cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1243079.10fu
title: SH1243079.10FU

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/sh1243081.10fu
title: SH1243081.10FU

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/sh1243082.10fu
title: SH1243082.10FU

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: 10.5281/zenodo.18184857
title: FFL-MPI-Data - measured dataset

description: FFL-MPI-Data - measured dataset

A public projection imaging dataset for field-free line magnetic particle imaging 

1. Data Storage Structure: Organized by phantom, each file contains all information for a single phantom, including data and metadata. Multi-domain data, such as sinograms and images, along with harmonic data for K = 2 to K = 7, are stored within data groups. Supplementary metadata facilitates user queries regarding the hardware systems and scan configurations used for phantom acquisition.

Data Storage Structure:FFL-MPI-Data (v2.0)| - measured dataset    | - phantom_1.h5    | - phantom_2.h5    | - ...    | - phantom_100.h5        | - data/image        | - data/sinogram        | - data/voltage        | - metadata| - simulated dataset    | - train dataset        | - phantom_1.h5        | - ....        | - phantom_60000.h5    | - test dataset        | - phantom_1.h5        | - ....        | - phantom_10000.h5

2. Data is stored in .h5 format. Users can access data as follows:

- Read image domain data: /data/image/imag (imaginary part), /data/image/real (real part)

- Reading sinogram domain data: /data/sinogram/imag (imaginary part), /data/sinogram/real (real part)

Metadata can also be read:

for example the following two attributes:

- /Project_Name (project name)

- /Dataset_type (dataset type: measured dataset or simulated data)

And other metadatas, users can view our GitHub project: BUAALGH/FFL-MPI-Data: Public projection imaging dataset for field free line magnetic particle imaging
DOI: 10.5281/zenodo.18184858
title: FFL-MPI-Data - measured dataset

description: FFL-MPI-Data - measured dataset

A public projection imaging dataset for field-free line magnetic particle imaging 

1. Data Storage Structure: Organized by phantom, each file contains all information for a single phantom, including data and metadata. Multi-domain data, such as sinograms and images, along with harmonic data for K = 2 to K = 7, are stored within data groups. Supplementary metadata facilitates user queries regarding the hardware systems and scan configurations used for phantom acquisition.

Data Storage Structure:FFL-MPI-Data (v2.0)| - measured dataset    | - phantom_1.h5    | - phantom_2.h5    | - ...    | - phantom_100.h5        | - data/image        | - data/sinogram        | - data/voltage        | - metadata| - simulated dataset    | - train dataset        | - phantom_1.h5        | - ....        | - phantom_60000.h5    | - test dataset        | - phantom_1.h5        | - ....        | - phantom_10000.h5

2. Data is stored in .h5 format. Users can access data as follows:

- Read image domain data: /data/image/imag (imaginary part), /data/image/real (real part)

- Reading sinogram domain data: /data/sinogram/imag (imaginary part), /data/sinogram/real (real part)

Metadata can also be read:

for example the following two attributes:

- /Project_Name (project name)

- /Dataset_type (dataset type: measured dataset or simulated data)

And other metadatas, users can view our GitHub project: BUAALGH/FFL-MPI-Data: Public projection imaging dataset for field free line magnetic particle imaging
DOI: 10.15156/bio/sh1243083.10fu
title: SH1243083.10FU

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/sh1243084.10fu
title: SH1243084.10FU

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/sh1243087.10fu
title: SH1243087.10FU

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: 10.71796/wits-figshare.30636092
title: <b>Species richness, composition and dominance of core and climate relicts of African Miombo woodlands</b>

description: The miombo woodlands, which span about 10% of the African continent, are essential for the ecosystem services they provide. These woodlands are mainly dominated by the genera <i>Julbernardia</i>, <i>Isoberlinia</i>, and <i>Brachystegia</i>. However, there is limited understanding of how species dominance and richness change in relict sites, which are far removed from the core miombo woodlands. In this study, we anticipated that relict sites would show reduced species diversity due to their isolation from the core miombo woodlands and their exposure to different species compositions. We sampled vegetation using modified Whittaker plots (50 m × 20 m) across four sites: core miombo woodland (n = 14), miombo edge (n = 19), Mozambique relict (n = 18), and South Africa relict (n = 21). Within each plot, we measured tree height, basal diameter, and canopy dimensions for mature trees; root collar diameter for saplings (20 m × 5 m subplots); and recorded seedling species and counts (in 5 m × 2 m subplots). Temperature and rainfall gradients were also assessed across the sites. Species richness, Shannon Wiener diversity, and species evenness were compared between sites using one-way analysis of variance (ANOVA). Species composition difference between sites were evaluated using analysis of similarity (ANOSIM). Our results revealed a pattern where species richness, the Shannon Wiener index, and evenness increased with decreasing relict size. Interestingly, evenness declined from juvenile to adult stages within sites, suggesting changes in species composition over time. Significant differences in species composition were observed between sites, with the most pronounced dissimilarities between the core miombo woodland and Mozambique relict. Our findings highlight that while key miombo species remained dominant and important, the relict sites demonstrated increased species richness. This suggests that these isolated sites might harbour high biodiversity, potentially due to their high perimeter-to-area ratio, which makes them more susceptible to species invasions. Additionally, the warmer temperatures recorded at the relict sites could be driving thermophilization, further contributing to the richness and diversity observed. These insights are crucial for informing conservation strategies for miombo woodlands and their relicts in the face of ongoing climate change.
DOI: 10.71796/wits-figshare.30636092.v1
title: <b>Species richness, composition and dominance of core and climate relicts of African Miombo woodlands</b>

description: The miombo woodlands, which span about 10% of the African continent, are essential for the ecosystem services they provide. These woodlands are mainly dominated by the genera <i>Julbernardia</i>, <i>Isoberlinia</i>, and <i>Brachystegia</i>. However, there is limited understanding of how species dominance and richness change in relict sites, which are far removed from the core miombo woodlands. In this study, we anticipated that relict sites would show reduced species diversity due to their isolation from the core miombo woodlands and their exposure to different species compositions. We sampled vegetation using modified Whittaker plots (50 m × 20 m) across four sites: core miombo woodland (n = 14), miombo edge (n = 19), Mozambique relict (n = 18), and South Africa relict (n = 21). Within each plot, we measured tree height, basal diameter, and canopy dimensions for mature trees; root collar diameter for saplings (20 m × 5 m subplots); and recorded seedling species and counts (in 5 m × 2 m subplots). Temperature and rainfall gradients were also assessed across the sites. Species richness, Shannon Wiener diversity, and species evenness were compared between sites using one-way analysis of variance (ANOVA). Species composition difference between sites were evaluated using analysis of similarity (ANOSIM). Our results revealed a pattern where species richness, the Shannon Wiener index, and evenness increased with decreasing relict size. Interestingly, evenness declined from juvenile to adult stages within sites, suggesting changes in species composition over time. Significant differences in species composition were observed between sites, with the most pronounced dissimilarities between the core miombo woodland and Mozambique relict. Our findings highlight that while key miombo species remained dominant and important, the relict sites demonstrated increased species richness. This suggests that these isolated sites might harbour high biodiversity, potentially due to their high perimeter-to-area ratio, which makes them more susceptible to species invasions. Additionally, the warmer temperatures recorded at the relict sites could be driving thermophilization, further contributing to the richness and diversity observed. These insights are crucial for informing conservation strategies for miombo woodlands and their relicts in the face of ongoing climate change.
DOI: 10.15156/bio/sh1243088.10fu
title: SH1243088.10FU

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/sh1243090.10fu
title: SH1243090.10FU

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.31047710
title: Detection of five viruses commonly implicated with bovine respiratory disease using loop-mediated isothermal amplification

description: Herein, we present novel quantitative loop-mediated isothermal amplification (qLAMP) and reverse-transcription qLAMP (RT-qLAMP) assays for the detection of five viruses implicated with the onset and progression of bovine respiratory disease (BRD): Bovine Alphaherpesvirus Type 1 (BHV-1), Bovine Adenovirus Type 3 (BAV-3), Bovine Respiratory Syncytial Virus (BRSV), Bovine Viral Diarrhea Virus Type 1 (BVDV-1), and Bovine Parainfluenza Virus Type 3 (BPIV-3). Using contrived samples spiked with whole viruses, our extraction-free assays have limits of detection between 30 and 1,057 copies per reaction (1.8% final sample concentration) with minimal sample processing. Using dual-tipped swabs and 1.4 mL resuspension volumes, limits of detection are on the order of 2 × 10<sup>5</sup> copies per swab for BAV-3 and BHV-1 and between 6.31 × 10<sup>6</sup> to 8.22 × 10<sup>6</sup> copies per swab for BPIV-3, BRSV, and BVDV-1. Analytical sensitivities ranged from 73 − 100% and analytical specificities ranged from 90 − 100%. Additionally, we introduced a streamlined pipeline to minimize the experimental workload to design, screen, select, and characterize LAMP performance for developing assays. Our assays support the development of colorimetric LAMP assays that enable the sensitive and specific detection of these viruses’ chute side to aid in diagnosing and treating BRD. The associated pipeline enables more rapid development of LAMP-based diagnostic tools targeting emerging pathogens.
DOI: 10.6084/m9.figshare.31047710.v1
title: Detection of five viruses commonly implicated with bovine respiratory disease using loop-mediated isothermal amplification

description: Herein, we present novel quantitative loop-mediated isothermal amplification (qLAMP) and reverse-transcription qLAMP (RT-qLAMP) assays for the detection of five viruses implicated with the onset and progression of bovine respiratory disease (BRD): Bovine Alphaherpesvirus Type 1 (BHV-1), Bovine Adenovirus Type 3 (BAV-3), Bovine Respiratory Syncytial Virus (BRSV), Bovine Viral Diarrhea Virus Type 1 (BVDV-1), and Bovine Parainfluenza Virus Type 3 (BPIV-3). Using contrived samples spiked with whole viruses, our extraction-free assays have limits of detection between 30 and 1,057 copies per reaction (1.8% final sample concentration) with minimal sample processing. Using dual-tipped swabs and 1.4 mL resuspension volumes, limits of detection are on the order of 2 × 10<sup>5</sup> copies per swab for BAV-3 and BHV-1 and between 6.31 × 10<sup>6</sup> to 8.22 × 10<sup>6</sup> copies per swab for BPIV-3, BRSV, and BVDV-1. Analytical sensitivities ranged from 73 − 100% and analytical specificities ranged from 90 − 100%. Additionally, we introduced a streamlined pipeline to minimize the experimental workload to design, screen, select, and characterize LAMP performance for developing assays. Our assays support the development of colorimetric LAMP assays that enable the sensitive and specific detection of these viruses’ chute side to aid in diagnosing and treating BRD. The associated pipeline enables more rapid development of LAMP-based diagnostic tools targeting emerging pathogens.
DOI: 10.15156/bio/sh1243092.10fu
title: SH1243092.10FU

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.