cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15131/shef.data.27210891
title: Biosynthesis, characterisation and biocompatibility of a unique and elastomeric medium chain-length polyhydroxyalkanoates for kidney glomerular tissue engineering

description: Polyhydroxyalkanoates (PHAs) are bacteria-derived polymers that are being actively explored for their potential in biomedical engineering applications. These polymers are not only highly biocompatible in nature but also sustainable, produced using renewable substrates, and hence considered future biomaterials. This study explores a medium chain-length PHA (mcl-PHA) produced by <em>Pseudomonas mendocina </em>CH50 by batch fermentation, fed with glucose as the sole carbon source. The polymer was extensively characterised, and it exhibited an elastomeric property of a typical mcl-PHA with 215 ± 52 % elongation at break. The mcl-PHA also had a low melting point, <em>T</em><sub>m</sub>,<sub> </sub>of around 55 °C, making it processable with various fabrication methods. The extracted mcl-PHA was prepared as a solvent-cast film and tested as a potential cell culture substrate for human glomerular cells, the conditionally immortalised human podocytes (CiHP) and conditionally immortalised human glomerular endothelial cells (CiGEnC). Initial resazurin assay under proliferative conditions showed promising cell metabolic activities of the cells cultured on the mcl-PHA film, comparable with those cultured on tissue culture plastic (TCP). Despite the decreased expression of collagen IV under proliferative conditions, the differentiated co-cultured cells on mcl-PHA had comparable values with those cells grown on TCP. These promising results verified the biocompatibility of the mcl-PHA produced by <em>P. mendocina </em>CH50 and established its potential as a bio-based sustainable alternative in biomedical applications including glomerular tissue engineering.
DOI: 10.15131/shef.data.27210891.v2
title: Biosynthesis, characterisation and biocompatibility of a unique and elastomeric medium chain-length polyhydroxyalkanoates for kidney glomerular tissue engineering

description: Polyhydroxyalkanoates (PHAs) are bacteria-derived polymers that are being actively explored for their potential in biomedical engineering applications. These polymers are not only highly biocompatible in nature but also sustainable, produced using renewable substrates, and hence considered future biomaterials. This study explores a medium chain-length PHA (mcl-PHA) produced by <em>Pseudomonas mendocina </em>CH50 by batch fermentation, fed with glucose as the sole carbon source. The polymer was extensively characterised, and it exhibited an elastomeric property of a typical mcl-PHA with 215 ± 52 % elongation at break. The mcl-PHA also had a low melting point, <em>T</em><sub>m</sub>,<sub> </sub>of around 55 °C, making it processable with various fabrication methods. The extracted mcl-PHA was prepared as a solvent-cast film and tested as a potential cell culture substrate for human glomerular cells, the conditionally immortalised human podocytes (CiHP) and conditionally immortalised human glomerular endothelial cells (CiGEnC). Initial resazurin assay under proliferative conditions showed promising cell metabolic activities of the cells cultured on the mcl-PHA film, comparable with those cultured on tissue culture plastic (TCP). Despite the decreased expression of collagen IV under proliferative conditions, the differentiated co-cultured cells on mcl-PHA had comparable values with those cells grown on TCP. These promising results verified the biocompatibility of the mcl-PHA produced by <em>P. mendocina </em>CH50 and established its potential as a bio-based sustainable alternative in biomedical applications including glomerular tissue engineering.
DOI: 10.15131/shef.data.27210891.v1
title: Regenerating the kidney glomerulus using a unique, elastomeric, bacteria-derived sustainable polymer

description: Polyhydroxyalkanoates (PHAs) are bacteria-derived polymers that are being actively explored for their potential in biomedical engineering applications. These polymers are not only highly biocompatible in nature but also sustainable, produced using renewable substrates, and hence considered future biomaterials. This study explores a medium chain-length PHA (mcl-PHA) produced by <em>Pseudomonas mendocina </em>CH50 by batch fermentation, fed with glucose as the sole carbon source. The polymer was extensively characterised, and it exhibited an elastomeric property of a typical mcl-PHA with 215 ± 52 % elongation at break. The mcl-PHA also had a low melting point, <em>T</em><sub>m</sub>,<sub> </sub>of around 55 °C, making it processable with various fabrication methods. The extracted mcl-PHA was prepared as a solvent-cast film and tested as a potential cell culture substrate for human glomerular cells, the conditionally immortalised human podocytes (CiHP) and conditionally immortalised human glomerular endothelial cells (CiGEnC). Initial resazurin assay under proliferative conditions showed promising cell metabolic activities of the cells cultured on the mcl-PHA film, comparable with those cultured on tissue culture plastic (TCP). Despite the decreased expression of collagen IV under proliferative conditions, the differentiated co-cultured cells on mcl-PHA had comparable values with those cells grown on TCP. These promising results verified the biocompatibility of the mcl-PHA produced by <em>P. mendocina </em>CH50 and established its potential as a bio-based sustainable alternative in biomedical applications including glomerular tissue engineering.
DOI: 10.5281/zenodo.15792951
title: Raw SEM and XRD Data Supporting the Use of Glass Fiber Filters for Particulate Phosphorus Measurements

description: This dataset includes:





Raw X-ray diffraction (XRD) data used to identify the crystalline phases present in the glass fiber filters.



RH R6_2024-11-20 09.23.56AM.ASC

 RH R8_2024-11-25 09.16.03AM.ASC

 RH R10_2024-11-27 09.13.53AM.ASC

 RH R12_2024-11-28 09.05.01AM.ASC

RH R14_2024-11-29 08.36.11AM.ASC





Energy-dispersive X-ray spectroscopy (EDS) readings providing elemental composition associated with SEM analyses.



EDS 20241204_position 1_3_5.docx

EDS 20241128_position 4.docx

EDS 20241126_position 1_2.docx





Scanning electron microscopy (SEM) images showing the surface morphology and structural integrity of the glass fiber filters before and after experimental treatments.



S11_002.tif

S22_006.tif

S33_003.tif

S55_001.tif




These data were collected to support the evaluation of glass fiber filters used in the quantification of total particulate phosphorus. All files are provided in their original formats as exported from the respective instruments.

These data support the findings in the manuscript "Enhancing the Thermal Resistance of Gass Fiber Filters in Measurement of Particulate Phosphorus using Extra High Temperature Combustion", submitted to Limnology and Oceanography: Methods.
DOI: 10.5281/zenodo.15792952
title: Raw SEM and XRD Data Supporting the Use of Glass Fiber Filters for Particulate Phosphorus Measurements

description: This dataset includes:





Raw X-ray diffraction (XRD) data used to identify the crystalline phases present in the glass fiber filters.



RH R6_2024-11-20 09.23.56AM.ASC

 RH R8_2024-11-25 09.16.03AM.ASC

 RH R10_2024-11-27 09.13.53AM.ASC

 RH R12_2024-11-28 09.05.01AM.ASC

RH R14_2024-11-29 08.36.11AM.ASC





Energy-dispersive X-ray spectroscopy (EDS) readings providing elemental composition associated with SEM analyses.



EDS 20241204_position 1_3_5.docx

EDS 20241128_position 4.docx

EDS 20241126_position 1_2.docx





Scanning electron microscopy (SEM) images showing the surface morphology and structural integrity of the glass fiber filters before and after experimental treatments.



S11_002.tif

S22_006.tif

S33_003.tif

S55_001.tif




These data were collected to support the evaluation of glass fiber filters used in the quantification of total particulate phosphorus. All files are provided in their original formats as exported from the respective instruments.

These data support the findings in the manuscript "Enhancing the Thermal Resistance of Gass Fiber Filters in Measurement of Particulate Phosphorus using Extra High Temperature Combustion", submitted to Limnology and Oceanography: Methods.
DOI: 10.15468/dl.b77xvx
title: Occurrence Download

description: A dataset containing 6942 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Chelonoidis denticulatus, Podocnemis expansa)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6942 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045169-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30246790
title: Optimal Run Order for Order-of-Addition Experiments

description: Order-of-addition experiments have emerged as a cornerstone in modern experimental design, yet the critical role of run-order has been entirely neglected in the literature. This oversight is surprising, given that the run order can significantly influence the cost, efficiency, and validity of the experiment. Certain run orders are inherently more economical and effective, while suboptimal orders may introduce unnecessary complexities or compromise results. To ensure experimental integrity, an optimal run order must minimize factor level changes, especially when transitions between levels are costly—and safeguard against the detrimental effects of time trends, which can skew factor effect estimates and undermine conclusions. Despite its importance, the relationship between run order and order-of-addition experiments remains poorly understood. Our research addresses this critical gap by deriving the theoretical lower bound on the total number of factor level changes for ordered order-of-addition designs. We introduce novel construction methods that achieve this minimum, ensuring both cost efficiency and practicality. Additionally, we develop a rigorous framework to eliminate the bias introduced by linear time trends, proposing robust methods to construct time trend-free ordered designs. These methods lead to the establishment of optimal ordered designs that excel under both criteria. The proposed designed orders go beyond theoretical elegance—they are robust to lurking variables in the external environment, making them invaluable for real-world applications. This study not only shines the spotlight on an overlooked dimension of order-of-addition experiments but also delivers solutions that redefine how these experiments should be conducted. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.30246790.v1
title: Optimal run order for order-of-addition experiments

description: Order-of-addition experiments have emerged as a cornerstone in modern experimental design, yet the critical role of run-order has been entirely neglected in the literature. This oversight is surprising, given that the run order can significantly influence the cost, efficiency, and validity of the experiment. Certain run orders are inherently more economical and effective, while suboptimal orders may introduce unnecessary complexities or compromise results. To ensure experimental integrity, an optimal run order must minimize factor level changes, especially when transitions between levels are costly–and safeguard against the detrimental effects of time trends, which can skew factor effect estimates and undermine conclusions. Despite its importance, the relationship between run order and order-of-addition experiments remains poorly understood. Our research addresses this critical gap by deriving the theoretical lower bound on the total number of factor level changes for ordered order-of-addition designs. We introduce novel construction methods that achieve this minimum, ensuring both cost efficiency and practicality. Additionally, we develop a rigorous framework to eliminate the bias introduced by linear time trends, proposing robust methods to construct time trend-free ordered designs. These methods lead to the establishment of optimal ordered designs that excel under both criteria. The proposed designed orders go beyond theoretical elegance–they are robust to lurking variables in the external environment, making them invaluable for real-world applications. This study not only shines the spotlight on an overlooked dimension of order-of-addition experiments but also delivers solutions that redefine how these experiments should be conducted.
DOI: 10.6084/m9.figshare.30246790.v2
title: Optimal Run Order for Order-of-Addition Experiments

description: Order-of-addition experiments have emerged as a cornerstone in modern experimental design, yet the critical role of run-order has been entirely neglected in the literature. This oversight is surprising, given that the run order can significantly influence the cost, efficiency, and validity of the experiment. Certain run orders are inherently more economical and effective, while suboptimal orders may introduce unnecessary complexities or compromise results. To ensure experimental integrity, an optimal run order must minimize factor level changes, especially when transitions between levels are costly—and safeguard against the detrimental effects of time trends, which can skew factor effect estimates and undermine conclusions. Despite its importance, the relationship between run order and order-of-addition experiments remains poorly understood. Our research addresses this critical gap by deriving the theoretical lower bound on the total number of factor level changes for ordered order-of-addition designs. We introduce novel construction methods that achieve this minimum, ensuring both cost efficiency and practicality. Additionally, we develop a rigorous framework to eliminate the bias introduced by linear time trends, proposing robust methods to construct time trend-free ordered designs. These methods lead to the establishment of optimal ordered designs that excel under both criteria. The proposed designed orders go beyond theoretical elegance—they are robust to lurking variables in the external environment, making them invaluable for real-world applications. This study not only shines the spotlight on an overlooked dimension of order-of-addition experiments but also delivers solutions that redefine how these experiments should be conducted. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.15468/dl.ezfkkn
title: Occurrence Download

description: A dataset containing 4711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((1.53985 45.87147,7.67243 45.87147,7.67243 48.13992,1.53985 48.13992,1.53985 45.87147))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lanius senator"
 ]
}

 The dataset includes 4711 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045170-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30329777
title: Cluster-Randomized Trials with Cross-Cluster Interference

description: The literature on cluster-randomized trials typically allows for interference within but not across clusters. This may be implausible when units are irregularly distributed across space without well-separated communities, as clusters in such cases may not align with significant geographic, social, or economic divisions. This article develops methods for reducing bias due to cross-cluster interference. We first propose an estimation strategy that excludes units not surrounded by clusters assigned to the same treatment arm. We show that this substantially reduces bias relative to conventional difference-in-means estimators without significant cost to variance. Second, we formally establish a bias-variance tradeoff in the choice of clusters: constructing fewer, larger clusters reduces bias due to interference but increases variance. We provide a rule for choosing the number of clusters to balance the asymptotic orders of the bias and variance of our estimator. Finally, we consider unsupervised learning for cluster construction and provide theoretical guarantees for <i>k</i>-medoids. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.30329777.v1
title: Cluster-Randomized Trials with Cross-Cluster Interference

description: The literature on cluster-randomized trials typically allows for interference within but not across clusters. This may be implausible when units are irregularly distributed across space without well-separated communities, as clusters in such cases may not align with significant geographic, social, or economic divisions. This article develops methods for reducing bias due to cross-cluster interference. We first propose an estimation strategy that excludes units not surrounded by clusters assigned to the same treatment arm. We show that this substantially reduces bias relative to conventional difference-in-means estimators without significant cost to variance. Second, we formally establish a bias-variance tradeoff in the choice of clusters: constructing fewer, larger clusters reduces bias due to interference but increases variance. We provide a rule for choosing the number of clusters to balance the asymptotic orders of the bias and variance of our estimator. Finally, we consider unsupervised learning for cluster construction and provide theoretical guarantees for <i>k</i>-medoids. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.26779570
title: Elephant long bone medical CT scan data (DICOMs)

description: from Bader, C., Gilardet, R., Rinder, N., Herridge, V., Hutchinson, J.R., Houssaye, A. 2025. Long bone microanatomy in elephants: microstructural insights into gigantic beasts. Zoological Journal of the Linnean Society 204:slaf008. https://doi.org/10.1093/zoolinnean/zlaf008602MB .zip archive of medical CT scans for RVC specimens2.77GB .zip archive of medical CT scans for NHMUK specimens146MB .zip archive of medical CT scans for UMZC specimens
DOI: 10.6084/m9.figshare.26779570.v2
title: Elephant long bone medical CT scan data (DICOMs)

description: from Bader, C., Gilardet, R., Rinder, N., Herridge, V., Hutchinson, J.R., Houssaye, A. 2025. Long bone microanatomy in elephants: microstructural insights into gigantic beasts. Zoological Journal of the Linnean Society 204:slaf008. https://doi.org/10.1093/zoolinnean/zlaf008602MB .zip archive of medical CT scans for RVC specimens2.77GB .zip archive of medical CT scans for NHMUK specimens146MB .zip archive of medical CT scans for UMZC specimens
DOI: 10.6084/m9.figshare.26779570.v1
title: Elephant long bone medical CT scan data (DICOMs)

description: from Bader, C., Gilardet, R., Rinder, N., Herridge, V., Hutchinson, J.R., Houssaye, A. 2025. Long bone microanatomy in elephants: microstructural insights into gigantic beasts. Zoological Journal of the Linnean Society 204:slaf008. https://doi.org/10.1093/zoolinnean/zlaf008602MB .zip archive of medical CT scans for RVC specimens2.77GB .zip archive of medical CT scans for NHMUK specimens146MB .zip archive of medical CT scans for UMZC specimens
DOI: 10.15468/dl.fj2zfd
title: Occurrence Download

description: A dataset containing 146 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Prionospio bocki",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 146 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045171-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30389136
title: Identification of blood-derived DNA methylation biomarkers of glaucoma and intraocular pressure measurements in three European ancestry cohorts including the Canadian longitudinal study on aging

description: Glaucoma is a major cause of blindness globally and its prevalence rises with age. This study explored systemic blood-derived DNA methylation epigenetic biomarkers for association with glaucoma and intraocular pressure (IOP). Blood-derived DNA methylation (DNAm) was analyzed in 1,201 European participants from the Canadian Longitudinal Study on Aging (CLSA; Illumina EPIC v1 array) and 843 European participants from TwinsUK (450k array). An Epigenome-Wide Association Study (EWAS) for glaucoma and IOP was conducted, adjusting for age, sex, tobacco smoking, and leukocyte cell types. DNAm-based EpiScores estimates for 108 plasma protein levels were evaluated for associations with glaucoma and IOP. Additionally, ‘biological’ age acceleration, estimated using five established DNAm ‘clocks,’ was assessed for glaucoma and IOP and replicated in The Health and Retirement Study (HRS; <i>n</i> = 3,453). EWAS analyses of glaucoma and IOP in individual cohorts did not identify genome-wide significant associations. However, a combined EWAS for overlapping probes in both cohorts identified two epigenome-wide significant CpGs: cg03498697 in the <i>FRMD3</i> promoter (<i>p</i> = 6.86x10<sup>−8</sup>) and cg06044751 intronically within <i>PALLD</i> (<i>p</i> = 1.76x10<sup>−7</sup>). EpiScore analysis revealed one IOP Bonferroni-significant association with TNFRSF1B levels in the meta-analysis of both cohorts (<i>p</i> = 1.31x10<sup>−4</sup>). DNAm ‘clock’ analysis in the HRS identified a GrimAge-positive age acceleration associated with glaucoma (<i>p</i> = 0.01). This study identified significant epigenetic blood-derived biomarkers that are associated with glaucoma and IOP. These findings warrant replication in larger and more diverse populations as well as via longitudinal analysis to assess their robustness and potential predictive power.