cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22664896.v2
title: Elements and dust input data from Hulugou peat in the northeastern Qinghai-Tibetan Plateau.xlsx

description: The resluts of elements was scanned by X-Ray Fluorescence (XRF) using the Geotek Multi-Sensor Core Loggers (MSCL) XRF core scanner. The grain size distributions of peat samples were determined by a laser-optical particle size analyzer Malvern Mastersizer-2000 and analyzed by parameterization End-member Modelling Analysis (EMA). We stacked a curve with EM1 and Ti components for the reconstructed dust input.
DOI: 10.35078/p6rj5h
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Varginha | Município: Oliveira

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es)
DOI: 10.5281/zenodo.7509384
title: To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design

description: This repository contains Materials and designed UCE probe sets for the manuscript entitled "To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design".
DOI: 10.5281/zenodo.7509385
title: To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design

description: This repository contains Supplementary Materials and designed UCE probe sets for the manuscript entitled "To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design".
DOI: 10.5281/zenodo.7926017
title: To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design

description: This repository contains Materials and designed UCE probe sets for the manuscript entitled "To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design".
DOI: 10.35078/7ynb0j
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Montes Claros | Município: Rubelita

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es)
DOI: 10.6084/m9.figshare.22806140
title: PAMpolinizadores.zip

description: A presence-absence matrix of 1,135 species of bees, hummingbirds, sphinx moths and bats for Mexico. On a 165,078 cells of 5' of degree. It is a zipped large CSV binary matrix, with two added columns of the longitude and latitude of the centroid of each one of the cells in the matrix.
DOI: 10.15784/601686
title: Post-molt emperor penguin foraging ecology

description: This dataset includes an inventory of emperor penguins captured after their molt in February 2023. Observations recorded include capture date, instrumentation, body mass, flipper length, and samples collected.
DOI: 10.15784/601688
title: Late chick-rearing foraging ecology of emperor penguins from the Cape Crozier colony

description: This dataset includes an inventory of emperor penguins captured during late chick rearing at the Cape Crozier colony in November 2022. Observations recorded include capture date, instrumentation, body mass, flipper length, and samples collected.
DOI: 10.13012/b2idb-3731847_v1
title: XSEDE: Allocations Awards and Usage for the NSF Cyberfrastructure Portfolio, 2004-2022

description: The XSEDE program manages the database of allocation awards for the portfolio of advanced research computing resources funded by the National Science Foundation (NSF). The database holds data for allocation awards dating to the start of the TeraGrid program in 2004 through the XSEDE operational period, which ended August 31, 2022. The project data include lead researcher and affiliation, title and abstract, field of science, and the start and end dates. Along with the project information, the data set includes resource allocation and usage data for each award associated with the project. The data show the transition of resources over a fifteen year span along with the evolution of researchers, fields of science, and institutional representation. Because the XSEDE program has ended, the allocation_award_history file includes all allocations activity initiated via XSEDE processes through August 31, 2022. The Resource Providers and successor program to XSEDE agreed to honor all project allocations made during XSEDE. Thus, allocation awards that extend beyond the end of XSEDE may not reflect all activity that may ultimately be part of the project award. Similarly, allocation usage data only reflects usage reported through August 31, 2022, and may not reflect all activity that may ultimately be conducted by projects that were active beyond XSEDE.
DOI: 10.5517/ccdc.csd.cc2dj302
title: CCDC 2220003: Experimental Crystal Structure Determination

description: Related Article: Samantha L. Piper, Craig M. Forsyth, Mega Kar, Callum Gassner, R. Vijayaraghavan, S. Mahadevan, Karolina Matuszek, Jennifer M. Pringle, Douglas R. MacFarlane|2023|RSC Sustainability|1|470|doi:10.1039/D2SU00111J
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.cc2dj313
title: CCDC 2220004: Experimental Crystal Structure Determination

description: Related Article: Samantha L. Piper, Craig M. Forsyth, Mega Kar, Callum Gassner, R. Vijayaraghavan, S. Mahadevan, Karolina Matuszek, Jennifer M. Pringle, Douglas R. MacFarlane|2023|RSC Sustainability|1|470|doi:10.1039/D2SU00111J
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.cc2fcvvj
title: CCDC 2245728: Experimental Crystal Structure Determination

description: Related Article: Indranil Halder, Akshay M. Nair, Chandra M. R. Volla|2023|Chem.Commun.|59|5862|doi:10.1039/D3CC01088K
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.cc2fk1wy
title: CCDC 2250720: Experimental Crystal Structure Determination

description: Related Article: Indranil Halder, Akshay M. Nair, Chandra M. R. Volla|2023|Chem.Commun.|59|5862|doi:10.1039/D3CC01088K
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: 10.35078/g2ovsw
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Montes Claros | Município: São João da Ponte

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es)
DOI: 10.6069/dhn4-vq23
title: PRM quantification of MCS proteins and viral proteins in HCMV virus microenvironment

description: The control of host processes which influence cell-cell communication is central to determining the outcome of a virus infection in tissue. Despite this, it remains unclear how cells either in close or distant proximity to an infected cell differentially respond to the primary infection. We established a virus infection microenvironment to resolve molecular features and functional consequences of cell spatial address within this localized niche by proteomic analyses, and identified differential regulations of membrane contact site (MCS) proteins in different cell populations. Here, we conducted targeted mass spectrometry (PRM) analyses for all MCS proteins representing every major organelle-organelle association, and identified elevation of MCS proteins in infected and neighboring cells. To check the contribution of extracellular vesicle (EV) dependent mechanism to the viral proteins detected in the neighboring cells, HCMV protein PRM analyses were conducted with or without EV inhibitors, GW4869 or manumycin A (MA), showing that EVs contribute to the viral protein levels in neighboring population.
DOI: 10.35078/mw1bi3
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Montes Claros | Município: Coração de Jesus

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es)
DOI: 10.15468/dl.3h8q25
title: Occurrence Download

description: A dataset containing 3585 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Kyllinga brevifolia"
 ]
}

 The dataset includes 3585 records from 175 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014862-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.43h3h4
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scandix pecten-veneris",
 "Country is Belarus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014864-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15115243
title: Human datasets and computational analysis: Prdm16_pos antigen-presenting cells

description: Prdm16-dependent antigen-presenting cells induce tolerance to gut antigens

This repository contains all code and computational analysis for the human datasets associated with the above paper. Items are organized as follows:



2024-03-13/ contains human lymph node raw sequencing data (our primary data).

Human_Node_Analysis/ contains all code in R to process finalized datasets, ultimately generating Figures 5b-c, and ExtData Fig 10a.

OUTPUT/ contains final RDS files as output by each workflow, to use as input for each Analysis script. A reader may choose to skip the majority of the above workflow, and only download these files to immediately generate the Figures and/or further explore the data.


In general, a reader can follow the A_import scripts to create initial Seurat objects, B_integrate scripts to integrate separate sequencing runs, C_annotate scripts to assign finalized cell types, and D_analysis scripts to generate all plots. Each workflow ostensibly only requires establishing certain library dependencies, as well as filepaths for INPUT and OUTPUT directories.

Please note, several of the Integration scripts are particularly computationally intensive.  These were successfully run by allocating 512 Gb of memory within our university’s supercomputing environment.

As emphasized within code annotations, this entire workflow is run with R 4.3.2 and Seurat 5.1.0— our computation makes use of that FindClusters implementation, a shared nearest neighbor modularity optimization based clustering algorithm (Seurat 5.2 is not compatible). We specify the Leiden algorithm at these steps, which differs from the default Louvain algorithm, which offers certain computational advantages (see PMID 30914743). While results with Louvain would likely reach the same biological conclusions, the final clusters and annotations we provide here are only useful with Leiden implementation. Finally, we are grateful to our institution’s supercomputer admins, who helped establish a virtual environment with R-Reticulate, which allows for calling the Leiden algorithm (implemented in Python). Readers will similarly need to establish this dependency based on their local environment.
DOI: 10.5281/zenodo.15115244
title: Human datasets and computational analysis: Prdm16_pos antigen-presenting cells

description: Prdm16-dependent antigen-presenting cells induce tolerance to gut antigens

This repository contains all code and computational analysis for the human datasets associated with the above paper. Items are organized as follows:



2024-03-13/ contains human lymph node raw sequencing data (our primary data).


In general, a reader can follow the A_import scripts to create initial Seurat objects, B_integrate scripts to integrate separate sequencing runs, C_annotate scripts to assign finalized cell types, and D_analysis scripts to generate all plots. Each workflow ostensibly only requires establishing certain library dependencies, as well as filepaths for INPUT and OUTPUT directories.

Please note, several of the Integration scripts are particularly computationally intensive.  These were successfully run by allocating 512 Gb of memory within our university’s supercomputing environment.

As emphasized within code annotations, this entire workflow is run with R 4.3.2 and Seurat 5.1.0— our computation makes use of that FindClusters implementation, a shared nearest neighbor modularity optimization based clustering algorithm (Seurat 5.2 is not compatible). We specify the Leiden algorithm at these steps, which differs from the default Louvain algorithm, which offers certain computational advantages (see PMID 30914743). While results with Louvain would likely reach the same biological conclusions, the final clusters and annotations we provide here are only useful with Leiden implementation. Finally, we are grateful to our institution’s supercomputer admins, who helped establish a virtual environment with R-Reticulate, which allows for calling the Leiden algorithm (implemented in Python). Readers will similarly need to establish this dependency based on their local environment.
DOI: 10.5281/zenodo.15211473
title: Human datasets and computational analysis: Prdm16_pos antigen-presenting cells

description: Prdm16-dependent antigen-presenting cells induce tolerance to gut antigens

This repository contains all code and computational analysis for the human datasets associated with the above paper. Items are organized as follows:



2024-03-13/ contains human lymph node raw sequencing data (our primary data).

Human_Node_Analysis/ contains all code in R to process finalized datasets, ultimately generating Figures 5b-c, and ExtData Fig 10a.

OUTPUT/ contains final RDS files as output by each workflow, to use as input for each Analysis script. A reader may choose to skip the majority of the above workflow, and only download these files to immediately generate the Figures and/or further explore the data.


In general, a reader can follow the A_import scripts to create initial Seurat objects, B_integrate scripts to integrate separate sequencing runs, C_annotate scripts to assign finalized cell types, and D_analysis scripts to generate all plots. Each workflow ostensibly only requires establishing certain library dependencies, as well as filepaths for INPUT and OUTPUT directories.

Please note, several of the Integration scripts are particularly computationally intensive.  These were successfully run by allocating 512 Gb of memory within our university’s supercomputing environment.

As emphasized within code annotations, this entire workflow is run with R 4.3.2 and Seurat 5.1.0— our computation makes use of that FindClusters implementation, a shared nearest neighbor modularity optimization based clustering algorithm (Seurat 5.2 is not compatible). We specify the Leiden algorithm at these steps, which differs from the default Louvain algorithm, which offers certain computational advantages (see PMID 30914743). While results with Louvain would likely reach the same biological conclusions, the final clusters and annotations we provide here are only useful with Leiden implementation. Finally, we are grateful to our institution’s supercomputer admins, who helped establish a virtual environment with R-Reticulate, which allows for calling the Leiden algorithm (implemented in Python). Readers will similarly need to establish this dependency based on their local environment.
DOI: 10.15468/dl.uwffwx
title: Occurrence Download

description: A dataset containing 465714 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "Month is greater than or equal to January",
 "Country is Malaysia",
 "TaxonKey is Passeriformes"
 ]
}

 The dataset includes 465714 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001809-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-56144
title: Redemption tidings, vol. 37, nos. 1-52, 1 Jan. - 22 Dec. 1961

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.5w2sv5
title: Occurrence Download

description: A dataset containing 105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Geranium saxatile Kar. & Kir.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 105 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0261889-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e397dc
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mimosa demissa Barneby"
 ]
}

 The dataset includes 8 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041327-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-56428
title: Redemption tidings, vol. 37, nos. 1-52, 1 Jan. - 22 Dec. 1961

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.ddzghm
title: Occurrence Download

description: A dataset containing 194 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Craugastor taylori (Lynch, 1966)",
 "TaxonKey is Craugastor pelorus (Campbell & Savage, 2000)",
 "TaxonKey is Craugastor palenque (Campbell & Savage, 2000)",
 "TaxonKey is Bolitoglossa stuarti Wake & Brame, 1969"
 ]
}

 The dataset includes 194 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015312-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k2bwds
title: Occurrence Download

description: A dataset containing 627902 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Esox lucius Linnaeus, 1758"
 ]
}

 The dataset includes 627902 records from 518 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0097699-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.