cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25405/data.ncl.29356565
title: Data sets for "Biohydrogen production through dark fermentation of agricultural waste: Novel strain and feedstock characterisation".

description: Data sets (as excel files) underpinning the figures presented in:Biohydrogen production through dark fermentation of agricultural waste: Novel strain and feedstock characterisation,Ariadna Vidal, Obaidullah Mohiuddin, Ella Chance, Sergio Serrano-Blanco, Thomas Howard, Jose Muñoz-Muñoz, Sharon Velasquez-Orta, Leonardo Rios-SolisBioresource Technology 2025, 132839, https://doi.org/10.1016/j.biortech.2025.132839.Hydrogen is a promising alternative energy source that could help reduce reliance on fossil fuels and support the transition to decarbonisation of the energy sector. Biohydrogen can be produced through biological processes such as dark fermentation of agricultural waste. Lignocellulosic biomass from willow, hay, wheat or barley, is abundant and contains approximately 40 % carbon, which if properly pretreated, can serve as an excellent feedstock for microorganisms. In this study, <i>Shewanella oneidensis</i> MR-1, <i>Cellvibrio japonicus</i> Ueda107 and <i>Sorangium cellulosum</i> So ce27 were tested for biohydrogen (H2) production through dark fermentation of lignocellulosic waste. Maximum biohydrogen concentrations were obtained for <i>S. oneidensis</i> with 787.6 ± 69.3 mL H2/L willow hydrolysate after 12 h, and <i>C. japonicus</i> with 851.6 ± 20.8 mL H2/L hay hydrolysate after 36 h of fermentation. The main metabolite produced by <i>S. oneidensis</i> was acetic acid with a maximum yield of 6.48 mmol/L in willow-derived media after 36 h. <i>C. japonicus</i> and <i>S. cellulosum</i> mainly produced isobutyric in wheat-derived media, with 9.7 ± 12.4 mmol/L and 15 ± 10.1 mmol/L, respectively. This study proposes novel feedstocks and strains for biohydrogen and metabolites production from agricultural waste.Keywords: Biohydrogen; Lignocellulosic biomass; Dark fermentation; Waste valorisation<br><br>The data sets deposited here contain the underpinning data used to generate Tables, Figures and SI Figures associated with this publication. Files are named after the relevant Table or Figure within the paper. All methods used to generate the data are presented in the paper.
DOI: 10.25405/data.ncl.29356565.v1
title: Data sets for "Biohydrogen production through dark fermentation of agricultural waste: Novel strain and feedstock characterisation".

description: Data sets (as excel files) underpinning the figures presented in:Biohydrogen production through dark fermentation of agricultural waste: Novel strain and feedstock characterisation,Ariadna Vidal, Obaidullah Mohiuddin, Ella Chance, Sergio Serrano-Blanco, Thomas Howard, Jose Muñoz-Muñoz, Sharon Velasquez-Orta, Leonardo Rios-SolisBioresource Technology 2025, 132839, https://doi.org/10.1016/j.biortech.2025.132839.Hydrogen is a promising alternative energy source that could help reduce reliance on fossil fuels and support the transition to decarbonisation of the energy sector. Biohydrogen can be produced through biological processes such as dark fermentation of agricultural waste. Lignocellulosic biomass from willow, hay, wheat or barley, is abundant and contains approximately 40 % carbon, which if properly pretreated, can serve as an excellent feedstock for microorganisms. In this study, <i>Shewanella oneidensis</i> MR-1, <i>Cellvibrio japonicus</i> Ueda107 and <i>Sorangium cellulosum</i> So ce27 were tested for biohydrogen (H2) production through dark fermentation of lignocellulosic waste. Maximum biohydrogen concentrations were obtained for <i>S. oneidensis</i> with 787.6 ± 69.3 mL H2/L willow hydrolysate after 12 h, and <i>C. japonicus</i> with 851.6 ± 20.8 mL H2/L hay hydrolysate after 36 h of fermentation. The main metabolite produced by <i>S. oneidensis</i> was acetic acid with a maximum yield of 6.48 mmol/L in willow-derived media after 36 h. <i>C. japonicus</i> and <i>S. cellulosum</i> mainly produced isobutyric in wheat-derived media, with 9.7 ± 12.4 mmol/L and 15 ± 10.1 mmol/L, respectively. This study proposes novel feedstocks and strains for biohydrogen and metabolites production from agricultural waste.Keywords: Biohydrogen; Lignocellulosic biomass; Dark fermentation; Waste valorisation<br><br>The data sets deposited here contain the underpinning data used to generate Tables, Figures and SI Figures associated with this publication. Files are named after the relevant Table or Figure within the paper. All methods used to generate the data are presented in the paper.
DOI: 10.15468/dl.9bukby
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Compsopogon Montagne, 1846",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((18.2339 -32.5266,18.1411 -32.657,18.1007 -32.7021,18.0224 -32.6366,17.8923 -32.6419,17.754 -32.8255,17.7723 -32.9007,20.509 -32.9007,20.509 -28.5786,16.2782 -28.5786,16.4358 -28.7202,16.726 -29.1235,17.1957 -30.3752,17.6655 -31.1743,18.1322 -31.7679,18.2495 -32.2638,18.2339 -32.5266))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064612-250525065834625/datasets/export for details.
DOI: 10.15468/dl.aktq2n
title: Occurrence Download

description: A dataset containing 585 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euagrus Ausserer, 1875"
 ]
}

 The dataset includes 585 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064611-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25442/hku.29231828
title: Supporting Data for "ZC3H8 regulates rDNA transcription by suppression of R loop formation"

description: <b>Project Overview:</b>This project investigates the role of ZC3H8, a nucleolar protein, in safeguarding genomic integrity during ribosome biogenesis. The nucleolus, as the site of ribosomal RNA (rRNA) synthesis, is one of the most transcriptionally active regions in the cell and is particularly vulnerable to genomic instability. Ribosomal DNA (rDNA), which resides in the nucleolus, is prone to the formation of R loops—three-stranded nucleic acid structures that can interfere with transcription, thereby threatening genome stability.The study demonstrates that ZC3H8 may play a critical role in suppressing R loop formation at rDNA loci. Mechanistically, ZC3H8 functions in concert with DHX9, an RNA helicase known to resolve R loops. ZC3H8 binds preferentially to single-stranded RNA, and this interaction is proposed to stabilize the RNA strand during DHX9-mediated unwinding of R loops. This cooperative mechanism supports efficient rRNA synthesis while preserving the structural and functional integrity of the rDNA.<b>Dataset Contents:</b>The dataset includes raw and processed experimental data organized by thesis chapters and figures. Data formats include high-resolution immunofluorescence images, Western blot scans, quantification files, RNA-seq datasets, and schematic illustrations. All files are arranged to mirror the thesis structure, ensuring clear correspondence between data and manuscript figures.<br><b>Key Directories and File Types:</b><b>Chapter 1 – Introduction (Figures 1.1–1.2):</b>Adobe Illustrator (.ai) schematics illustrating rDNA structure and nucleolar functions.<b>Chapter 3 – Experimental Results (Figures 3.1–3.13):</b><b>Raw Data:</b>Immunofluorescence images (.tif, .rar)Western blot scans (Image Lab format)RNA-seq analysis files (.csv, .xlsx, .txt)EMSA gel imagesQuantification data (.pzfx, .pzf) from GraphPad PrismProtein structure prediction outputs (AlphaFold, PyMOL)<b>Organised Data:</b>Finalized figure panels (.tif)Schematics (.ai) and processed visualizations used directly in the thesis manuscript.<br><b>Software and Equipment Used:</b>Image Analysis: Fiji (ImageJ v1.53f51)Quantitative Analysis: GraphPad Prism (v7.0 or higher)Microscopy: Zeiss LSM 780 confocal microscope<br><b>Intended Use:</b>The dataset supports reproducibility and transparency of the thesis findings. It is intended for researchers interested in rDNA transcription, nucleolar biology, RNA processing, and protein–nucleic acid interactions. The detailed file organization facilitates targeted reuse of specific data elements (e.g., IF quantifications, RNA-seq processing).
DOI: 10.25442/hku.29231828.v1
title: Supporting Data for "ZC3H8 regulates rDNA transcription by suppression of R loop formation"

description: <b>Project Overview:</b>This project investigates the role of ZC3H8, a nucleolar protein, in safeguarding genomic integrity during ribosome biogenesis. The nucleolus, as the site of ribosomal RNA (rRNA) synthesis, is one of the most transcriptionally active regions in the cell and is particularly vulnerable to genomic instability. Ribosomal DNA (rDNA), which resides in the nucleolus, is prone to the formation of R loops—three-stranded nucleic acid structures that can interfere with transcription, thereby threatening genome stability.The study demonstrates that ZC3H8 may play a critical role in suppressing R loop formation at rDNA loci. Mechanistically, ZC3H8 functions in concert with DHX9, an RNA helicase known to resolve R loops. ZC3H8 binds preferentially to single-stranded RNA, and this interaction is proposed to stabilize the RNA strand during DHX9-mediated unwinding of R loops. This cooperative mechanism supports efficient rRNA synthesis while preserving the structural and functional integrity of the rDNA.<b>Dataset Contents:</b>The dataset includes raw and processed experimental data organized by thesis chapters and figures. Data formats include high-resolution immunofluorescence images, Western blot scans, quantification files, RNA-seq datasets, and schematic illustrations. All files are arranged to mirror the thesis structure, ensuring clear correspondence between data and manuscript figures.<br><b>Key Directories and File Types:</b><b>Chapter 1 – Introduction (Figures 1.1–1.2):</b>Adobe Illustrator (.ai) schematics illustrating rDNA structure and nucleolar functions.<b>Chapter 3 – Experimental Results (Figures 3.1–3.13):</b><b>Raw Data:</b>Immunofluorescence images (.tif, .rar)Western blot scans (Image Lab format)RNA-seq analysis files (.csv, .xlsx, .txt)EMSA gel imagesQuantification data (.pzfx, .pzf) from GraphPad PrismProtein structure prediction outputs (AlphaFold, PyMOL)<b>Organised Data:</b>Finalized figure panels (.tif)Schematics (.ai) and processed visualizations used directly in the thesis manuscript.<br><b>Software and Equipment Used:</b>Image Analysis: Fiji (ImageJ v1.53f51)Quantitative Analysis: GraphPad Prism (v7.0 or higher)Microscopy: Zeiss LSM 780 confocal microscope<br><b>Intended Use:</b>The dataset supports reproducibility and transparency of the thesis findings. It is intended for researchers interested in rDNA transcription, nucleolar biology, RNA processing, and protein–nucleic acid interactions. The detailed file organization facilitates targeted reuse of specific data elements (e.g., IF quantifications, RNA-seq processing).
DOI: 10.5255/ukda-sn-857823
title: A Service Evaluation of Psycho-Social Support Pathways within Trans and Gender Diverse Healthcare: Interview Data, 2025

description: Trans and gender diverse (TGD) people experience poorer health outcomes in comparison to their cisgender counterparts. These poor health outcomes for TGD young people are, in part, explained by exposure to minority stress (e.g., discrimination due to their minoritized identities). 

Positively, research suggests that social support can be helpful for mediating this relationship between minority stress and poor health outcomes, highlighting that it may be beneficial to integrate social support into gender-affirming care. However, this social support needs to be meaningful (i.e., offer them a sense of belonging and access to psychological support that groups can provide) in order to mitigate against negative health outcomes. 

Resultantly, this research conducted a service evaluation of one gender clinic in England. They are the first gender clinic to begin incorporating social support into their model of care. Open-ended survey data was collected from 30 service users, reflecting 10% of total service users. 

This evaluation allowed to understand whether social support delivered through an NHS pathway allows meaningful social connections that enhance health to be developed, or whether these are experienced as too artificial in comparison to finding social support through their own volition.
DOI: 10.25442/hku.29235293
title: Supporting data for “Exercise ameliorates obesity-related periodontal bone loss via modulating gut microbiota homeostasis”

description: This dataset was generated as part of a research project investigating the effects of exercise and gut microbiota on periodontal and systemic bone health, particularly in the context of obesity-associated periodontitis. The study involved both in vivo and in vitro components. In the animal experiments, male C57BL/6 mice (n = 64) were assigned to different experimental groups, including high-fat diet (HFD), exercise intervention (high-intensity interval training), and periodontitis induction via ligature placement. Additional groups received fecal microbiota transplantation (FMT) to assess the transmissible effects of gut microbiota from obese or exercise-conditioned donors.Fecal, serum, and tissue samples were collected from these animals and analyzed using 16S rRNA gene sequencing for microbial profiling. Micro-computed tomography (micro-CT) and histological staining were used to assess bone parameters in both femoral and alveolar bone. Serum cytokines and SCFAs were also quantified using ELISA and targeted metabolomics.In parallel, human periodontal ligament stem cells (PDLSCs) were cultured and treated with various concentrations of acetate to investigate its role in osteogenic and adipogenic differentiation. Gene and protein expression analyses, including Western blotting, and immunofluorescence, were performed to explore underlying mechanisms.
DOI: 10.25442/hku.29235293.v1
title: Supporting data for “Exercise ameliorates obesity-related periodontal bone loss via modulating gut microbiota homeostasis”

description: This dataset was generated as part of a research project investigating the effects of exercise and gut microbiota on periodontal and systemic bone health, particularly in the context of obesity-associated periodontitis. The study involved both in vivo and in vitro components. In the animal experiments, male C57BL/6 mice (n = 64) were assigned to different experimental groups, including high-fat diet (HFD), exercise intervention (high-intensity interval training), and periodontitis induction via ligature placement. Additional groups received fecal microbiota transplantation (FMT) to assess the transmissible effects of gut microbiota from obese or exercise-conditioned donors.Fecal, serum, and tissue samples were collected from these animals and analyzed using 16S rRNA gene sequencing for microbial profiling. Micro-computed tomography (micro-CT) and histological staining were used to assess bone parameters in both femoral and alveolar bone. Serum cytokines and SCFAs were also quantified using ELISA and targeted metabolomics.In parallel, human periodontal ligament stem cells (PDLSCs) were cultured and treated with various concentrations of acetate to investigate its role in osteogenic and adipogenic differentiation. Gene and protein expression analyses, including Western blotting, and immunofluorescence, were performed to explore underlying mechanisms.
DOI: 10.15468/dl.ruqvjg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Compsopogon Montagne, 1846",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((15.6372 -28.0032,16.2782 -28.5786,20.509 -28.5786,20.509 -24.0715,15.4933 -24.0715,15.4945 -24.1257,16.0509 -25.6631,15.6372 -28.0032))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064613-250525065834625/datasets/export for details.
DOI: 10.34740/kaggle/dsv/12254785
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.nckkq5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Compsopogon Montagne, 1846",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((15.4784 -23.4046,15.4933 -24.0715,20.509 -24.0715,20.509 -24.0455,20.0952 -23.5072,19.9968 -23.017,19.7843 -22.5405,19.1988 -21.8785,18.5972 -21.5447,17.8859 -21.3993,17.1626 -21.4805,16.5332 -21.7596,16.1257 -22.0882,15.8234 -22.4662,15.606 -22.8993,15.4784 -23.4046))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064615-250525065834625/datasets/export for details.
DOI: 10.15468/dl.ttgfea
title: Occurrence Download

description: A dataset containing 13479 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "PublishingOrg is 5299c15f-07ad-4ef6-8d6a-b3acbb90ce93"
 ]
}

 The dataset includes 13479 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064616-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9jm35v
title: Occurrence Download

description: A dataset containing 105255 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Accipitriformes, Anseriformes, Apodiformes, Bucerotiformes, Caprimulgiformes, Charadriiformes, Ciconiiformes, Columbiformes, Coraciiformes, Cuculiformes, Falconiformes, Galliformes, Gaviiformes, Gruiformes, Otidiformes, Passeriformes, Passeriformes, Pelecaniformes, Phaethontiformes, Piciformes, Podicipediformes, Procellariiformes, Psittaciformes, Strigiformes, Suliformes, Sphenisciformes, Apterygiformes, Casuariiformes, Musophagiformes, Tinamiformes, Phoenicopteriformes, Rheiformes, Eurypygiformes, Struthioniformes, Trogoniformes, Cariamiformes, Opisthocomiformes)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 "Year is greater than or equal to 1970",
 "CoordinateUncertaintyInMeters is less than 3000"
 ]
}

 The dataset includes 105255 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064608-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.765u5y
title: Occurrence Download

description: A dataset containing 3752 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Oryx gazella (Linnaeus, 1758)"
 ]
}

 The dataset includes 3752 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064619-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vxhyfw
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Compsopogon Montagne, 1846",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((25.5395 -28.5786,20.509 -28.5786,20.509 -32.9007,25.5395 -32.9007,25.5395 -28.5786))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064618-250525065834625/datasets/export for details.
DOI: 10.25442/hku.29245232
title: Supporting data for “Utilizing AlphaFold Predictions for Enhancing X-ray Crystallographic Structure Determination”

description: High-resolution X-ray diffraction remains central to macromolecular structure determination; however, traditional phase determination methods, such as molecular replacement with homologous structures or experimental techniques like single-wavelength anomalous dispersion, possess inherent limitations. The emergence of accurate de novo structural models generated by AlphaFold, even for proteins without existing homologs, promises significant advancement in crystallographic phasing by providing reliable initial models. Concurrently, technological innovations, including rapid pixel array detectors and automated beamline systems, have enabled high-throughput crystallography, necessitating the development of similarly automated structure determination pipelines.AutoPD, an open-source meta-pipeline leveraging AlphaFold predictions for automated crystallographic analysis, is presented. This pipeline streamlines the entire workflow, progressing from raw diffraction images and protein sequences to refined structural models. AlphaFold-assisted molecular replacement is integrated to establish initial phasing, followed by a dual-space iterative refinement method combining real-space and reciprocal-space approaches. Adaptive decision-making dynamically selects optimal processing pathways based on data quality and interim results. Collectively, these innovations allow structures to be solved automatically, significantly reducing manual intervention and addressing critical bottlenecks in conventional methods.
DOI: 10.25442/hku.29245232.v1
title: Supporting data for “Utilizing AlphaFold Predictions for Enhancing X-ray Crystallographic Structure Determination”

description: High-resolution X-ray diffraction remains central to macromolecular structure determination; however, traditional phase determination methods, such as molecular replacement with homologous structures or experimental techniques like single-wavelength anomalous dispersion, possess inherent limitations. The emergence of accurate de novo structural models generated by AlphaFold, even for proteins without existing homologs, promises significant advancement in crystallographic phasing by providing reliable initial models. Concurrently, technological innovations, including rapid pixel array detectors and automated beamline systems, have enabled high-throughput crystallography, necessitating the development of similarly automated structure determination pipelines.AutoPD, an open-source meta-pipeline leveraging AlphaFold predictions for automated crystallographic analysis, is presented. This pipeline streamlines the entire workflow, progressing from raw diffraction images and protein sequences to refined structural models. AlphaFold-assisted molecular replacement is integrated to establish initial phasing, followed by a dual-space iterative refinement method combining real-space and reciprocal-space approaches. Adaptive decision-making dynamically selects optimal processing pathways based on data quality and interim results. Collectively, these innovations allow structures to be solved automatically, significantly reducing manual intervention and addressing critical bottlenecks in conventional methods.