cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26500419
title: Melatonin Improves Oxidative Stress Injury in Retinopathy of Prematurity by Targeting miR-23a-3p/Nrf2

description: Melatonin has promising protective effects for retinopathy. However, its roles in retinopathy of prematurity (ROP) and the underlying mechanisms remain unknown. We aimed to explore its roles and mechanisms in a ROP model. Hematoxylin and eosin staining were used to observe the morphology of the retina. Immunofluorescence was used to detect positive (Nrf2+ and VEGF+) cells. Immunohistochemistry was used to detect the level of nuclear expression of PCNA in retinal tissue. Transmission electron microscope (TEM) was used to observe the morphology and structure of pigment cells. qRT-PCR was used to assay the expression of miR-23a-3p, Nrf2, and HO-1. Western blotting was used to detect the expression of Nrf2, HO-1, β-actin, and Lamin B1. Melatonin or miR-23a-3p antagomir treatment could ameliorate the Oxygen-induced pathological changes, increased the expression of Nrf2 and HO-1, SOD, and GSH-Px, and decreased the expression of VEGF, miR-23a-3p, MDA and the apoptosis in the ROP model. Further target prediction and luciferase reporter assays confirmed the targeted binding relationship between miR-23a-3p and Nrf2. Our study showed that melatonin could ameliorate H<sub>2</sub>O<sub>2</sub>-induced apoptosis and oxidative stress injury in RGC cells by mediating miR-23a-3p/Nrf2 signaling pathway, thereby improving retinal degeneration.
DOI: 10.6084/m9.figshare.26500419.v1
title: Melatonin Improves Oxidative Stress Injury in Retinopathy of Prematurity by Targeting miR-23a-3p/Nrf2

description: Melatonin has promising protective effects for retinopathy. However, its roles in retinopathy of prematurity (ROP) and the underlying mechanisms remain unknown. We aimed to explore its roles and mechanisms in a ROP model. Hematoxylin and eosin staining were used to observe the morphology of the retina. Immunofluorescence was used to detect positive (Nrf2+ and VEGF+) cells. Immunohistochemistry was used to detect the level of nuclear expression of PCNA in retinal tissue. Transmission electron microscope (TEM) was used to observe the morphology and structure of pigment cells. qRT-PCR was used to assay the expression of miR-23a-3p, Nrf2, and HO-1. Western blotting was used to detect the expression of Nrf2, HO-1, β-actin, and Lamin B1. Melatonin or miR-23a-3p antagomir treatment could ameliorate the Oxygen-induced pathological changes, increased the expression of Nrf2 and HO-1, SOD, and GSH-Px, and decreased the expression of VEGF, miR-23a-3p, MDA and the apoptosis in the ROP model. Further target prediction and luciferase reporter assays confirmed the targeted binding relationship between miR-23a-3p and Nrf2. Our study showed that melatonin could ameliorate H<sub>2</sub>O<sub>2</sub>-induced apoptosis and oxidative stress injury in RGC cells by mediating miR-23a-3p/Nrf2 signaling pathway, thereby improving retinal degeneration.
DOI: 10.15468/dl.2bnewm
title: Occurrence Download

description: A dataset listing the 34 species recorded in GBIF matching the query:
{
 "and" : [
 "Year is 2010",
 "TaxonKey is Litoria Tschudi, 1838"
 ]
}

 The dataset's 34 records were derived from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011013-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2ujs3u
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year is 1900",
 "TaxonKey is Vulpes vulpes (Linnaeus, 1758)"
 ]
}

 The dataset includes 70 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011017-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14792463
title: DynamicAtlas Demo Dataset

description: This data respository contains the Demo Dataset used in the tutorial for the MATLAB-based code in DynamicAtlas.
DOI: 10.5281/zenodo.14649141
title: A 2,000-year-long record of reproduction in Santa Barbara Basin benthic foraminifera

description: This dataset accompanies a submission to Proceedings of the Royal Society B entitled "A nineteenth and twentieth century reproductive regime shift in benthic foraminifera from the Santa Barbara Basin, California."

The dataset includes measurements of individual reproductive life history traits for 20,293 individuals. Specifically, these are reproductive mode (megalospheric or microspheric, via the the size of the proloculus, or first chamber) and accumulation rate (a time- and area-normalized test count).

Paper Abstract: Long-term records that span the past several centuries and capture within-population variation are critical for distinguishing ephemeral ecosystem changes from regime shifts. Using a ~2 kyr record of reproductive life history from the central Santa Barbara Basin, we examined population trends in reproductive mode and accumulation rate (i.e., reproductive output) across four species in the biserial benthic foraminiferan genus Bolivina. Bolivina populations were consistently dominated by asexually-produced individuals until the mid-nineteenth century, after which they exhibit an increase in variance and decrease in mean proportion of asexualy-produced individuals. At the same time, they rundergo an order-of-magnitude decline in accumulation rate. The magnitude and persistence of these changes suggests that the nineteenth and twentieth century represent a life history regime shift. Compounding effects of anthropogenic impacts and long-term trends in the California Current system (such as heightened deoxygenation and altered sedimentation regimes) may have pushed Santa Barbara Basin towards increased investment in sexual reproduction.
DOI: 10.5281/zenodo.14649140
title: A 2,000-year-long record of reproduction in Santa Barbara Basin benthic foraminifera

description: This dataset accompanies a submission to Proceedings of the Royal Society B entitled "A nineteenth and twentieth century reproductive regime shift in benthic foraminifera from the Santa Barbara Basin, California."

The dataset includes measurements of individual reproductive life history traits for 20,293 individuals. Specifically, these are reproductive mode (megalospheric or microspheric, via the the size of the proloculus, or first chamber) and accumulation rate (a time- and area-normalized test count).

Paper Abstract: Long-term records that span the past several centuries and capture within-population variation are critical for distinguishing ephemeral ecosystem changes from regime shifts. Using a ~2 kyr record of reproductive life history from the central Santa Barbara Basin, we examined population trends in reproductive mode and accumulation rate (i.e., reproductive output) across four species in the biserial benthic foraminiferan genus Bolivina. Bolivina populations were consistently dominated by asexually-produced individuals until the mid-nineteenth century, after which they exhibit an increase in variance and decrease in mean proportion of asexualy-produced individuals. At the same time, they rundergo an order-of-magnitude decline in accumulation rate. The magnitude and persistence of these changes suggests that the nineteenth and twentieth century represent a life history regime shift. Compounding effects of anthropogenic impacts and long-term trends in the California Current system (such as heightened deoxygenation and altered sedimentation regimes) may have pushed Santa Barbara Basin towards increased investment in sexual reproduction.
DOI: 10.5281/zenodo.14799313
title: A 2,000-year-long record of reproduction in Santa Barbara Basin benthic foraminifera

description: This dataset accompanies a submission to Proceedings of the Royal Society B entitled "A nineteenth and twentieth century reproductive regime shift in benthic foraminifera from the Santa Barbara Basin, California."

The dataset includes measurements of individual reproductive life history traits for 20,293 individuals. Specifically, these are reproductive mode (megalospheric or microspheric, via the the size of the proloculus, or first chamber) and accumulation rate (a time- and area-normalized test count).

Paper Abstract: Long-term records that span the past several centuries and capture within-population variation are critical for distinguishing ephemeral ecosystem changes from regime shifts. Using a ~2 kyr record of reproductive life history from the central Santa Barbara Basin, we examined population trends in reproductive mode and accumulation rate (i.e., reproductive output) across four species in the biserial benthic foraminiferan genus Bolivina. Bolivina populations were consistently dominated by asexually-produced individuals until the mid-nineteenth century, after which they exhibit an increase in variance and decrease in mean proportion of asexualy-produced individuals. At the same time, they rundergo an order-of-magnitude decline in accumulation rate. The magnitude and persistence of these changes suggests that the nineteenth and twentieth century represent a life history regime shift. Compounding effects of anthropogenic impacts and long-term trends in the California Current system (such as heightened deoxygenation and altered sedimentation regimes) may have pushed Santa Barbara Basin towards increased investment in sexual reproduction.
DOI: 10.15468/dl.m74cut
title: Occurrence Download

description: A dataset containing 307 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhina Bloch & Schneider, 1801"
 ]
}

 The dataset includes 307 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011018-250127130748423/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.28340757
title: Additional file 2 of Activity-based chemical proteomics reveals caffeic acid ameliorates pentylenetetrazol-induced seizures by covalently targeting aconitate decarboxylase 1

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.28340757.v1
title: Additional file 2 of Activity-based chemical proteomics reveals caffeic acid ameliorates pentylenetetrazol-induced seizures by covalently targeting aconitate decarboxylase 1

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.28340760
title: Additional file 3 of Activity-based chemical proteomics reveals caffeic acid ameliorates pentylenetetrazol-induced seizures by covalently targeting aconitate decarboxylase 1

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.28340760.v1
title: Additional file 3 of Activity-based chemical proteomics reveals caffeic acid ameliorates pentylenetetrazol-induced seizures by covalently targeting aconitate decarboxylase 1

description: Supplementary Material 3
DOI: 10.15468/dl.m3bseg
title: Occurrence Download

description: A dataset containing 368052 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2024-12-09",
 "EventDate is less than or equal to 2025-01-08",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 368052 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011005-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m9g4zr
title: Occurrence Download

description: A dataset containing 2777 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Dominica",
 "PublishingOrg is one of (bc092ff0-02e4-11dc-991f-b8a03c50a862, b4640710-8e03-11d8-b956-b8a03c50a862, 66522820-055c-11d8-b84e-b8a03c50a862, b554c320-0560-11d8-b851-b8a03c50a862, 8483a1f0-1032-11db-ae00-b8a03c50a862, 2b8e48b0-812d-11de-86fe-b8a03c50a862, ff418020-1d67-11d9-8435-b8a03c50a862, ccd1ddc0-6c21-11de-8224-b8a03c50a862, 845f3630-812c-11de-86fe-b8a03c50a862)",
 "TaxonKey is Anolis oculatus (Cope, 1879)"
 ]
}

 The dataset includes 2777 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011020-250127130748423/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.28340835.v1
title: Additional file 1 of Integrative analysis of immunogenic PANoptosis and experimental validation of cinobufagin-induced activation to enhance glioma immunotherapy

description: Supplementary Material 1.
DOI: 10.34740/kaggle/dsv/10656843
title: Layline Shareholder activism dataset
DOI: 10.15468/dl.ucmtdr
title: Occurrence Download

description: A dataset containing 49325 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2025-01-09",
 "EventDate is less than or equal to 2025-02-08",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 49325 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011021-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x7h8f5
title: Occurrence Download

description: A dataset containing 652 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lycium afrum L."
 ]
}

 The dataset includes 652 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011022-250127130748423/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.28340898
title: Additional file 2 of Engineering a bacterial toxin deaminase from the DYW-family into a novel cytosine base editor for plants and mammalian cells

description: Additional file 2: Supplementary tables S1-S6. Table S1. Genotyping results of regenerated T0 plants transformed with SsdAG103S-v1-CBE or hA3A-CBE. Table S2. Inheritance of mutations in rice T1 lines. Table S3. Analyzing potential Cas-dependent off-target editing of SsdAG103S-v1-CBE in T0 plants. Table S4. Plasmids used in this study. Table S5. Oligos used in this study. Table S6. Top 50 candidates from the AlphaFold Protein Structure Database (AFDB50) with structural similarity to SsdAtox.
DOI: 10.6084/m9.figshare.28340901
title: Additional file 1 of Regulatory signatures involved in the cell cycle pathway contribute to egg production heterosis in chicken

description: Additional file 1: Fig. S1 The summary of sample sequence statistics including clean reads, clean bases, Q20, Q30, GC content and overall mapping rate. Fig. S2 The PCA for transcriptome profiles of purebreds and crossbreds in each laying stage. Fig. S3 Scale independence and mean connectivity for purebreds and crossbreds using various soft threshold powers. Fig. S4 Venn diagram showing the overlapped GO terms enriched by EN-related module genes in each genetic group. Fig. S5 Pairwise module preservation of gene co-expression networks between the crossbreds and their parents. Dashed red and blue lines represent the Zsummary thresholds for strong (Zsummary &gt; 10) and weak to moderate (2 &lt; Zsummary &lt; 10) preservation levels, respectively. Colored dots represent the corresponding modules in the reference network, and the module size is the number of overlapped genes within each reference module. Fig. S6 The cluster profiles of consensus modules (CMs) and group-specific modules for crossbred WY (a) and crossbred YW (b) compared to their parents, respectively. Fig. S7 The consensus and divergence of gene co-expression networks between the crossbred YW and its parents (WW and YY) during the 5 laying stages. (a) Hierarchical cluster dendrogram showing consensus gene co-expression modules (CMs) among WW, YY and YW. The red line above is the cut height (0.995) for CM identification. CM colors are labeled independent of the separately identified modules in each group. (b) The relationships between global and group specific co-expression networks. The vertical axis represents CMs. The horizontal axis represents modules within each group (c) The relationships among eigengenes of CMs in each group. (d) The expression patterns of eigengenes of CMs in WW, YY and YW during 5 laying stages. Blue and red represent lesser and greater expression, respectively. (e) Heatmap showing KEGG pathways significantly enriched by genes in each CM. Color intensity represents the significance of enrichment. Fig. S8. Hub genes in the preserved gene co-expression network underlying the dynamic egg production heterosis. (a) Upset plot showing the common hub genes among WW, YY and YW. (b) KEGG pathways enrichment analysis for the common hub genes. The color bar represents the ratio of gene numbers in each pathway, and the black dot represents the significance (adjusted P value) of the KEGG pathway. (c) The differential expression patterns during 5 laying stages for hub genes involved in the cell cycle. The cell colors represent differential expression patterns, and the colors on the left represent the corresponding CM and KEGG pathway to which each gene belongs, respectively.
DOI: 10.6084/m9.figshare.28340903.v1
title: Additional file 1 of Successful management of catheter injury or refractory infection by partial replantation of peritoneal dialysis catheters: a retrospective observational study

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.28340904.v1
title: Additional file 2 of Regulatory signatures involved in the cell cycle pathway contribute to egg production heterosis in chicken

description: Additional file 2: Table S1 The summary of population phenotypic value in the 5 sampling weeks. Table S2a Significant GO terms enriched by genes in the modules related to the egg number for purebreds and crossbreds; Table S2b Significant KEGG pathways enriched by genes in the modules related to the egg number for purebreds and crossbreds. Table S3a The consensus genes and their connectivity (kME) among WW, WY and YY; Table S3b The consensus genes and their connectivity (kME) among WW, YW and YY. Table S4a Significant KEGG pathways enriched by genes in the consensus modules (CMs) detected for WW, YY and WY; Table S4b Significant KEGG pathways enriched by genes in the consensus modules (CMs) detected for WW, YY and YW. Table S5a Hub genes of WW screened by module membership value (kME) and its P value; Table S5b Hub genes of YY screened by module membership value (kME) and its P value; Table S5c Hub genes of WY screened by module membership value (kME) and its P value. Table S6a Significant GO terms enriched by hub genes shared by WW, YY and WY; Table S6b Significant GO terms enriched by hub genes shared by WW, YY and YW. Table S7a Significant KEGG pathways enriched by hub genes shared by WW, YY and WY; Table S7b Significant KEGG pathways enriched by hub genes shared by WW, YY and YW.
DOI: 10.6084/m9.figshare.28340898.v1
title: Additional file 2 of Engineering a bacterial toxin deaminase from the DYW-family into a novel cytosine base editor for plants and mammalian cells

description: Additional file 2: Supplementary tables S1-S6. Table S1. Genotyping results of regenerated T0 plants transformed with SsdAG103S-v1-CBE or hA3A-CBE. Table S2. Inheritance of mutations in rice T1 lines. Table S3. Analyzing potential Cas-dependent off-target editing of SsdAG103S-v1-CBE in T0 plants. Table S4. Plasmids used in this study. Table S5. Oligos used in this study. Table S6. Top 50 candidates from the AlphaFold Protein Structure Database (AFDB50) with structural similarity to SsdAtox.
DOI: 10.6084/m9.figshare.28340901.v1
title: Additional file 1 of Regulatory signatures involved in the cell cycle pathway contribute to egg production heterosis in chicken

description: Additional file 1: Fig. S1 The summary of sample sequence statistics including clean reads, clean bases, Q20, Q30, GC content and overall mapping rate. Fig. S2 The PCA for transcriptome profiles of purebreds and crossbreds in each laying stage. Fig. S3 Scale independence and mean connectivity for purebreds and crossbreds using various soft threshold powers. Fig. S4 Venn diagram showing the overlapped GO terms enriched by EN-related module genes in each genetic group. Fig. S5 Pairwise module preservation of gene co-expression networks between the crossbreds and their parents. Dashed red and blue lines represent the Zsummary thresholds for strong (Zsummary &gt; 10) and weak to moderate (2 &lt; Zsummary &lt; 10) preservation levels, respectively. Colored dots represent the corresponding modules in the reference network, and the module size is the number of overlapped genes within each reference module. Fig. S6 The cluster profiles of consensus modules (CMs) and group-specific modules for crossbred WY (a) and crossbred YW (b) compared to their parents, respectively. Fig. S7 The consensus and divergence of gene co-expression networks between the crossbred YW and its parents (WW and YY) during the 5 laying stages. (a) Hierarchical cluster dendrogram showing consensus gene co-expression modules (CMs) among WW, YY and YW. The red line above is the cut height (0.995) for CM identification. CM colors are labeled independent of the separately identified modules in each group. (b) The relationships between global and group specific co-expression networks. The vertical axis represents CMs. The horizontal axis represents modules within each group (c) The relationships among eigengenes of CMs in each group. (d) The expression patterns of eigengenes of CMs in WW, YY and YW during 5 laying stages. Blue and red represent lesser and greater expression, respectively. (e) Heatmap showing KEGG pathways significantly enriched by genes in each CM. Color intensity represents the significance of enrichment. Fig. S8. Hub genes in the preserved gene co-expression network underlying the dynamic egg production heterosis. (a) Upset plot showing the common hub genes among WW, YY and YW. (b) KEGG pathways enrichment analysis for the common hub genes. The color bar represents the ratio of gene numbers in each pathway, and the black dot represents the significance (adjusted P value) of the KEGG pathway. (c) The differential expression patterns during 5 laying stages for hub genes involved in the cell cycle. The cell colors represent differential expression patterns, and the colors on the left represent the corresponding CM and KEGG pathway to which each gene belongs, respectively.
DOI: 10.6084/m9.figshare.28340903
title: Additional file 1 of Successful management of catheter injury or refractory infection by partial replantation of peritoneal dialysis catheters: a retrospective observational study

description: Supplementary Material 1