cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28136880.v1
title: Prediction of survival after pancreatoduodenectomy for distal cholangiocarcinoma: independent external validation of a prognostic model for 3-year overall survival in Sweden

description: The only treatment with curative potential for distal cholangiocarcinoma (dCCA) is radical surgery which can be complemented with adjuvant chemotherapy. The aim of the present study was to perform an independent external validation of a prognostic model for 3-year overall survival based on routine clinicopathological variables for patients treated with pancreatoduodenectomy for dCCA. All patients with a histopathological confirmed dCCA that underwent pancreatoduodenectomy in Sweden from 2009 through 2019 were identified in the Swedish National Registry for Pancreatic and Periampullary Cancer. Model performance was estimated using the C-index and calibration plots. In total 220 patients were included in the study. The median survival was 33 months (IQR 26–40) and 3-year survival rate 47% (95% CI 40–53%). The prognostic model had a C-index of 0.69 (95% CI 0.62–0.72). Calibration plots revealed overestimated risk of death across risk groups in the full cohort. Calibration was good in the subgroup of patients that did not receive adjuvant treatment. The prognostic model showed reasonable discriminative ability but some miscalibration likely since the effect of adjuvant treatment is not included in the model. Given that the model was developed in cohorts treated prior to the current adjuvant standard of care the model can be used to estimate baseline risk prior to risk/benefit decision for adjuvant treatment as well as stratification for clinical trials but with a risk to underestimate 3-year overall survival for patients that receive adjuvant treatment.
DOI: 10.6084/m9.figshare.28151367
title: Mitochondrial dysfunction and lipid alterations in primary sclerosing cholangitis

description: Indications of mitochondrial dysfunction are commonly seen in liver diseases, but data are scarce in primary sclerosing cholangitis (PSC). Analyzing circulating and liver-resident molecules indirectly reflecting mitochondrial dysfunction, we aimed to comprehensively characterize this deficit in PSC, and whether this was PSC specific or associated with cholestasis. We retrospectively included plasma from 191 non-transplant patients with large-duct PSC and 100 healthy controls and explanted liver tissue extracts from 24 PSC patients and 18 non-cholestatic liver disease controls. Using mass spectroscopy, we profiled lipids and fatty acids, carnitine, acylcarnitines, and metabolites in the tryptophan-kynurenine-nicotinamide pathway. Hierarchal clustering of fatty acid levels identified patients with PSC and healthy controls as separate clusters. Compared to healthy controls, PSC patients had increased levels of monounsaturated fatty acids (MUFA) and palmitate (C16:0) in plasma, but reduced levels of long-chain saturated fatty acids (SFAs). These findings were more pronounced in PSC patients with cholestasis. Several n-3 polyunsaturated fatty acids were elevated in PSC but not associated with cholestasis. Acylcarnitine ratios C2/C5 and C2/C3 were elevated while C2/C16 was reduced in PSC, indicating impaired mitochondrial fatty acid oxidation of medium-long chained fatty acids. Levels of intermediates in the tryptophan-kynurenine pathway indicated impaired NAD biosynthesis, suggesting impaired energy supply to mitochondria in PSC. We found that mitochondrial dysfunction was prominent in PSC and associated with increasing cholestasis. Whether this is merely a marker of liver disease and severity, or an underlying driver and potential therapeutic target in PSC remains to be explored.
DOI: 10.6084/m9.figshare.28152241
title: Efficacy and safety of anticoagulation in asymptomatic cirrhotic patients with portal vein thrombosis: a systematic review and meta-analysis

description: The role of anticoagulation in asymptomatic cirrhotic patients with portal vein thrombosis (PVT) remains unclear. This study aims to evaluate the efficacy and safety of anticoagulation in this patient population. We systematically searched PubMed, Web of Science, Cochrane Library, and Embase up to August 2024. The primary outcomes analyzed were PVT recanalization, progression of PVT, bleeding events, and mortality. Odds ratios (OR) with 95% confidence intervals (CI) were calculated for dichotomous variables. Seventeen studies, including randomized controlled trials (RCTs) and observational studies, were included in the analysis. Compared to no intervention, anticoagulation significantly increased the PVT recanalization rate (OR = 3.89, <i>p</i> &lt; .001) and decreased the PVT progression rate (OR = 0.28, <i>p</i> &lt; .001) as well as overall mortality (OR = 0.66, <i>p</i> = .008). Importantly, anticoagulation did not significantly increase the bleeding rate (OR = 1.21, <i>p</i> = .41). Subgroup analysis revealed a greater benefit in PVT recanalization within the short-term treatment subgroup (≤ 6 months) compared to long-term treatment subgroup (&gt; 6 months), and in the Asian subgroup compared to the European or United States of America (USA) subgroup. In the Warfarin subgroup, while the total bleeding rate increased significantly, there was no significant rise in major bleeding events. Additionally, a downward trend in variceal bleeding was observed in the Asian subgroup (OR = 0.44; 95% CI: 0.19–1.04; <i>p</i> = .06). Anticoagulation is both safe and effective for asymptomatic cirrhotic patients with PVT. It not only treats PVT and reduces all-cause mortality, but also does so without significantly increasing the risk of bleeding events.
DOI: 10.6084/m9.figshare.28152241.v1
title: Efficacy and safety of anticoagulation in asymptomatic cirrhotic patients with portal vein thrombosis: a systematic review and meta-analysis

description: The role of anticoagulation in asymptomatic cirrhotic patients with portal vein thrombosis (PVT) remains unclear. This study aims to evaluate the efficacy and safety of anticoagulation in this patient population. We systematically searched PubMed, Web of Science, Cochrane Library, and Embase up to August 2024. The primary outcomes analyzed were PVT recanalization, progression of PVT, bleeding events, and mortality. Odds ratios (OR) with 95% confidence intervals (CI) were calculated for dichotomous variables. Seventeen studies, including randomized controlled trials (RCTs) and observational studies, were included in the analysis. Compared to no intervention, anticoagulation significantly increased the PVT recanalization rate (OR = 3.89, <i>p</i> &lt; .001) and decreased the PVT progression rate (OR = 0.28, <i>p</i> &lt; .001) as well as overall mortality (OR = 0.66, <i>p</i> = .008). Importantly, anticoagulation did not significantly increase the bleeding rate (OR = 1.21, <i>p</i> = .41). Subgroup analysis revealed a greater benefit in PVT recanalization within the short-term treatment subgroup (≤ 6 months) compared to long-term treatment subgroup (&gt; 6 months), and in the Asian subgroup compared to the European or United States of America (USA) subgroup. In the Warfarin subgroup, while the total bleeding rate increased significantly, there was no significant rise in major bleeding events. Additionally, a downward trend in variceal bleeding was observed in the Asian subgroup (OR = 0.44; 95% CI: 0.19–1.04; <i>p</i> = .06). Anticoagulation is both safe and effective for asymptomatic cirrhotic patients with PVT. It not only treats PVT and reduces all-cause mortality, but also does so without significantly increasing the risk of bleeding events.
DOI: 10.6084/m9.figshare.28151367.v1
title: Mitochondrial dysfunction and lipid alterations in primary sclerosing cholangitis

description: Indications of mitochondrial dysfunction are commonly seen in liver diseases, but data are scarce in primary sclerosing cholangitis (PSC). Analyzing circulating and liver-resident molecules indirectly reflecting mitochondrial dysfunction, we aimed to comprehensively characterize this deficit in PSC, and whether this was PSC specific or associated with cholestasis. We retrospectively included plasma from 191 non-transplant patients with large-duct PSC and 100 healthy controls and explanted liver tissue extracts from 24 PSC patients and 18 non-cholestatic liver disease controls. Using mass spectroscopy, we profiled lipids and fatty acids, carnitine, acylcarnitines, and metabolites in the tryptophan-kynurenine-nicotinamide pathway. Hierarchal clustering of fatty acid levels identified patients with PSC and healthy controls as separate clusters. Compared to healthy controls, PSC patients had increased levels of monounsaturated fatty acids (MUFA) and palmitate (C16:0) in plasma, but reduced levels of long-chain saturated fatty acids (SFAs). These findings were more pronounced in PSC patients with cholestasis. Several n-3 polyunsaturated fatty acids were elevated in PSC but not associated with cholestasis. Acylcarnitine ratios C2/C5 and C2/C3 were elevated while C2/C16 was reduced in PSC, indicating impaired mitochondrial fatty acid oxidation of medium-long chained fatty acids. Levels of intermediates in the tryptophan-kynurenine pathway indicated impaired NAD biosynthesis, suggesting impaired energy supply to mitochondria in PSC. We found that mitochondrial dysfunction was prominent in PSC and associated with increasing cholestasis. Whether this is merely a marker of liver disease and severity, or an underlying driver and potential therapeutic target in PSC remains to be explored.
DOI: 10.15468/dl.rx7qvb
title: Occurrence Download

description: A dataset containing 15778 records in GBIF matching the query:
 SELECT "year", countryCode, GBIF_EEARGCode( 1000, decimalLatitude, decimalLongitude, COALESCE(coordinateUncertaintyInMeters, 1000) ) AS eeaCellCode, classKey, class, speciesKey, species, COUNT(*) AS occurrences, MIN(COALESCE(coordinateUncertaintyInMeters, 1000)) AS minCoordinateUncertaintyInMeters, MIN(GBIF_TemporalUncertainty(eventDate)) AS minTemporalUncertainty, IF(ISNULL(classKey), NULL, SUM(COUNT(*)) OVER (PARTITION BY classKey)) AS classCount FROM occurrence WHERE occurrenceStatus = 'PRESENT' AND speciesKey IN ( 5218786, 5217334 ) AND continent = 'EUROPE' AND "year" &gt;= 1950 AND hasCoordinate = TRUE AND speciesKey IS NOT NULL AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE') AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE') AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID') AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH') AND ( LOWER(identificationVerificationStatus) NOT IN ( 'unverified', 'unvalidated', 'not validated', 'under validation', 'not able to validate', 'control could not be conclusive due to insufficient knowledge', 'uncertain', 'unconfirmed', 'unconfirmed - not reviewed', 'validation requested' ) OR identificationVerificationStatus IS NULL ) GROUP BY "year", countryCode, eeaCellCode, classKey, class, speciesKey, species ORDER BY "year" DESC, eeaCellCode ASC, speciesKey ASC; 

 The dataset's 15778 records were derived from 197 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011427-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cwdfyn
title: Occurrence Download

description: A dataset containing 6415 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Cranioleuca albicapilla (Cabanis, 1873)"
 ]
}

 The dataset includes 6415 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011447-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25716/gude.1fr1-v7h7
title: Exploring the modulation of the complex folding landscape of Human Telomeric DNA by low molecular weight ligands

description: Telomeric DNA forms G-quadruplex (G4) structures. G4s are crucial for genomic stability and therapeutic targeting. Using time-resolved NMR and CD spectroscopies, we investigated how the ligand Phen-DC3 modulates the folding of the human telomeric repeat 23TAG DNA sequence into G4. The kinetics are modulated by the ligand and by the presence of potassium cations (K+). Ligand binding to G4 occurs via a triphasic process with fast and slow phases. Notably, for the G4 structure in the presence of K+, the slow rate is ten times slower than without K+. These findings offer key insights into the modulation of the complex folding landscape of G4s by ligands, advancing our understanding of G4-ligand interactions for potential therapeutic applications.
description: Kinetic traces obtained from CD and pseudo-2D NMR measurements (raw data). Traces were fitted in Figures 2, S1, S2, S3, S4, S5 and S6.
DOI: 10.15468/dl.qntv8u
title: Occurrence Download

description: A dataset containing 3294766 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Ukraine"
 ]
}

 The dataset includes 3294766 records from 1345 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011437-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5yvagk
title: Occurrence Download

description: A dataset containing 1932718 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Bulgaria"
 ]
}

 The dataset includes 1932718 records from 924 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011434-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh0178357.10fu
title: SH0178357.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0178358.10fu
title: SH0178358.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0178359.10fu
title: SH0178359.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0178360.10fu
title: SH0178360.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0178361.10fu
title: SH0178361.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0178362.10fu
title: SH0178362.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0178363.10fu
title: SH0178363.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0178364.10fu
title: SH0178364.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0178365.10fu
title: SH0178365.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.