986 to 2/198711Ardley Cove62.203258.93954007 February 198712Ardley Cove62.204558.94361509 February 198713Ardley Cove62.203258.93975001 March 198714Ardley Cove62.203258.93277001 March 198715Ardley Cove62.204158.92959007 March 1987
description: Published as part of Zettler, Michael L. & Bick, Andreas, 2025, Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records, pp. 403 in Zootaxa 5631 (3) on page 403, DOI: 10.11646/zootaxa.5631.3.1, http://zenodo.org/record/15370912
DOI: 10.5281/zenodo.15375663
title: TABLE 1. Sampling stations during the 31 in Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records

description: TABLE 1. Sampling stations during the 31 st Soviet Antarctic expedition in 1986/87 where molluscs were found.
StationAreaSouthWestDepth (m)Date1Fildes Strait62.233259.00125018 January 19862Fildes Strait62.233258.99857031 January 19863Ardley Cove62.202558.918710028 February 19864Krestianka Point62.198258.95040.58 times from 12/1986 to 03/19875Ardley Cove62.201658.94861506 January 19876Ardley Cove62.201958.916710006 January 19877Ardley Cove62.200058.94725009 January 19878Ardley Cove62.203258.94103513 January 19879Lapidary Point62.196958.93570.53 times from 1/1987 to 2/198710Ardley Cove62.201958.9393602 times from 1/1986 to 2/198711Ardley Cove62.203258.93954007 February 198712Ardley Cove62.204558.94361509 February 198713Ardley Cove62.203258.93975001 March 198714Ardley Cove62.203258.93277001 March 198715Ardley Cove62.204158.92959007 March 1987
description: Published as part of Zettler, Michael L. & Bick, Andreas, 2025, Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records, pp. 403 in Zootaxa 5631 (3) on page 403, DOI: 10.11646/zootaxa.5631.3.1, http://zenodo.org/record/15370912
DOI: 10.5281/zenodo.15375664
title: TABLE 2 in Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records

description: TABLE 2. Species abundance sorted according to their frequency per depth. Species marked with an asterisk (*) are first records for King George Island.
Species0.5m15m35m40m50m60m70m90m100mLaevilitorina umbilicata Pfeffer, 18865641Kidderia subquadrata (Pelseneer, 1903)236Laevilitorina caliginosa (A. Gould, 1849)54
description: Published as part of Zettler, Michael L. & Bick, Andreas, 2025, Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records, pp. 404 in Zootaxa 5631 (3) on page 404, DOI: 10.11646/zootaxa.5631.3.1, http://zenodo.org/record/15370912
DOI: 10.5281/zenodo.15375665
title: TABLE 2 in Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records

description: TABLE 2. Species abundance sorted according to their frequency per depth. Species marked with an asterisk (*) are first records for King George Island.
Species0.5m15m35m40m50m60m70m90m100mLaevilitorina umbilicata Pfeffer, 18865641Kidderia subquadrata (Pelseneer, 1903)236Laevilitorina caliginosa (A. Gould, 1849)54
description: Published as part of Zettler, Michael L. & Bick, Andreas, 2025, Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records, pp. 404 in Zootaxa 5631 (3) on page 404, DOI: 10.11646/zootaxa.5631.3.1, http://zenodo.org/record/15370912
DOI: 10.5281/zenodo.15375668
title: TABLE 3 in Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records

description: TABLE 3. Additional species, not found by us, which were discovered by Rauschert during the 26 th and 30 th Soviet Antarctic expedition in Maxwell Bay and published by Engl (2012) or are kept in the Zoological Museum Hamburg (ZMH).
TaxonClassEngl (2012ZMHAmauropsis rossiana E. A. Smith, 1907GastropodaxxAustrodoris kerguelenensis (Bergh, 1884)GastropodaxCerithiella astrolabiensis (Strebel, 1908)Gastropodax (30 m)Chitonina Thiele, 1909PolyplacophoraxChlanidota signeyana A. W. B. Powell, 1951GastropodaxCurnon granulosa (Vayssière, 1906)GastropodaxDiaphana paessleri (Strebel, 1905)GastropodaxEatoniella cana Ponder, 1983Gastropodax (10 m)xFalsimohnia innocens (E. A. Smith, 1907)GastropodaxxHarpovoluta charcoti (E. Lamy, 1910)GastropodaxLaevilacunaria bennetti (Preston, 1916)GastropodaxxLaevilitorina antarctica (E. A. Smith, 1902)GastropodaxLaevilitorina wandelensis (E. Lamy, 1906)GastropodaxxLeptochiton kerguelensis Haddon, 1886PolyplacophoraxLissotesta strebeli (Thiele, 1912)GastropodaxMicrodiscula vanhoeffeni Thiele, 1912GastropodaxMunditia meridionalis (Melvill & Standen, 1912)Gastropodax (5 m)xNeobuccinum eatoni (E. A. Smith, 1875)GastropodaxOmalogyra antarctica Egorova, 1991Gastropodax (15-20 m)xOnoba grisea (E. von Martens, 1885)GastropodaxxPellilitorina setosa (E. A. Smith, 1875)GastropodaxxPickenia signyensis Ponder, 1983Gastropodax (5-10 m)xProsipho astrolabiensis (Strebel, 1908)GastropodaxxProsipho enricoi Engl, 2004Gastropodax (type) (15-50 m)xProsipho harrietae Engl & Schwabe, 2003Gastropodax (type) (30 m)xPuncturella spirigera Thiele, 1912GastropodaxRissoella powelli Ponder, 1983Gastropodax (10-30 m)xScissurella petermannensis E. Lamy, 1910Gastropodax (3 m)xToledonia globosa Hedley, 1916GastropodaxTrilirata macmurdensis (Hedley, 1911)GastropodaxVolvarina hyalina (Thiele, 1912)Gastropodax
description: Published as part of Zettler, Michael L. & Bick, Andreas, 2025, Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records, pp. 444 in Zootaxa 5631 (3) on page 444, DOI: 10.11646/zootaxa.5631.3.1, http://zenodo.org/record/15370912
DOI: 10.5281/zenodo.15375669
title: TABLE 3 in Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records

description: TABLE 3. Additional species, not found by us, which were discovered by Rauschert during the 26 th and 30 th Soviet Antarctic expedition in Maxwell Bay and published by Engl (2012) or are kept in the Zoological Museum Hamburg (ZMH).
TaxonClassEngl (2012ZMHAmauropsis rossiana E. A. Smith, 1907GastropodaxxAustrodoris kerguelenensis (Bergh, 1884)GastropodaxCerithiella astrolabiensis (Strebel, 1908)Gastropodax (30 m)Chitonina Thiele, 1909PolyplacophoraxChlanidota signeyana A. W. B. Powell, 1951GastropodaxCurnon granulosa (Vayssière, 1906)GastropodaxDiaphana paessleri (Strebel, 1905)GastropodaxEatoniella cana Ponder, 1983Gastropodax (10 m)xFalsimohnia innocens (E. A. Smith, 1907)GastropodaxxHarpovoluta charcoti (E. Lamy, 1910)GastropodaxLaevilacunaria bennetti (Preston, 1916)GastropodaxxLaevilitorina antarctica (E. A. Smith, 1902)GastropodaxLaevilitorina wandelensis (E. Lamy, 1906)GastropodaxxLeptochiton kerguelensis Haddon, 1886PolyplacophoraxLissotesta strebeli (Thiele, 1912)GastropodaxMicrodiscula vanhoeffeni Thiele, 1912GastropodaxMunditia meridionalis (Melvill & Standen, 1912)Gastropodax (5 m)xNeobuccinum eatoni (E. A. Smith, 1875)GastropodaxOmalogyra antarctica Egorova, 1991Gastropodax (15-20 m)xOnoba grisea (E. von Martens, 1885)GastropodaxxPellilitorina setosa (E. A. Smith, 1875)GastropodaxxPickenia signyensis Ponder, 1983Gastropodax (5-10 m)xProsipho astrolabiensis (Strebel, 1908)GastropodaxxProsipho enricoi Engl, 2004Gastropodax (type) (15-50 m)xProsipho harrietae Engl & Schwabe, 2003Gastropodax (type) (30 m)xPuncturella spirigera Thiele, 1912GastropodaxRissoella powelli Ponder, 1983Gastropodax (10-30 m)xScissurella petermannensis E. Lamy, 1910Gastropodax (3 m)xToledonia globosa Hedley, 1916GastropodaxTrilirata macmurdensis (Hedley, 1911)GastropodaxVolvarina hyalina (Thiele, 1912)Gastropodax
description: Published as part of Zettler, Michael L. & Bick, Andreas, 2025, Molluscs from a shallow bay of King George Island (Antarctica, South Shetland Islands): An annotated checklist with new distributional records, pp. 444 in Zootaxa 5631 (3) on page 444, DOI: 10.11646/zootaxa.5631.3.1, http://zenodo.org/record/15370912
DOI: 10.21233/d6fj-wh73
title: Trout Peatland I testate amoebae surface sample dataset

description: Raw data for the Trout Peatland I testate amoebae surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.