cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17028/rd.lboro.31205845.v1
title: Supplementary information files for "Perioperative medicine for older people undergoing surgery scale up (POPS-SUp): study protocol"

description: Supplementary files for article "Perioperative medicine for older people undergoing surgery scale up (POPS-SUp): study protocol"<br><br><b>Background</b>Surgery provides definitive management of many age-related diseases, relieving symptoms or extending life. Age-related physiological decline, multimorbidity, and frailty predispose older people to postoperative complications and incomplete functional recovery, with resultant health and social care costs. These age-related conditions can be optimized using Comprehensive Geriatric Assessment (CGA), thus mitigating perioperative risk to improve clinical outcomes with cost-effectiveness. National organizations advocate CGA-based services for older surgical patients. However, there is variation in the provision of CGA-based perioperative medicine for older people undergoing surgery (POPS) services across the UK National Health Service, resulting in inequitable access for older surgical patients at higher risk, unnecessary deaths, complications, and financial cost. The aim of the POPS Scale Up (POPS-SUp) study is to determine whether CGA-based POPS services can be implemented at scale to cost-effectively improve clinical outcomes for older patients undergoing surgery.<b>Methods</b>A mixed-methods hybrid implementation–effectiveness interrupted time series study will examine the use of a coproduced implementation strategy to embed CGA-based POPS services at scale in the UK. Co-primary implementation–effectiveness outcomes will be used, namely reach and length of hospital stay, respectively. Evaluation will include an embedded process evaluation, quantitative evaluation of clinical effectiveness and cost-effectiveness, and qualitative appraisal of patient and staff experience. The proposed analysis is to embed a process evaluation using real-time framework analysis, enabling iterative refinement and evaluation of the implementation strategy. Accepted interrupted time series analysis will be used to examine and compare outcomes per participating site. A predefined dissemination strategy has been co-designed with patients/carers, clinical community of practice, and organizational bodies.<b>Conclusion</b>The anticipation is that POPS-SUp will have impact at the individual (patient and clinician), organizational, and policy levels in the perioperative setting, but with additional potential application to other clinical settings.Registration numbers: ISRCTN 45327 (https://www.isrctn.com/); NIHR 157443 (https://www.nihr.ac.uk/).
DOI: 10.15468/dl.7zab39
title: Occurrence Download

description: A dataset containing 338 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Portugal",
 "TaxonKey is Alosa fallax"
 ]
}

 The dataset includes 338 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001716-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/jyhk5f
title: Table_S5.xlsx

description: Table S5. Differentially expressed genes between groups in each cell type 
List of the differentially expressed genes (DEGs) between conditions (submerged (control) vs air-liquid interface (ALI)) in each cell type (presented in separate tabs) identified by fitting Negative Binomial generalized linear models on pseudo-bulk data in each cell type independently. The col-umns give the gene name, the log2(fold change) (logFC), the log counts per million (CPM) reads (logCPM), the likelihood ratio (LR), the p-value (LR test) (pvalue), the adjusted p-value (Benjamini-Hochberg procedure) (p.adjust), and the over or under-expressed state of the gene in the “ALI” condition versus the “control” condition (state), respectively. TA: transit amplifying cells.
DOI: 10.5281/zenodo.18429228
title: Research trends and perspectives on the use of mesocosms in ecology and ecotoxicology of amphibians and reptiles – A meta-analytic review_Database
DOI: 10.5281/zenodo.18429229
title: Research trends and perspectives on the use of mesocosms in ecology and ecotoxicology of amphibians and reptiles – A meta-analytic review_Database
DOI: 10.57745/iwdmyh
title: Table_S6.xlsx

description: Table S6. Biological pathways enriched in differentially expressed genes between conditions in each cell type. 
List of biological pathways enriched in differentially expressed genes (DEGs) between conditions (submerged (control) vs air-liquid interface (ALI)) per cell type. Columns give the identifier of the gene ontology (ID), the pathway name (Description), the number of marker genes over the number of genes in the biological pathway (GeneRatio), total number of genes in the biological pathway over the total number of genes expressed in the single-cell RNA-sequencing dataset (BgRatio), the p-value (pvalue) and the adjusted p-value (p.adjust) (Benjamini-Hochberg procedure) of the fisher exact test, and the list of DEGs in the biological pathway (geneID). TA: transit amplifying cells.
DOI: 10.57745/jbl1xi
title: Table_S9.xlsm

description: Table S9. Sequences of qPCR primers
Forward and reverse sequences of primers used for qPCR analysis of rabbit genes.
DOI: 10.57745/zzjkep
title: Table_S4.xlsx

description: Table S4. Biological pathways enriched in the marker genes of each cell type in the air-liquid interface condition
List of biological pathways enriched in the marker genes of each cell type (presented in separate tabs) in the organoid cell monolayers under air-liquid interface conditions. Columns give the identi-fier of the gene ontology (ID), the pathway name (Description), the number of marker genes over the number of genes in the biological pathway (GeneRatio), total number of genes in the biological pathway over the total number of genes expressed in the single-cell RNA-sequencing dataset (BgRa-tio), the p-value (pvalue) and the adjusted p-value (p.adjust) (Benjamini-Hochberg procedure) of the fisher exact test, and the list of marker genes in the biological pathway (geneID), respectively. TA: transit amplifying cells.
DOI: 10.57745/ew8wyv
title: Table_S3.xlsx

description: Table S3. Biological pathways enriched in the marker genes of each cell type in the control con-dition
List of biological pathways enriched in the marker genes of each cell type (presented in separate tabs) in the organoid cell monolayers under submerged conditions. Columns give the identifier of the gene ontology (ID), the pathway name (Description), the number of marker genes over the number of genes in the biological pathway (GeneRatio), total number of genes in the biological pathway over the total number of genes expressed in the single-cell RNA-sequencing dataset (BgRa-tio), the p-value (pvalue) and the adjusted p-value (p.adjust) (Benjamini-Hochberg procedure) of the Fisher exact test, and the list of marker genes in the biological pathway (geneID), respectively. TA: transit amplifying cells.
DOI: 10.57745/uvbvko
title: Table_S1.xlsx

description: Table S1. Marker genes of each cell type in the control condition
List of the marker genes of each cell type (presented in separate tabs) in the organoid cell monolay-ers under submerged conditions identified by using the FindAllMarkers function of Seurat. Col-umns give the gene name (gene), the p-value of the Wilcoxon rank test (pvalue), the adjusted p-value (Bonferroni procedure) (p.adjust), the average log2 fold-change (avg_log2FC), the percentage of cells expressing the gene in the cell type indicated in the tab name (pct.1) and the percentage of cells expressing the gene in all other cell types (pct.2). TA: transit amplifying cells.
DOI: 10.57745/7wniyj
title: Table_S7.tab

description: Table S7. Cell-cell communication probabilities across cellular pathways for the in vivo, the con-trol and the air-liquid interface conditions
List of the communication probabilities between all pairs of cell types for multiple signaling path-ways for the submerged (control) and air-liquid interface conditions (presented in separate tabs). Columns provide the names of the senders (Senders), receivers (Receivers), the pathways in which the senders and the receivers are involved in (Pathway), and the estimated probability of communi-cation between the senders and the receivers (Probability of communication).
DOI: 10.57745/qu0ca4
title: Table_S2.xlsx

description: Table S2. Marker genes of each cell type in the air-liquid interface condition
List of the marker genes of each cell type (presented in separate tabs) in the organoid cell monolay-ers under air-liquid interface conditions identified by using the FindAllMarkers function of Seurat. Columns give the gene name (gene), the p-value of the Wilcoxon rank test (pvalue), the adjusted p-value (Bonferroni procedure) (p.adjust), the average log2 fold-change (avg_log2FC), the percentage of cells expressing the gene in the cell type indicated in the tab name (pct.1) and the percentage of cells expressing the gene in all other cell types (pct.2). TA: transit amplifying cells.
DOI: 10.57745/oq41nu
title: Table_S8.tab

description: Table S8. Cell-cell communication probabilities based on the expression of ligand-receptor pairs for the in vivo, the control and the air-liquid interface conditions
List of the communication probabilities between all pairs of cell types based on several pairs of ligand-receptors for the submerged (control) and air-liquid interface (presented in separate tabs). Columns provide the names of the senders (Senders), the receivers (Receivers), the pathways in which the senders and the receivers are involved in (Pathway), the ligand-receptor pairs (Ligand-receptor pairs) and the estimated probability of communication between the senders and the receiv-ers (Probability of communication).
DOI: 10.57745/xvpqxj
title: Figure S1.TIF

description: Figure S1: Quality controls of the organoid single-cell transcriptomics
(A) Number of expressed genes, counts, and percentage of mitochondrial gene reads per cell and sample before (top panels) and after (bottom panels) filtering for the submerged (control) and air-liquid interface (ALI) conditions.
(B) Uniform Manifold Approximation and Projection (UMAP) of cells from individual samples (inserts) of the control and ALI conditions colored per conditions. 
(C) UMAP colored by the number of expressed genes, total counts, or percentage of mitochondrial gene reads per cell for the control and ALI conditions.
(D) UMAP colored by the clusters identified with the FindClusters function and expression of the top 10 genes with the highest average log2(fold change) of each cluster. For a given cluster, markers were ordered by decreasing log2(fold change) of the expression between this cluster and the other clusters. Numbers and colored bars on the top indicate cell clusters.
DOI: 10.15468/dl.xpch6k
title: Occurrence Download

description: A dataset containing 349 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((13.57286 -1.63611,13.54883 -1.62792,13.52882 -1.62667,13.51118 -1.62041,13.49896 -1.62222,13.48562 -1.62653,13.47215 -1.62542,13.4627 -1.62389,13.45812 -1.61958,13.45242 -1.61666,13.44228 -1.6175,13.43797 -1.6243,13.42922 -1.6375,13.43339 -1.64375,13.44839 -1.64667,13.46159 -1.65209,13.48458 -1.65375,13.49055 -1.64917,13.5 -1.65306,13.50945 -1.64917,13.51486 -1.64514,13.52278 -1.64987,13.52778 -1.64764,13.53195 -1.64486,13.53918 -1.64653,13.54918 -1.65112,13.55821 -1.65556,13.56335 -1.65292,13.57557 -1.6482,13.57286 -1.63611))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 349 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001718-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/rarrsy
title: Figure S3.TIF

description: Figure S3: The air-liquid condition promotes the differentiation of enteroendocrine cells 
Uniform Manifold Approximation and Projection (UMAP) of integrated single cell transcriptomics datasets of caecum epithelial cells in vivo and of organoid cell monolayers cultured submerged (control) or with air-liquid interface (ALI), colored by the expression of the enteroendocrine cell markers CHGA and CHGB with all cells (first row), or only with cells from each condition (other rows). The dotted circle highlights the localization of in vivo enteroendocrine cells on the UMAP.
DOI: 10.57745/7xvmhm
title: Figure S4.TIF

description: Figure S4: Morphology of organoid cell monolayers cultured in immerged or ALI conditions
Confocal microscopy observation of organoid cell monolayers stained with DAPI (nuclei, blue), phalloidin (actin, pink), and UEA-1 (fucosylated glycoconjugates). Two representative cross-sections (xz) are shown in each condition. Scale bars represent 20 µm. 
(A) Immerged condition (day 5 after cell seeding)
(B) ALI condition (day 5 after cell seeding, 48 hours after removal of the apical medium)
(C) ALI condition (day 7 after cell seeding, 96 hours after removal of the apical medium)
DOI: 10.57745/pcloq4
title: Figure S2.TIF

description: Figure S2: Genes involved in oxidative phosphorylation modulated by the culture in air-liquid interface across cell types in organoid cell monolayers
Differentially expressed genes from the KEGG pathway hsa00190 “Oxidative phosphorylation” are represented with the significance (log10(adjusted P value, color) and fold change sign (red for over expressed and blue for under expressed genes in the air-liquid interface condition compared to submerged condition). The size of the dot corresponds to the percentage of cells expressing the gene in the cell type.
DOI: 10.57745/ucqqvk
title: Single cell transcriptomics reveals that air-liquid interface culture promotes goblet cell differen-tiation and inhibits glycolysis in organoid cell monolayers

description: Faithfully recapitulating the cellular heterogeneity of the intestinal epithelium is essential when using organoid models. Air-liquid interface (ALI) culture has been shown to promote secretory cell dif-ferentiation but its impact on gene expression in each epithelial cell type remains unclear. In this study, we used single-cell RNA sequencing (scRNA-seq) to characterize the cellular heterogeneity of rabbit caecum-derived organoid monolayers grown under immerged or ALI conditions. We then compared these organoid cell type-specific gene expression profiles to a scRNA-seq atlas of the rabbit caecal epithelium in vivo. We selected the rabbit model notably because, unlike mice, it pos-sesses BEST4⁺ epithelial cells, a newly discovered subset of mature absorptive cells. Our analysis revealed a high degree of transcriptomic similarity between in vivo and organoid-derived stem and transit-amplifying cells. ALI culture markedly enhanced the differentiation of the secretory lineage, especially goblet cells, which transcriptome closely resembled that of in vivo goblet cells. Further-more, ALI was the only condition allowing the detection of enteroendocrine cells. BEST4⁺ cells, however, were absent from organoids in immerged or ALI conditions despite their presence in vivo. In addition, ALI culture led to a consistent downregulation of hypoxia and glycolysis-associated genes across all cell types, which suggests a metabolic shift likely driven by increased oxygen avail-ability in ALI conditions. Cell-cell communication analyses further indicated that ALI more closely mirrored in vivo patterns than immerged condition. Altogether, these results demonstrate that ALI culture allows to better recapitulate the in vivo cellular heterogeneity and molecular signatures of the intestinal epithelium.
DOI: 10.15468/dl.65hzkn
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Psychine stylosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 42 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001719-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mkdvkz
title: Occurrence Download

description: A dataset containing 1080 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acrostichum aureum",
 "HasCoordinate is true",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2010",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "not" : {
 "HasGeospatialIssue" : [
 "is true"
 ]
 }
 }
 ]
}

 The dataset includes 1080 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001720-260129131611470/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.31205083
title: In Silico Plasticity Ceiling Mapping of the MERS-CoV Nucleocapsid SR-Linker (aa 181 - 248): CPS-Guided Boundary Instantiation Reveals Structural Constraints That Block Autonomous Backbone Optimization

description: This dataset documents in-silico boundary mapping of the MERS-CoV nucleocapsid (N) gene's sole permissive zone that is the <b>SR-linker </b>(aa <b>181-248</b>) using Codon Permissiveness Score (<b>CPS</b>) constraints derived from <b>1,746</b> global isolates (Zenodo 10.5281/zenodo.18209279). We computationally instantiate <b>four theoretical enhancement vectors</b><b> </b>at the absolute viable limit permitted by purifying selection: (<b>1</b>) phase separation via S/T expansion, (<b>2</b>) nuclear localization signal (<b>NLS</b>) gain via K/R enrichment, (<b>3</b>) weak IFN antagonism via phospho-mimetic D/E substitutions, (<b>4</b>) silent codon optimization for human adaptation. Critically, the SR-linker's architecture permissive residues (<b>σ ≥ 0.15</b>) interspersed with constrained "guardrails" (σ &lt; 0.15) structurally blocks contiguous homopolymer expansion and dense basic residue clustering, permitting only dispersed substitutions (e.g., 5 phospho-mimetics viable; ≥8 contiguous S/T residues impossible). This constraint architecture acts as an <b>evolutionary brake </b>against autonomous N-mediated backbone enhancement. Outputs include boundary-sequence FASTAs, residue-level CPS annotations, and sentinel rules for genomic surveillance (e.g., N-SR-IFN-1: ≥3 D/E at positions 192/195/198/204/210). All instantiations are strictly computational, no experimental protocols or synthesis instructions are provided. This work supports defensive anticipatory surveillance logic for early-warning detection of natural isolates approaching theoretical fitness ceilings.<b>Note:</b>This dataset is part of a series of MERS-CoV genomic surveillance studies conducted independently by Tahir HB for pandemic preparedness, acknowledging that historically constrained pathogens may pose global risk under exceptional evolutionary or epidemiological conditions.
DOI: 10.6084/m9.figshare.31205083.v1
title: In Silico Plasticity Ceiling Mapping of the MERS-CoV Nucleocapsid SR-Linker (aa 181 - 248): CPS-Guided Boundary Instantiation Reveals Structural Constraints That Block Autonomous Backbone Optimization

description: This dataset documents in-silico boundary mapping of the MERS-CoV nucleocapsid (N) gene's sole permissive zone that is the <b>SR-linker </b>(aa <b>181-248</b>) using Codon Permissiveness Score (<b>CPS</b>) constraints derived from <b>1,746</b> global isolates (Zenodo 10.5281/zenodo.18209279). We computationally instantiate <b>four theoretical enhancement vectors</b><b> </b>at the absolute viable limit permitted by purifying selection: (<b>1</b>) phase separation via S/T expansion, (<b>2</b>) nuclear localization signal (<b>NLS</b>) gain via K/R enrichment, (<b>3</b>) weak IFN antagonism via phospho-mimetic D/E substitutions, (<b>4</b>) silent codon optimization for human adaptation. Critically, the SR-linker's architecture permissive residues (<b>σ ≥ 0.15</b>) interspersed with constrained "guardrails" (σ &lt; 0.15) structurally blocks contiguous homopolymer expansion and dense basic residue clustering, permitting only dispersed substitutions (e.g., 5 phospho-mimetics viable; ≥8 contiguous S/T residues impossible). This constraint architecture acts as an <b>evolutionary brake </b>against autonomous N-mediated backbone enhancement. Outputs include boundary-sequence FASTAs, residue-level CPS annotations, and sentinel rules for genomic surveillance (e.g., N-SR-IFN-1: ≥3 D/E at positions 192/195/198/204/210). All instantiations are strictly computational, no experimental protocols or synthesis instructions are provided. This work supports defensive anticipatory surveillance logic for early-warning detection of natural isolates approaching theoretical fitness ceilings.<b>Note:</b>This dataset is part of a series of MERS-CoV genomic surveillance studies conducted independently by Tahir HB for pandemic preparedness, acknowledging that historically constrained pathogens may pose global risk under exceptional evolutionary or epidemiological conditions.
DOI: 10.15468/dl.wnxg7b
title: Occurrence Download

description: A dataset listing the 1039 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-1.32908 47.04221,-1.32476 47.04008,-1.32401 47.03974,-1.31959 47.0379,-1.31497 47.03631,-1.31018 47.03497,-1.30526 47.03389,-1.30023 47.03308,-1.29512 47.03254,-1.28996 47.03228,-1.28479 47.03229,-1.27964 47.03258,-1.27454 47.03315,-1.26951 47.03399,-1.2646 47.03509,-1.25983 47.03645,-1.25523 47.03807,-1.25083 47.03993,-1.24666 47.04202,-1.24274 47.04432,-1.23909 47.04683,-1.23575 47.04952,-1.23272 47.05239,-1.23215 47.05298,-1.22947 47.05598,-1.22715 47.05912,-1.22519 47.06237,-1.22361 47.06571,-1.22242 47.06913,-1.22161 47.07261,-1.22121 47.07611,-1.22121 47.07963,-1.22161 47.08313,-1.22241 47.0866,-1.22361 47.09002,-1.22519 47.09337,-1.22715 47.09662,-1.22947 47.09975,-1.23215 47.10276,-1.23516 47.10561,-1.23849 47.10829,-1.23977 47.10917,-1.24123 47.11029,-1.2449 47.11271,-1.24504 47.1128,-1.24891 47.11498,-1.25301 47.11695,-1.25732 47.1187,-1.26181 47.12023,-1.26645 47.12152,-1.27123 47.12256,-1.27611 47.12336,-1.27618 47.12337,-1.28217 47.12398,-1.28821 47.12422,-1.2891 47.12423,-1.2942 47.12413,-1.29928 47.12377,-1.3043 47.12314,-1.30923 47.12224,-1.31405 47.12109,-1.31872 47.11969,-1.32322 47.11804,-1.32752 47.11617,-1.33159 47.11407,-1.33541 47.11176,-1.33896 47.10925,-1.34222 47.10657,-1.34516 47.10372,-1.34777 47.10073,-1.35003 47.09761,-1.35193 47.09437,-1.35346 47.09105,-1.35461 47.08766,-1.35537 47.08421,-1.35573 47.08074,-1.35576 47.08021,-1.35573 47.07668,-1.35529 47.07317,-1.35446 47.06968,-1.35323 47.06626,-1.3516 47.06291,-1.3496 47.05965,-1.34724 47.05652,-1.34452 47.05352,-1.34147 47.05067,-1.3381 47.048,-1.33718 47.04738,-1.3369 47.04715,-1.33314 47.04457,-1.32908 47.04221))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is 1928bdf0-f5d2-11dc-8c12-b8a03c50a862",
 "Year 2005-2026"
 ]
}

 The dataset's 1039 records were derived from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001713-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.