cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24139509.v2
title: Supplemental File 9

description: <b>Pre-curation trees. </b>Newick-string tree files containing the initial trees from which were selected robust clades unique to foraminifera (see methods).
DOI: 10.6084/m9.figshare.24139509.v1
title: Supplemental File S9

description: <b>Pre-curation trees. </b>Newick-string tree files containing the initial trees from which were selected robust clades unique to foraminifera (see methods).
DOI: 10.6084/m9.figshare.24139506
title: Supplemental File 8

description: <b>Pre-curation sequences. </b>A fasta file containing the initial set of nucleotide sequences that was filtered through selection of robust clades and other steps (see methods and legend for File S4 above) to produce File S5. These are identified as coding regions and do not contain UTRs.
DOI: 10.6084/m9.figshare.24139506.v1
title: Supplemental File S8

description: <b>Pre-curation sequences. </b>A fasta file containing the initial set of nucleotide sequences that was filtered through selection of robust clades and other steps (see methods and legend for File S4 above) to produce File S5. These are identified as coding regions and do not contain UTRs.
DOI: 10.6084/m9.figshare.24139506.v2
title: Supplemental File 8

description: <b>Pre-curation sequences. </b>A fasta file containing the initial set of nucleotide sequences that was filtered through selection of robust clades and other steps (see methods and legend for File S4 above) to produce File S5. These are identified as coding regions and do not contain UTRs.
DOI: 10.6084/m9.figshare.24139500
title: Supplemental File 7

description: <b>Curated alignments.</b>The final set of amino acid alignments (rebuilt clades) used in constructing trees (File S6) to identify robust sequences.
DOI: 10.6084/m9.figshare.24139500.v1
title: Supplemental File S7

description: <b>Curated alignments.</b>The final set of amino acid alignments (rebuilt clades) used in constructing trees (File S6) to identify robust sequences.
DOI: 10.6084/m9.figshare.24139500.v2
title: Supplemental File 7

description: <b>Curated alignments.</b>The final set of amino acid alignments (rebuilt clades) used in constructing trees (File S6) to identify robust sequences.
DOI: 10.6084/m9.figshare.24139497
title: Supplemental File 6

description: <b>Curated trees. </b>The final set of trees (rebuilt clades) used in identifying robust sequences.
DOI: 10.6084/m9.figshare.24139497.v2
title: Supplemental File 6

description: <b>Curated trees. </b>The final set of trees (rebuilt clades) used in identifying robust sequences.
DOI: 10.6084/m9.figshare.24139497.v1
title: Supplemental File S6

description: <b>Curated trees. </b>The final set of trees (rebuilt clades) used in identifying robust sequences.
DOI: 10.6084/m9.figshare.24139413
title: Supplemental File 5

description: <b>Curated sequences. </b>A fasta file containing the final set of 41,291 nucleotide sequences used in compositional analysis. These are identified as coding regions and do not contain UTRs.
DOI: 10.6084/m9.figshare.24139413.v2
title: Supplemental File 5

description: <b>Curated sequences. </b>A fasta file containing the final set of 41,291 nucleotide sequences used in compositional analysis. These are identified as coding regions and do not contain UTRs.
DOI: 10.6084/m9.figshare.24139413.v1
title: Supplemental File S5

description: <b>Curated sequences. </b>A fasta file containing the final set of 41,291 nucleotide sequences used in compositional analysis. These are identified as coding regions and do not contain UTRs.
DOI: 10.6084/m9.figshare.24139407
title: Supplemental File 4

description: Sequences removed during curation. These sequences are found in the pre-curation sequence and tree data (Supplementary files 8-9) but were removed during curation, as described in the methods section. Under the “reason removed” columns, “Low coverage compositional outlier” indicates sequences with a significantly outlying Malahonobis distance in the GC3S versus ENc distribution and with k-mer coverage &lt;10 or with a more highly covered paralogous sequence in the same clade; “Identical pair with differential coverage” indicates sequences at least 95% identical at the nucleotide level over at least 67% of their length with a sequence from another taxon that is more highly covered, as long as the k-mer coverage of the more lowly covered sequence is below a taxon-dependent threshold as determined by manual inspection of the data (50 for Bolivina and Nonionella, 20 for Hippocrepinella hirudina and Psammophaga fuegia, and 100 for Ammodiscus and sample Mf03 (Milliammina), and other wise 10); “Lowly covered paralog” indicates sequences with a more highly covered paralog in the same clade that covers at least 80% of the alignment length for the clade; “Sister genus and lab of origin” indicates sequences from taxa for which we have more than one sample available directly sister in the rebuilt clade tree to a taxon of a different genus (and not sister to any taxa of the same genus), as long as all the sister samples originate from the same lab as the sequence to be removed.
DOI: 10.6084/m9.figshare.24139407.v1
title: Supplemental File S4

description: Sequences removed during curation. These sequences are found in the pre-curation sequence and tree data (Supplementary files S8-S9) but were removed during curation, as described in the methods section. Under the “reason removed” columns, “Low coverage compositional outlier” indicates sequences with a significantly outlying Malahonobis distance in the GC3S versus ENc distribution and with k-mer coverage &lt;10 or with a more highly covered paralogous sequence in the same clade; “Identical pair with differential coverage” indicates sequences at least 95% identical at the nucleotide level over at least 67% of their length with a sequence from another taxon that is more highly covered, as long as the k-mer coverage of the more lowly covered sequence is below a taxon-dependent threshold as determined by manual inspection of the data (50 for Bolivina and Nonionella, 20 for Hippocrepinella hirudina and Psammophaga fuegia, and 100 for Ammodiscus and sample Mf03 (Milliammina), and other wise 10); “Lowly covered paralog” indicates sequences with a more highly covered paralog in the same clade that covers at least 80% of the alignment length for the clade; “Sister genus and lab of origin” indicates sequences from taxa for which we have more than one sample available directly sister in the rebuilt clade tree to a taxon of a different genus (and not sister to any taxa of the same genus), as long as all the sister samples originate from the same lab as the sequence to be removed.
DOI: 10.6084/m9.figshare.24139407.v2
title: Supplemental File 4

description: Sequences removed during curation. These sequences are found in the pre-curation sequence and tree data (Supplementary files 8-9) but were removed during curation, as described in the methods section. Under the “reason removed” columns, “Low coverage compositional outlier” indicates sequences with a significantly outlying Malahonobis distance in the GC3S versus ENc distribution and with k-mer coverage &lt;10 or with a more highly covered paralogous sequence in the same clade; “Identical pair with differential coverage” indicates sequences at least 95% identical at the nucleotide level over at least 67% of their length with a sequence from another taxon that is more highly covered, as long as the k-mer coverage of the more lowly covered sequence is below a taxon-dependent threshold as determined by manual inspection of the data (50 for Bolivina and Nonionella, 20 for Hippocrepinella hirudina and Psammophaga fuegia, and 100 for Ammodiscus and sample Mf03 (Milliammina), and other wise 10); “Lowly covered paralog” indicates sequences with a more highly covered paralog in the same clade that covers at least 80% of the alignment length for the clade; “Sister genus and lab of origin” indicates sequences from taxa for which we have more than one sample available directly sister in the rebuilt clade tree to a taxon of a different genus (and not sister to any taxa of the same genus), as long as all the sister samples originate from the same lab as the sequence to be removed.
DOI: 10.6084/m9.figshare.24139377
title: Supplemental File 3

description: <b>Composition statistics for each foraminiferan sequence that survived curation. </b>The ‘Raw transcript number’ can be used to correspond sequences to their UTRs, as well as to the pre-curation sequence files and pre- and post-curation trees.
DOI: 10.6084/m9.figshare.24139377.v2
title: Supplemental File 3

description: <b>Composition statistics for each foraminiferan sequence that survived curation. </b>The ‘Raw transcript number’ can be used to correspond sequences to their UTRs, as well as to the pre-curation sequence files and pre- and post-curation trees.
DOI: 10.6084/m9.figshare.24139377.v1
title: Supplemental File S3

description: <b>Composition statistics for each foraminiferan sequence that survived curation. </b>The ‘Raw transcript number’ can be used to correspond sequences to their UTRs, as well as to the pre-curation sequence files and pre- and post-curation trees.
DOI: 10.6084/m9.figshare.24139356
title: Supplemental Files 1-2

description: <b>File 1. Summary composition statistics for each foraminiferan sample.</b> Best-hit rDNAs were identified <i>via</i> BLASTn against the non-redundant databases through NCBI. P-values determined using the Spearman rank correlation test.<b>File 2. Summary composition statistics for non-foraminifera taxa</b>. Data correspond to those presented in Fig 2.
DOI: 10.6084/m9.figshare.24139356.v1
title: Supplemental Files S1-S2

description: <b>Summary composition statistics for each foraminiferan sample.</b> Best-hit rDNAs were identified <i>via</i> BLASTn against the non-redundant databases through NCBI. P-values determined using the Spearman rank correlation test.
DOI: 10.6084/m9.figshare.24139356.v2
title: Supplemental Files 1-2

description: <b>File 1. Summary composition statistics for each foraminiferan sample.</b> Best-hit rDNAs were identified <i>via</i> BLASTn against the non-redundant databases through NCBI. P-values determined using the Spearman rank correlation test.<b>File 2. Summary composition statistics for non-foraminifera taxa</b>. Data correspond to those presented in Fig 2.
DOI: 10.18434/mds2-2951
title: Data Publication: Data from NIST IR "Report on VAMAS Round Robin of ISO 13067: Microbeam Analysis - Electron Backscatter Diffraction - Measurement of Average Grain Size"
DOI: 10.5255/ukda-sn-855998
title: GCRF Centre for Sustainable, Healthy and Learning Cities and Neighbourhoods: Household Survey and Neighbourhood Focus Group Data from Seven Asian and African Countries, 2021-2022

description: In order to bring a thorough and comprehensive understanding of social, economic and environmental sustainability challenges faced by cities and local communities in the developing countries, the SHLC team conducted a major household survey followed by a neighbourhood focus group interview in seven Asian and African countries from late 2021 to early 2022. In each country the study includes two case study cities: one large city and one smaller regional cities. Within each case study cities, neighbourhoods were identified and categorised into five income and wealth bands: the rich, upper middle income, middle income, lower middle and low income neighbourhoods. A household survey was carried out face to face by trained interviewers with a random adult member of the household. The 20 page common questionnaire was designed and adopted by all teams, which cover topics of housing, residence, living conditions, migration, education, health, neighbourhood infrastructure, facilities, governance and relations, income and employments, gender equality and impacts from Covid-19. The sample was distributed in the city to representative the five neighbourhood types. The survey was completed in 13 of the 14 case study cities (fieldwork in Chongqing in China was delayed by the Covid-19 lockdowns and implemented in August 2023). The target sample for each city was 1000; the total sample in the database (SPSS and STATA) include 14245 households. The survey was followed by focus group interviews. A carefully designed and agreed common interview guide was used by all team. The target was to have one focus group for one neighbourhood in each income band in each city. A total of 74 focus group interviews were conducted (Fieldwork in Datong and Chongqing in China was delayed). The transcripts are the qualitative data shared here.
DOI: 10.15151/esrf-es-1330481602
title: IBS BAG

description: The IBS BAG includes in this proposal IBS teams and external groups from CEA-Cadarache (St Paul lez Durance) and IRBA (Brétigny-sur-Orge). We study structure-function relationships of proteins emphasizing in human health, biotechnology and methodology. Most of the projects are a continuation of the MX-2398 proposal and can be grouped into different topics as follows: host-pathogen interaction, new drug targets, fundamental cellular mechanisms, membrane proteins, biotechnological applications and methodology. Some of these projects use integrative approaches (X-ray crystallography, SAXS, NMR (and cryo-EM), together with other biophysical studies) with the aim to fully understand the complexity of the biological macromolecular systems on study.
DOI: 10.5281/zenodo.8255547
title: Archaeological sites in Taiwan during the Neolithic and Metal Age

description: Coordinates marked by asterisks were added in the current study (see Data and methods section for details). Chinese site names are romanised following the Wade-Giles system. Site names in indigenous peoples' languages are given in romanised form followed by the Chinese name in parentheses, if available. Archaeological cultures represented by the respective site are indicated by the value "1".
DOI: 10.5281/zenodo.8255546
title: Archaeological sites in Taiwan during the Neolithic and Metal Age

description: Coordinates marked by asterisks were added in the current study (see Data and methods section for details). Chinese site names are romanised following the Wade-Giles system. Site names in indigenous peoples' languages are given in romanised form followed by the Chinese name in parentheses, if available. Archaeological cultures represented by the respective site are indicated by the value "1".
DOI: 10.6073/pasta/93436a5ebe22529ee014c25e56f5ac11
title: Surface Water Quality Monitoring Data collected in South Florida Coastal Waters (FCE LTER), Florida, USA, June 1989-ongoing

description: The Southeast Environmental Research Center at Florida International University operates a network of 331 fixed sampling sites distributed throughout the estuarine and coastal ecosystems of south Florida. The purpose of this network is to address concerns in regional water quality which cross and overlap separate political boundaries. Funding has come from different sources with individual programs being added as funding became available. Biscayne Bay, Florida Bay, Whitewater Bay, Ten Thousand Islands, Rookery Bay, Estero Bay, and Pine Island Sound are sampled monthly while the Florida Keys National Marine Sanctuary (FKNMS) and the southwest shelf are sampled quarterly. Variables currently being measured include surface and bottom temperature, salinity, dissolved oxygen, nitrate, nitrite, ammonium, total nitrogen, total organic nitrogen, total phosphorus, soluble reactive phosphorus, total organic carbon, total silicate, chlorophyll a, alkaline phosphatase activity, turbidity, and light extinction. The purpose of this network is to address concerns in regional water quality which cross and overlap separate political boundaries. One of the products is a quasi-synoptic big picture of nutrient and phytoplankton biomass distributions over the South Florida Coastal Waters. The SERC network will, in time, provide us with the data necessary to determine whether conditions within the estuaries and sanctuary are improving or declining.
DOI: 10.6084/m9.figshare.24179823
title: BASE DE DATOS_Cta.Adaptativa-SIN DATOS PERDIDOS.xlsx

description: It is a database on the measurement of adaptive behavior for people with intellectual disabilities, applied through caregivers. It comes from the Peruvian jungle and the districts of Lima-Peru. Information on the caregiver and the person with intellectual disabilities is included, and it also includes data from a Quality of Life test.
DOI: 10.6084/m9.figshare.24179823.v2
title: BASE DE DATOS_Cta.Adaptativa-SIN DATOS PERDIDOS.xlsx

description: It is a database on the measurement of adaptive behavior for people with intellectual disabilities, applied through caregivers. It comes from the Peruvian jungle and the districts of Lima-Peru. Information on the caregiver and the person with intellectual disabilities is included, and it also includes data from a Quality of Life test.
DOI: 10.6084/m9.figshare.24179823.v1
title: BASE DE DATOS_Cta.Adaptativa-SIN DATOS PERDIDOS.xlsx

description: It is a database on the measurement of adaptive behavior for people with intellectual disabilities, applied through caregivers. It comes from the Peruvian jungle and the districts of Lima-Peru. Information on the caregiver and the person with intellectual disabilities is included, and it also includes data from a Quality of Life test.
DOI: 10.6084/m9.figshare.24179799
title: Atom Simulations N01-N96 Plus.pdf

description: <i>Scale 3D models (1 trillion to 1) of atoms 1 through 96 with a Periodic </i>Atom<i> Crystal Table (PACT). It clearly </i>identifies<i> the exact position of each electron (element) and the exact bonding points of each atom. It also shows that each element from carbon on has eight bonding points </i>because the last two layers are available for bonding.
DOI: 10.6084/m9.figshare.24179799.v1
title: Atom Simulations N01-N96 Plus.pdf

description: <i>Scale 3D models (1 trillion to 1) of atoms 1 through 96 with a Periodic </i>Atom<i> Crystal Table (PACT). It clearly </i>identifies<i> the exact position of each electron (element) and the exact bonding points of each atom. It also shows that each element from carbon on has eight bonding points </i>because the last two layers are available for bonding.
DOI: 10.25345/c5901zs2j
title: MassIVE MSV000092931 - Motrpac - Endurance Exercise Training Study In 6 Months Old Rats (Protein Ubiquitination In Heart And Liver)
title: This proteomics dataset focuses on the study of changes in protein ubiquitination in the following tissues: liver and heart. The dataset is a subset of an endurance exercise training study that targets young adult (6-month-old) rats. Specifically, male and female Fischer 344 rats (n = 12) were subjected to progressive treadmill endurance exercise training for 1, 2, 4, or 8 weeks, with tissues collected 48 hours after the last exercise bout. Sex-matched sedentary, untrained rats were used as controls. This study contributes to MoTrPAC's broader mission, which is to identify molecular changes occurring due to exercise. The ultimate goal is to understand how physical activity can improve and sustain health across various ages and fitness levels. The program is supported by the NIH Common Fund. For additional information, visit the MoTrPAC Data Hub at https://motrpac-data.org/.
DOI: 10.5281/zenodo.8368693
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Cicely Kate Bertram, http://www.wikidata.org/entity/Q6375370. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q6375370
DOI: 10.5281/zenodo.8368692
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Cicely Kate Bertram, http://www.wikidata.org/entity/Q6375370. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q6375370
DOI: 10.5281/zenodo.8368695
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Daphne Aubertin, http://www.wikidata.org/entity/Q86636785. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q86636785
DOI: 10.21227/w9mp-5w63
title: Aoralscan3 tooth segmentation dataset

description: The Aoralscan3 dataset includes 1573, 244, and 244 videos for the corresponding sets. The uniform size of the images in the dataset is 640 × 480 pixels.  LabelMe software is employed to accurately mark the boundary and classify the region of each tooth in the datasets.  This dataset is usef for orthodontic treatment. which is one of the research direction of artificial intelligence using current images and previous 3D models to estimate the relative position of individual teeth before and after orthodontic treatment. This dataset can also be used for point cloud-based instance segmentation and for varifying the effectiveness and efficiency of the proposed methods.
DOI: 10.6084/m9.figshare.23611818.v2
title: Data for: Evolution of rarity and phylogeny determine above- and belowground biomass in plant-plant interactions

description: <br>Dataset was initially utilized in Senior et al. 2013 (https://doi.org/10.1371/journal.pone.0060088); data from this paper were recategorized through the addition of rarity levels and reanalyzed to address untested hypotheses and provide new results unrelated to Senior et al. 2013. Both datasets provide information regarding the above- and beloground biomass of 25 species of Tasmanian <i>Eucalyptus</i> grown in community mixtures in a common garden varying in phylogenetic relatedness and rarity. The dataset titled “Eucalyptus Community Full” contains the full dataset used in the analyses and the dataset titled “Eucalyptus Community No Monocultures” contains the data for all plant-plant interactions with the omission of monocultures. The full dataset is used to test the hypotheses: 1) Above- and belowground plant biomass is related to the phylogenetic relatedness of interacting species; 2) Above- and belowground plant biomass is related to the rarity level of interacting plant species. The no monoculture dataset is used to perform t-tests on the standardized interaction strengths of species biomass in mixtures to test for non-additive responses in plant-plant interactions.
DOI: 10.5281/zenodo.8368707
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Vladimír Úlehla, http://www.wikidata.org/entity/Q20056772. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q20056772
DOI: 10.5281/zenodo.8368706
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Vladimír Úlehla, http://www.wikidata.org/entity/Q20056772. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q20056772