cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23540937
title: Revealing common differential mRNAs, signaling pathways, and immune cells in blood, glomeruli, and tubulointerstitium of lupus nephritis patients based on transcriptomic data

description: Lupus nephritis (LN) is a potentially fatal autoimmune disease. The purpose of this study was to find potential key molecular markers of LN to aid in the early diagnosis and management of the disease. Datasets GSE99967_blood, GSE32591_glomeruli, and GSE32591_tubulointerstitium were included in this study. Differentially expressed mRNAs (DEmRNAs) were identified between the normal control and LN groups using the limma package in R. Common DEmRNAs in the three datasets were taken. Subsequently, functional enrichment analysis, immune correlation analysis, receiver operating characteristic (ROC) curve analysis and real-time polymerase chain reaction (RT-PCR) verification were performed. In this study, 11 common DEmRNAs were obtained and all of them were up-regulated. In protein–protein interaction (PPI) networks, we found that MX dynamin like GTPase 1 (MX1) and radical S-adenosyl methionine domain containing 2 (RSAD2) had the highest interaction score (0.997). Functional enrichment analysis revealed that MX1 and RSAD2 were enriched in influenza A and hepatitis C signaling pathways. The area under the curve (AUC) values of interferon-induced protein 44 (IFI44) and MX1 in GSE32591_glomeruli and GSE32591_tubulointerstitium datasets are 1, which is worthy of further study on their diagnostic value and molecular mechanism. The xCell analysis showed abnormal distribution of granulocyte-macrophage progenitor (GMP) cells in blood, glomeruli, and tubulointerstitium. Pearson’s correlation analysis found that GMP cells were significantly correlated with lactotransferrin (LTF) and cell cycle. Identification of common DEmRNAs and key pathways in the blood, glomeruli, and tubulointerstitium of patients with LN provides potential research directions for exploring the molecular mechanisms of the disease.
DOI: 10.6084/m9.figshare.23735522.v1
title: Rituximab treatment for refractory nephrotic syndrome in adults: a multicenter retrospective study

description: The treatment of refractory nephrotic syndrome (RNS) is full of challenges and the role of rituximab (RTX) is not well-established, thus this study aims to demonstrate the role of RTX in RNS. This was a multicenter retrospective study of all adult patients receiving RTX for RNS. Patients enrolled were divided into two groups according to pathological pattern: 20 patients as a group of podocytopathy (including minimal change disease [MCD] and focal and segmental glomerulosclerosis [FSGS]), and 26 patients as membranous nephropathy (MN) group. The remission rate, relapse rate, adverse effects, and predictors of remission were analyzed. A total of 75 patients received RTX for RNS and 48 were available for analysis after exclusion criteria. No significant difference in the remission rate at 6 or 12 months was observed between the MCD/FSGS and MN cases (<i>p</i> &gt; 0.05). The median duration of the first complete remission (CR) was 1 month in the podocytopathy group and 12.5 months in the MN group. Three relapses were associated with infection as the ultimate outcome, and 6 out of 48 remained refractory representing a response rate of 87.5% in RNS. Clinical predictors of cumulative CR were estimated glomerular filtration rate (eGFR) &lt;60 mL/min/1.73 m<sup>2</sup> and mean arterial pressure (MAP) ≤103 mmHg at the beginning of therapy in patients with MN. No serious adverse effects were reported. RTX appears to be effective in RNS across various clinical and pathological subtypes, exhibiting a low relapse rate and minimal significant side effects in the majority of patients.
DOI: 10.6084/m9.figshare.23702696
title: CircTLK1 alleviates oxygen-glucose deprivation/reperfusion induced apoptosis in HK-2 cells through miR-136-5p/Bcl2 signal axis

description: The biological functions of circTLK1 in acute kidney injury (AKI), which mainly results from renal ischemia-reperfusion (IR), remain largely unknown. HK-2 cell treatment with oxygen and glucose deprivation, reoxygenation, and glucose (OGD/R) was used to simulate an AKI model that was mainly caused by renal IR. Then, the circTLK1 expression level in HK-2 cells treated with OGD/R was assessed by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Functional experiments were performed with circTLK1 knockdown of HK-2 cells <i>via</i> Cell Counting Kit-8 (CCK8), flow cytometry (FCM), RT-qPCR, and western blotting. The circTLK1-miRNAs-mRNAs network was constructed following the ceRNA mechanism and visualized by Cytoscape software to investigate the mechanism of circTLK1 in AKI. RT-qPCR was performed to verify the relationship between circTLK1, miR-136-5p, and Bcl2. The level of miR-136-5p was knocked down to ensure its function in OGD/R-triggered apoptosis through experiments, including CCK8, FCM, RT-qPCR, and western blotting. CircTLK1 was downregulated in HK-2 cells subjected to OGD/R treatment and in mouse kidney tissues after renal IR, but the expression of miR-136-5p was the opposite. Interference with circTLK1 expression accelerated HK-2 cell apoptosis, which was overturned by miR-136-5p inhibitors. CircTLK1 targets miR-136-5p to upregulate Bcl2 expression and attenuate apoptosis in HK-2 cells. These data revealed the possible role of circTLK1 as a new biomarker for diagnosis as well as a target in AKI through the miR-136-5p/Bcl2 signaling axis.
DOI: 10.6084/m9.figshare.23599234
title: The gut microbiome and metabolome in kidney transplant recipients with normal and moderately decreased kidney function

description: The kidney transplant recipients (KTRs) were diagnosed with Chronic Kidney Disease after transplantation (CKD-T). CKD-T can be affected by the microbial composition and metabolites. The present study integrates the analysis of gut microbiome and metabolites to further identify the characteristics of CKD-T. We collected 100 fecal samples of KTRs and divided them into two groups according to the stage progression of CKD-T. Among them, 55 samples were analyzed by Hiseq sequencing, and 100 samples were used for non-targeted metabolomics analysis. The gut microbiome and metabolomics of KTRs were comprehensively characterized. As well as significant differences in gut microbiome diversity between the CKD G1-2T group and CKD G3T group. Eight flora including Akkermansia were found to be enriched in CKD G3T group. As compared with CKD G1-2T group, the relative abundance of some amino acid metabolism, glycerophospholipid metabolism, amino acid biosynthesis, carbohydrate metabolism and purine metabolism in CKD G3T group were differential expressed significantly. In addition, fecal metabolome analysis indicated that CKD G3T group had a unique metabolite distribution characteristic. Two differentially expressed metabolites, N-acetylornithine and 5-deoxy-5'-(Methylthio) Adenosine, were highly correlated with serum creatinine, eGFR and cystatin C. The enrichment of gut microbial function in CKD-T is correlated with the expression of gut metabolites. Gut microbiome and metabolites in the progression of CKD-T display some unique distribution and expression characteristics. The composition of the gut microbiome and their metabolites appears to be different between patients with CKD G3T and those with CKD G1-2T.
DOI: 10.15468/dl.9rv2nz
title: Occurrence Download

description: A dataset containing 24073 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Month is one of (March, April, May, June, July, August, September, October, November, December)",
 "OccurrenceStatus is Present",
 "TaxonKey is Corvus frugilegus Linnaeus, 1758",
 "Year 2010-2010"
 ]
}

 The dataset includes 24073 records from 152 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022988-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/4r8h-2s11
title: Coyote Pond pollen surface sample dataset

description: Raw data for the Coyote Pond pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.6084/m9.figshare.23599234.v1
title: The gut microbiome and metabolome in kidney transplant recipients with normal and moderately decreased kidney function

description: The kidney transplant recipients (KTRs) were diagnosed with Chronic Kidney Disease after transplantation (CKD-T). CKD-T can be affected by the microbial composition and metabolites. The present study integrates the analysis of gut microbiome and metabolites to further identify the characteristics of CKD-T. We collected 100 fecal samples of KTRs and divided them into two groups according to the stage progression of CKD-T. Among them, 55 samples were analyzed by Hiseq sequencing, and 100 samples were used for non-targeted metabolomics analysis. The gut microbiome and metabolomics of KTRs were comprehensively characterized. As well as significant differences in gut microbiome diversity between the CKD G1-2T group and CKD G3T group. Eight flora including Akkermansia were found to be enriched in CKD G3T group. As compared with CKD G1-2T group, the relative abundance of some amino acid metabolism, glycerophospholipid metabolism, amino acid biosynthesis, carbohydrate metabolism and purine metabolism in CKD G3T group were differential expressed significantly. In addition, fecal metabolome analysis indicated that CKD G3T group had a unique metabolite distribution characteristic. Two differentially expressed metabolites, N-acetylornithine and 5-deoxy-5'-(Methylthio) Adenosine, were highly correlated with serum creatinine, eGFR and cystatin C. The enrichment of gut microbial function in CKD-T is correlated with the expression of gut metabolites. Gut microbiome and metabolites in the progression of CKD-T display some unique distribution and expression characteristics. The composition of the gut microbiome and their metabolites appears to be different between patients with CKD G3T and those with CKD G1-2T.
DOI: 10.21233/yt8f-zp08
title: Olympic Park ostracode surface sample dataset

description: Raw data for the Olympic Park ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.6084/m9.figshare.23540937.v1
title: Revealing common differential mRNAs, signaling pathways, and immune cells in blood, glomeruli, and tubulointerstitium of lupus nephritis patients based on transcriptomic data

description: Lupus nephritis (LN) is a potentially fatal autoimmune disease. The purpose of this study was to find potential key molecular markers of LN to aid in the early diagnosis and management of the disease. Datasets GSE99967_blood, GSE32591_glomeruli, and GSE32591_tubulointerstitium were included in this study. Differentially expressed mRNAs (DEmRNAs) were identified between the normal control and LN groups using the limma package in R. Common DEmRNAs in the three datasets were taken. Subsequently, functional enrichment analysis, immune correlation analysis, receiver operating characteristic (ROC) curve analysis and real-time polymerase chain reaction (RT-PCR) verification were performed. In this study, 11 common DEmRNAs were obtained and all of them were up-regulated. In protein–protein interaction (PPI) networks, we found that MX dynamin like GTPase 1 (MX1) and radical S-adenosyl methionine domain containing 2 (RSAD2) had the highest interaction score (0.997). Functional enrichment analysis revealed that MX1 and RSAD2 were enriched in influenza A and hepatitis C signaling pathways. The area under the curve (AUC) values of interferon-induced protein 44 (IFI44) and MX1 in GSE32591_glomeruli and GSE32591_tubulointerstitium datasets are 1, which is worthy of further study on their diagnostic value and molecular mechanism. The xCell analysis showed abnormal distribution of granulocyte-macrophage progenitor (GMP) cells in blood, glomeruli, and tubulointerstitium. Pearson’s correlation analysis found that GMP cells were significantly correlated with lactotransferrin (LTF) and cell cycle. Identification of common DEmRNAs and key pathways in the blood, glomeruli, and tubulointerstitium of patients with LN provides potential research directions for exploring the molecular mechanisms of the disease.
DOI: 10.21233/2ex8-x739
title: Yawgoo Millpond diatom surface sample dataset

description: Raw data for the Yawgoo Millpond diatom surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/p6w6-4666
title: Lac Disson diatom surface sample dataset

description: Raw data for the Lac Disson diatom surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.6084/m9.figshare.28981298
title: Replication data for Only a Moment in Time? The Changing Effectiveness of Mass Mobilization on Transitions to Democracy

description: This archive provides access to the raw data and routines in the empirical analyses reported in "Only a Moment in Time? The Changing Effectiveness of Mass Mobilization on Transitions to Democracy"All the data used are from fully open sources. A full replication archive will be made available on publication of the article
DOI: 10.15468/dl.v4h564
title: Occurrence Download

description: A dataset containing 218 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Larus cachinnans Pallas, 1811",
 "Year is greater than or equal to 2000",
 "Country is China",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 218 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022991-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.juhb9h
title: Occurrence Download

description: A dataset containing 6193 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Month is one of (January, February)",
 "OccurrenceStatus is Present",
 "TaxonKey is Corvus frugilegus Linnaeus, 1758",
 "Year 2011-2011"
 ]
}

 The dataset includes 6193 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022990-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/xgv4-x338
title: Boiler Lake water chemistry dataset

description: Raw data for the Boiler Lake water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/4p66-1f04
title: Hahanudan Lake (RkIk-5), [MLZ-00013], [Two House Site] vertebrate fauna dataset

description: Raw data for the Hahanudan Lake (RkIk-5), [MLZ-00013], [Two House Site] vertebrate fauna dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.xb7t3c
title: Occurrence Download

description: A dataset containing 26794 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hemaris fuciformis Linnaeus, 1758"
 ]
}

 The dataset includes 26794 records from 605 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022989-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/0bdh-em33
title: Wiccopee Reservoir (N) diatom bottom sample dataset

description: Raw data for the Wiccopee Reservoir (N) diatom bottom sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/1fga-tk17
title: Prall Shelter [3BE187] vertebrate fauna dataset

description: Raw data for the Prall Shelter [3BE187] vertebrate fauna dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/x5tm-5873
title: Painted Hand Pueblo pollen dataset

description: Raw data for the Painted Hand Pueblo pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.r4hrjj
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Hydrocoloeus minutus (Pallas, 1776)",
 "Year is greater than or equal to 2000",
 "Country is China",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 67 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022993-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/dw7x-3g60
title: LDDsite4313 ostracode surface sample dataset

description: Raw data for the LDDsite4313 ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/09kf-9481
title: Dal der Steenwijker A (KA) pollen dataset

description: Raw data for the Dal der Steenwijker A (KA) pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.17028/rd.lboro.28980959
title: Supplementary information files for "Seabed seismographs reveal duration and structure of longest runout sediment flows on earth"

description: Supplementary files for article "Seabed seismographs reveal duration and structure of longest runout sediment flows on earth"Turbidity currents carve the deepest canyons on Earth, deposit its largest sediment accumulations, and break seabed telecommunication cables. Powerful canyon-flushing turbidity currents break sensors placed in their path, making them notoriously challenging to measure, and thus poorly understood. This study provides the first remote measurements of canyon-flushing flows, using ocean-bottom seismographs located outside the flow's destructive path, revolutionizing flow monitoring. We recorded the internal dynamics of the longest sediment flows yet monitored on Earth, which traveled &gt;1,000 km down the Congo Canyon-Channel at 3.7–7.6 m s−1 and lasted &gt;3 weeks. These observations allow us to test fundamental models for turbidity current behavior and reveal that flows contain dense and fast frontal-zones up to ∼400 km in length. These frontal-zones developed near-uniform durations and speeds for hundreds of kilometres despite substantial seabed erosion, enabling flows to rapidly transport prodigious volumes of organic carbon, sediment, and warm water to the deep-sea.<br><br>© The Author(s), CC BY 4.0
DOI: 10.17028/rd.lboro.28980959.v1
title: Supplementary information files for "Seabed seismographs reveal duration and structure of longest runout sediment flows on earth"

description: Supplementary files for article "Seabed seismographs reveal duration and structure of longest runout sediment flows on earth"Turbidity currents carve the deepest canyons on Earth, deposit its largest sediment accumulations, and break seabed telecommunication cables. Powerful canyon-flushing turbidity currents break sensors placed in their path, making them notoriously challenging to measure, and thus poorly understood. This study provides the first remote measurements of canyon-flushing flows, using ocean-bottom seismographs located outside the flow's destructive path, revolutionizing flow monitoring. We recorded the internal dynamics of the longest sediment flows yet monitored on Earth, which traveled &gt;1,000 km down the Congo Canyon-Channel at 3.7–7.6 m s−1 and lasted &gt;3 weeks. These observations allow us to test fundamental models for turbidity current behavior and reveal that flows contain dense and fast frontal-zones up to ∼400 km in length. These frontal-zones developed near-uniform durations and speeds for hundreds of kilometres despite substantial seabed erosion, enabling flows to rapidly transport prodigious volumes of organic carbon, sediment, and warm water to the deep-sea.<br><br>© The Author(s), CC BY 4.0
DOI: 10.15468/dl.248deq
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Lao People’s Democratic Republic",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nephila pilipes (Fabricius, 1793)"
 ]
}

 The dataset includes 101 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022992-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.