cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/w4mkdmwvn6.1
title: Recent evolution of the developing human intestine impacts metabolic and barrier functions

description: This is the additional supporting data for the manuscript titled as "Recent evolution of the developing human intestine impacts metabolic and barrier functions". It contains 
1) comprehensive annotation of open chromatin regions detected in developing human or chimp intestine organoids or tissue; 
2) cell type enriched features, including (A) developing human proximal small intestine tissue cell type marker genes and regions, (B) in vitro and transplanted HIO cell type enriched genes and regions, (C) in vitro and transplanted CIO cell type enriched genes and regions, (D) developing mouse epithelial cell type marker genes; 
3) amino acid substitution rate (dN/dS) and epithelial cell type expression specificity (Tau) of epithelial cell class and specific cell type marker genes; 
4) differentially expressed genes (DEG) between species, including (A) human-chimp DEGs of each intestinal epithelial cell type of in vitro or transplanted organoids, (B) human-mouse DEGs of epithelial cell type between developing human and mouse tissues, (C) developing human and mouse tissue DEG along stem-cell-to-enterocyte pseudotime trajectory, (D) human-chimp DEGs based on consensus genome; (E) human-chimp DEGs after stem cell to enterocyte differentiation pseudotime alignment; 
5) collected evolutionary selection signatures for composite annotation of open chromatin regions.
DOI: 10.17632/w4mkdmwvn6.2
title: Recent evolution of the developing human intestine impacts metabolic and barrier functions

description: This is the additional supporting data for the manuscript titled as "Recent evolution of the developing human intestine impacts metabolic and barrier functions". It contains 
1) comprehensive annotation of open chromatin regions detected in developing human or chimp intestine organoids or tissue; 
2) cell type enriched features, including (A) developing human proximal small intestine tissue cell type marker genes and regions, (B) in vitro and transplanted HIO cell type enriched genes and regions, (C) in vitro and transplanted CIO cell type enriched genes and regions, (D) developing mouse epithelial cell type marker genes; 
3) amino acid substitution rate (dN/dS) and epithelial cell type expression specificity (Tau) of epithelial cell class and specific cell type marker genes; 
4) differentially expressed genes (DEG) between species, including (A) human-chimp DEGs of each intestinal epithelial cell type of in vitro or transplanted organoids, (B) human-mouse DEGs of epithelial cell type between developing human and mouse tissues, (C) developing human and mouse tissue DEG along stem-cell-to-enterocyte pseudotime trajectory, (D) human-chimp DEGs based on consensus genome; (E) human-chimp DEGs after stem cell to enterocyte differentiation pseudotime alignment; 
5) collected evolutionary selection signatures for composite annotation of open chromatin regions
6) Seurat objects of scSTARR-seq experiments and the table for the calculation of the normalized CRE activity
7) Seurat objects of human, chimpanzee, mouse data
8) Human, chimpanzee, and mouse stem cell to enterocyte pseudotime (Pt) aligned expression matrix
DOI: 10.17632/w4mkdmwvn6.3
title: Recent evolution of the developing human intestine impacts metabolic and barrier functions

description: This is the additional supporting data for the manuscript titled as "Recent evolution of the developing human intestine impacts metabolic and barrier functions". It contains 
1) comprehensive annotation of open chromatin regions detected in developing human or chimp intestine organoids or tissue; 
2) cell type enriched features, including (A) developing human proximal small intestine tissue cell type marker genes and regions, (B) in vitro and transplanted HIO cell type enriched genes and regions, (C) in vitro and transplanted CIO cell type enriched genes and regions, (D) developing mouse epithelial cell type marker genes; 
3) amino acid substitution rate (dN/dS) and epithelial cell type expression specificity (Tau) of epithelial cell class and specific cell type marker genes; 
4) differentially expressed genes (DEG) between species, including (A) human-chimp DEGs of each intestinal epithelial cell type of in vitro or transplanted organoids, (B) human-mouse DEGs of epithelial cell type between developing human and mouse tissues, (C) developing human and mouse tissue DEG along stem-cell-to-enterocyte pseudotime trajectory, (D) human-chimp DEGs based on consensus genome; (E) human-chimp DEGs after stem cell to enterocyte differentiation pseudotime alignment; 
5) collected evolutionary selection signatures for composite annotation of open chromatin regions
6) Seurat objects of scSTARR-seq experiments and the table for the calculation of the normalized CRE activity
7) Seurat objects of human, chimpanzee, mouse data
8) Human, chimpanzee, and mouse stem cell to enterocyte pseudotime (Pt) aligned expression matrix
DOI: 10.21233/4d87-cc35
title: Moninea testate amoebae surface sample dataset

description: Raw data for the Moninea 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.6qrvez
title: Occurrence Download

description: A dataset containing 33823 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Milvus milvus (Linnaeus, 1758)",
 "Year 2017-2019"
 ]
}

 The dataset includes 33823 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021222-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/q95g-2x92
title: Bruckmisse pollen dataset

description: Raw data for the Bruckmisse 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.6mj3mg
title: Occurrence Download

description: A dataset containing 3848 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Vincetoxicum rossicum (Kleopow) Barbar.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is Canada",
 "Year is one of (1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907, 1908, 1909, 1910, 1911, 1912, 1913, 1914, 1915, 1916, 1917, 1918, 1919, 1920, 1921, 1922, 1923, 1924, 1925, 1926, 1927, 1928, 1929, 1930, 1931, 1932, 1933, 1934, 1935, 1936, 1937, 1938, 1939, 1940, 1941, 1942, 1943, 1944, 1945, 1946, 1947, 1948, 1949, 1950, 1951, 1952, 1953, 1954, 1955, 1956, 1957, 1958, 1959, 1960, 1961, 1962, 1963, 1964, 1965, 1966, 1967, 1968, 1969, 1970, 1971, 1972, 1973, 1974, 1975, 1976, 1977, 1978, 1979, 1980, 1981, 1982, 1983, 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024)"
 ]
}

 The dataset includes 3848 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021223-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/72y0-8t05
title: Awl Site midden pollen dataset

description: Raw data for the Awl Site midden 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: 10.6084/m9.figshare.27909663
title: Raw, normalised, preprocessed and segmented IMC images

description: Output images generated by the automated image processing software SIMPLI (https://github.com/ciccalab/SIMPLI - https://doi.org/10.1038/s41467-022-28470-x).<b>Raw</b>: original images generated by the IMC acquisition. <b>Normalised</b>: raw images individually processed with 99th percentile normalisation by SIMPLI.<b>Preprocesed</b>: normalised images adjusted by threshold and masking by SIMPLI using a pre-defined Cell Profilier pipeline. Images generated in this step are used for the consecutive pixel-based (area_measurements.csv) and cell-based (clustered_cells.csv) analyses.<b>Segmentation</b>: output files from segmentation of the DNA1 channel performed by SIMPLI using StarDist. This step is necessary to identify all areas corresponding to individual nuclei and to proceed with cell-based analyses (clustered_cells.csv).<br>
DOI: 10.15468/dl.4sh8t4
title: Occurrence Download

description: A dataset containing 3848 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Vincetoxicum rossicum (Kleopow) Barbar.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is Canada",
 "Year is one of (1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907, 1908, 1909, 1910, 1911, 1912, 1913, 1914, 1915, 1916, 1917, 1918, 1919, 1920, 1921, 1922, 1923, 1924, 1925, 1926, 1927, 1928, 1929, 1930, 1931, 1932, 1933, 1934, 1935, 1936, 1937, 1938, 1939, 1940, 1941, 1942, 1943, 1944, 1945, 1946, 1947, 1948, 1949, 1950, 1951, 1952, 1953, 1954, 1955, 1956, 1957, 1958, 1959, 1960, 1961, 1962, 1963, 1964, 1965, 1966, 1967, 1968, 1969, 1970, 1971, 1972, 1973, 1974, 1975, 1976, 1977, 1978, 1979, 1980, 1981, 1982, 1983, 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024)"
 ]
}

 The dataset includes 3848 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021224-250426092105405/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.27901113
title: SIMPLI output files

description: Output files generated by the automated image processing software SIMPLI (https://github.com/ciccalab/SIMPLI - https://doi.org/10.1038/s41467-022-28470-x).<b>area_measurements: </b>quantification of total pixel area in the ROI positive for each marker used. These quantification was used to determine the total deposition of amyloid-b and pTau (Fig. S4.B-I), as well as synapses markers (NTNG2 and Synaprophysin; Fig. S3.A) and myelin (PLP1; Fig. S6.E).<b>clustered_cells: </b>list of all nuclei segmented in all ROIs (rows). Mean signal instensity per marker analysed is indicated in the "Intensity_MeanIntensity_" columns. This quantification was used for nuclei clustering by Seurat integrated in SIMPLI (cluster # to which each cell was assiged is indicated in the "res_0.9_ids" column, which indicate the clustering resolution; Fig. S2.A). X and Y location of segmented nuclei in the ROI is also indicated in the "Location_Center_X" and "Location_Center_Y" columns, which was used to determine nuclei distribution in each cortical layer (Fig. 2.D; Fig. 3. B,D,F; Fig. S6.H). The quantification of mean signal instensity in the "Intensity_MeanIntensity_Ab" and "Intensity_MeanIntensity_pTau" columns was used to quantify intracellular signal for amyloid-b and pTau respectively (Fig. 4).<b>all_cells-clusters: </b>same as clustered_cells.csv file but with the correct format to be used for spatial interactions analyses using the imcRtools package built by the Bodenmiller group. Spatial interactions were quantified between neuronal and glial populations (Fig. 5.e and Fig. S6.f,g).<br><br>
DOI: 10.21233/gf2d-1y68
title: LDDsite3082 water chemistry dataset

description: Raw data for the LDDsite3082 water chemistry 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/n1eq-wj23
title: Runway Ruin pollen dataset

description: Raw data for the Runway Ruin 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.fj6uw9
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cheirochela Hope, 1841"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021225-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/0x7r-w944
title: Falling Water Falls [3PP40] vertebrate fauna dataset

description: Raw data for the Falling Water Falls [3PP40] 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: 10.21233/62nr-me38
title: LDDsite1484 ostracode surface sample dataset

description: Raw data for the LDDsite1484 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/kv9d-px78
title: Lough Keeran pollen surface sample dataset

description: Raw data for the Lough Keeran 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: 10.21233/6c4z-gq06
title: Lake12 pollen surface sample dataset

description: Raw data for the Lake12 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/b7rq-2908
title: Don Brickyard Interglacial Section insect dataset

description: Raw data for the Don Brickyard Interglacial Section insect 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: 10.21233/2vyw-2h54
title: Alter Rachelsee pollen dataset

description: Raw data for the Alter Rachelsee 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: 10.21233/4277-dc83
title: Bay of Quinte/Wallbridge Point ostracode surface sample dataset

description: Raw data for the Bay of Quinte/Wallbridge Point 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: 10.21233/8jzw-7e29
title: Jinbei testate amoebae surface sample dataset

description: Raw data for the Jinbei 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/mzmz-zt36
title: French Creek water chemistry dataset

description: Raw data for the French Creek water chemistry 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/mf7s-6841
title: Kreighle Lake diatom dataset

description: Raw data for the Kreighle Lake 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/y9x2-wn62
title: Welsh Lake diatom surface sample dataset

description: Raw data for the Welsh Lake 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: 10.23668/psycharchives.16347
title: Interactive Technologies in Education

description: The research investigates the impact of interactive learning technologies on development of moral reasoning in higher education students.
DOI: 10.21233/bze7-fc80
title: Blackhawk Lake water chemistry dataset

description: Raw data for the Blackhawk Lake water chemistry 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: 10.21233/5twb-qz96
title: Burns Bog testate amoebae surface sample dataset

description: Raw data for the Burns Bog 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: 10.5517/ccdc.csd.cc2jt2hy
title: CCDC 2347800: Experimental Crystal Structure Determination

description: Related Article: Wenxuan Li, Jianjia He, Yilan Zhang, Le Ye, Guoying Yao, Zixuan Zhang, Shiang Li, Xinhui Lu, Haipeng Lu, Tao Zeng, Zhenyu Yang|2025|Cell Reports Physical Science|6|102509|doi:10.1016/j.xcrp.2025.102509
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lphph
title: CCDC 2403947: Experimental Crystal Structure Determination

description: Related Article: Enrique Aguilar-Ramírez, José Rivera-Chávez, Mario Yair Miranda-Rosas, Diego Martínez-Otero|2025|Org.Biomol.Chem.|23|4525|doi:10.1039/D5OB00115C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.21233/ysd5-0011
title: Pammel Creek [47LC61] macroinvertebrate dataset

description: Raw data for the Pammel Creek [47LC61] macroinvertebrate 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: 10.5517/ccdc.csd.cc2mhx57
title: CCDC 2428359: Experimental Crystal Structure Determination

description: Related Article: Lisa Zimmermann, Michael A. Land, Christoph Riesinger, Charles L. B. Macdonald, Manfred Scheer|2025|Chem.Commun.|61|6973|doi:10.1039/D5CC01162K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mhx68
title: CCDC 2428360: Experimental Crystal Structure Determination

description: Related Article: Lisa Zimmermann, Michael A. Land, Christoph Riesinger, Charles L. B. Macdonald, Manfred Scheer|2025|Chem.Commun.|61|6973|doi:10.1039/D5CC01162K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mhx79
title: CCDC 2428361: Experimental Crystal Structure Determination

description: Related Article: Lisa Zimmermann, Michael A. Land, Christoph Riesinger, Charles L. B. Macdonald, Manfred Scheer|2025|Chem.Commun.|61|6973|doi:10.1039/D5CC01162K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mhx8b
title: CCDC 2428362: Experimental Crystal Structure Determination

description: Related Article: Lisa Zimmermann, Michael A. Land, Christoph Riesinger, Charles L. B. Macdonald, Manfred Scheer|2025|Chem.Commun.|61|6973|doi:10.1039/D5CC01162K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.