cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh2730850.08fu
title: SH2730850.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5517/ccdc.csd.cc1pgn1v
title: CCDC 1563207: Experimental Crystal Structure Determination

description: Related Article: Tetsuji Moriguchi, Hiromasa Kawata, Venkataprasad Jalli|2021|Cryst.Struct.Theory Appl.|10|1|doi:10.4236/csta.2021.101001
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: 10.15156/bio/sh2730851.08fu
title: SH2730851.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2730852.08fu
title: SH2730852.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2730853.08fu
title: SH2730853.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2730854.08fu
title: SH2730854.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5517/ccdc.csd.cc25rnqb
title: CCDC 2018742: Experimental Crystal Structure Determination

description: Related Article: Chang Shen, Wasihun Menberu Dagnaw, Ching Wai Fong, Kai Chung Lau, Cheuk-Fai Chow|2022|Chem.Commun.|58|10627|doi:10.1039/D2CC02924C
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: 10.15156/bio/sh2730855.08fu
title: SH2730855.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2730856.08fu
title: SH2730856.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2730857.08fu
title: SH2730857.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.9034454
title: Dendrobium nutritional characteristics.xlsx

description: Dendrobium polysaccharideDendrobium total alkaloidDendrobium amino acidsDendrobium trace elements
DOI: 10.6084/m9.figshare.9034451
title: ocean_ch4.nc

description: This netcdf file accompanies the manuscript "Global ocean methane emissions dominated by shallow coastal waters", authors T. Weber, N. Wiseman, A. Kock. See README for file details. <br>
DOI: 10.6084/m9.figshare.9034454.v2
title: Dendrobium nutritional characteristics.xlsx

description: Dendrobium polysaccharideDendrobium total alkaloidDendrobium amino acidsDendrobium trace elements
DOI: 10.6084/m9.figshare.9034352
title: Codebook

description: Codebook describing all variables in the main data file for "Do Democratic Governors Lower Economic Freedom? A Regression Discontinuity Approach."
DOI: 10.6084/m9.figshare.9034352.v1
title: Codebook

description: Codebook describing all variables in the main data file for "Do Democratic Governors Lower Economic Freedom? A Regression Discontinuity Approach."
DOI: 10.6084/m9.figshare.9034331.v2
title: Parallelization of a Common Changepoint Detection Method

description: In recent years, various means of efficiently detecting changepoints have been proposed, with one popular approach involving minimizing a penalized cost function using dynamic programming. In some situations, these algorithms can have an expected computational cost that is linear in the number of data points; however, the worst case cost remains quadratic. We introduce two means of improving the computational performance of these methods, both based on parallelizing the dynamic programming approach. We establish that parallelization can give substantial computational improvements: in some situations the computational cost decreases roughly quadratically in the number of cores used. These parallel implementations are no longer guaranteed to find the true minimum of the penalized cost; however, we show that they retain the same asymptotic guarantees in terms of their accuracy in estimating the number and location of the changes. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.9034331.v1
title: Parallelisation of a Common Changepoint Detection Method

description: In recent years, various means of efficiently detecting changepoints have been proposed, with one popular approach involving minimising a penalised cost function using dynamic programming. In some situations, these algorithms can have an expected computational cost that is linear in the number of data points; however, the worst case cost remains quadratic. We introduce two means of improving the computational performance of these methods, both based on parallelising the dynamic programming approach. We establish that parallelisation can give substantial computational improvements: in some situations the computational cost decreases roughly quadratically in the number of cores used. These parallel implementations are no longer guaranteed to find the true minimum of the penalised cost; however, we show that they retain the same asymptotic guarantees in terms of their accuracy in estimating the number and location of the changes. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.9034256
title: Main Data File

description: This file includes all data needed to reproduce the findings in the article "Do Democratic Governors Lower Economic Freedom? A Regression Discontinuity Approach."
DOI: 10.6084/m9.figshare.9034256.v1
title: Main Data File

description: This file includes all data needed to reproduce the findings in the article "Do Democratic Governors Lower Economic Freedom? A Regression Discontinuity Approach."
DOI: 10.6084/m9.figshare.9034232
title: Supplementary Tables for "Testing the role of SOX15 in human primordial germ cell fate"

description: Oligonucleotides used in this study are listed in Supplemental Table 1. Antibodies (primary and secondary) used for immunofluorescence are listed in Supplemental Table 2. PGCLC fraction counts by flow cytometry are listed in Supplemental Tables 3–5. ∆∆Ct values from qPCR experiments are listed in Supplemental Tables 6–8. Raw Ct values are listed in Supplemental Table 9.
DOI: 10.6084/m9.figshare.9034199
title: Plasmids for "Testing the role of SOX15 in human primordial germ cell fate"

description: These plasmids were used to generate cell lines as described in "Testing the role of SOX15 in human primordial germ cell fate"<br>
DOI: 10.6084/m9.figshare.9034232.v1
title: Supplementary Tables for "Testing the role of SOX15 in human primordial germ cell fate"

description: Oligonucleotides used in this study are listed in Supplemental Table 1. Primary antibodies used for immunofluorescence are listed in Supplemental Table 2. PGCLC fraction counts by flow cytometry are listed in Supplemental Tables 3–5. ∆∆Ct values from qPCR experiments are listed in Supplemental Tables 6–8. Raw Ct values are listed in Supplemental Table 9.
DOI: 10.6084/m9.figshare.9034202
title: Secondary structures of rfam eukaryotic group II introns

description: Structures of eukaryotic group II introns of RFAM RF00029 family
DOI: 10.6084/m9.figshare.9034199.v1
title: Plasmids for "Testing the role of SOX15 in human primordial germ cell fate"

description: These plasmids were used to generate cell lines as described in "Testing the role of SOX15 in human primordial germ cell fate"<br>
DOI: 10.6084/m9.figshare.9034166
title: Cross-species transmission of poultry pathogens in backyard farms: ducks as carriers of chicken viruses

description: In backyard farms of Lao People’s Democratic Republic, mixed-species rearing of poultry is a breeding-ground for cross-species transmission. Here, the epidemiology of viruses circulating among backyard poultry in Vientiane Province was assessed to guide future control strategies. Oral/tracheal and cloacal swabs, collected from 605 poultry (308 ducks, 297 chickens) between 2011 and 2015, were screened by PCR for Newcastle disease virus (NDV), coronavirus (CoV) and chicken anaemia virus (CAV). Chicken sera were screened for anti-NDV antibodies by ELISA. Statistical and phylogenetic analyses revealed transmission patterns and relationships. Closely related strains co-circulated in chickens and ducks. While CoV RNA was detected in oral/tracheal swabs of 9.3% of the chickens and 2.4% of the ducks, rates were higher in faecal swabs of both species (27.3% and 48.2%). RNA of infectious bronchitis virus (IBV) and duck CoV was found in faecal swabs of chickens (19.7% and 7.1%) and ducks (4.1% and 44.1%). Moreover, DNA of the generally chicken-specific CAV was detected in oral/tracheal swabs of chickens (18.1%) and, sporadically, of ducks (2.4%). Despite serological evidence of NDV circulation or vaccination (86.9%), NDV RNA was not detected. We found a high prevalence and indication for cross-species transmission of different CoV strains in backyard poultry. Interestingly, ducks served as biological, or at least mechanical, carriers of viral strains closely related not only to IBV, but also to CAV. Bird containment and poultry species separation could be first steps to avoid cross-species transmission and emergence of novel strains with broad host range and enhanced pathogenicity. <b>RESEARCH HIGHLIGHTS</b>High rates of avian viruses were detected by PCR in backyard poultry from Lao PDR.Diverse coronavirus and chicken anemia virus strains co-circulated.Phylogenetic analyses suggested virus transmission between chickens and ducks.Serological evidence of Newcastle disease was found, but viral RNA was not detected. High rates of avian viruses were detected by PCR in backyard poultry from Lao PDR. Diverse coronavirus and chicken anemia virus strains co-circulated. Phylogenetic analyses suggested virus transmission between chickens and ducks. Serological evidence of Newcastle disease was found, but viral RNA was not detected.
DOI: 10.6084/m9.figshare.9034184
title: Secondary structures of the training set of eukatyotic group II introns

description: Secondary structures of the training set of eukaryotic group II introns
DOI: 10.6084/m9.figshare.9034232.v2
title: Supplementary Tables for "Testing the role of SOX15 in human primordial germ cell fate"

description: Oligonucleotides used in this study are listed in Supplemental Table 1. Primary antibodies used for immunofluorescence are listed in Supplemental Table 2. PGCLC fraction counts by flow cytometry are listed in Supplemental Tables 3–5. ∆∆Ct values from qPCR experiments are listed in Supplemental Tables 6–8. Raw Ct values are listed in Supplemental Table 9.
DOI: 10.6084/m9.figshare.9034202.v1
title: Secondary structures of rfam eukaryotic group II introns

description: Structures of eukaryotic group II introns of RFAM RF00029 family
DOI: 10.6084/m9.figshare.9034166.v2
title: Cross-species transmission of poultry pathogens in backyard farms: ducks as carriers of chicken viruses

description: In backyard farms of Lao People’s Democratic Republic, mixed-species rearing of poultry is a breeding-ground for cross-species transmission. Here, the epidemiology of viruses circulating among backyard poultry in Vientiane Province was assessed to guide future control strategies. Oral/tracheal and cloacal swabs, collected from 605 poultry (308 ducks, 297 chickens) between 2011 and 2015, were screened by PCR for Newcastle disease virus (NDV), coronavirus (CoV) and chicken anaemia virus (CAV). Chicken sera were screened for anti-NDV antibodies by ELISA. Statistical and phylogenetic analyses revealed transmission patterns and relationships. Closely related strains co-circulated in chickens and ducks. While CoV RNA was detected in oral/tracheal swabs of 9.3% of the chickens and 2.4% of the ducks, rates were higher in faecal swabs of both species (27.3% and 48.2%). RNA of infectious bronchitis virus (IBV) and duck CoV was found in faecal swabs of chickens (19.7% and 7.1%) and ducks (4.1% and 44.1%). Moreover, DNA of the generally chicken-specific CAV was detected in oral/tracheal swabs of chickens (18.1%) and, sporadically, of ducks (2.4%). Despite serological evidence of NDV circulation or vaccination (86.9%), NDV RNA was not detected. We found a high prevalence and indication for cross-species transmission of different CoV strains in backyard poultry. Interestingly, ducks served as biological, or at least mechanical, carriers of viral strains closely related not only to IBV, but also to CAV. Bird containment and poultry species separation could be first steps to avoid cross-species transmission and emergence of novel strains with broad host range and enhanced pathogenicity. <b>RESEARCH HIGHLIGHTS</b>High rates of avian viruses were detected by PCR in backyard poultry from Lao PDR.Diverse coronavirus and chicken anemia virus strains co-circulated.Phylogenetic analyses suggested virus transmission between chickens and ducks.Serological evidence of Newcastle disease was found, but viral RNA was not detected. High rates of avian viruses were detected by PCR in backyard poultry from Lao PDR. Diverse coronavirus and chicken anemia virus strains co-circulated. Phylogenetic analyses suggested virus transmission between chickens and ducks. Serological evidence of Newcastle disease was found, but viral RNA was not detected.
DOI: 10.6084/m9.figshare.9034184.v1
title: Secondary structures of the training set of eukatyotic group II introns

description: Secondary structures of the training set of eukaryotic group II introns
DOI: 10.6084/m9.figshare.9034232.v3
title: Supplementary Tables for "Testing the role of SOX15 in human primordial germ cell fate"

description: Oligonucleotides used in this study are listed in Supplemental Table 1. Primary antibodies used for immunofluorescence are listed in Supplemental Table 2. PGCLC fraction counts by flow cytometry are listed in Supplemental Tables 3–5. ∆∆Ct values from qPCR experiments are listed in Supplemental Tables 6–8. Raw Ct values are listed in Supplemental Table 9.