cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28538768
title: Supplementary Material for: In situ and in silico localization of major satellite DNAs in the genome of the red-eared slider (Trachemys scripta elegans, Emydidae, Testudines)

description: Introduction. Satellite DNA is an important component of the eukaryotic genome. Some satellite DNAs plays an important role in various biological processes. The red-eared slider (Trachemys scripta elegans, 2n=50, C=1.43 pg) belongs to the American freshwater turtle family and is recognised as one of the world's most invasive species. In the T. s. elegans chromosome-level genome assembly, which has been recently published, satellite DNAs comprise only 0.1%. From the repetitive repertoire of the T. elegans genome, only ribosomal DNA genes and telomeric repeats have been localised on the species' chromosomes.
Methods. Using publicly available short-read sequencing data, we conducted de novo identification of the most abundant satellite DNAs in T. s. elegans using TAREAN pipeline. We combined bioinformatics (using blastn) and chromosome mapping by fluorescence in situ hybridization to describe the distribution of major tandem repetitive DNAs. The diversity and distribution of satDNA in the assembled genome of T. s. elegans were explored using the SatXplor pipeline.
Results. Six major satellite sequences occupying approximately 0.8% of the genome were identified in the genome data, all of which were successfully localised both in situ and in silico on T. s. elegans chromosomes and in silico on chromosomal scaffolds. We revealed a complex structural organisation of these sequences: monomers may be moderately or highly variable and they may contain regions homologous to retrotransposons. Cytogenetic mapping showed the accumulation of satellite DNAs in the pericentromeric regions of most chromosomes and in the distal regions of the short arms of submetacentric chromosomes. Comparisons between cytogenetic maps and genome assembly data revealed discrepancies in the number and chromosomal locations of the identified satellite DNA clusters.
Conclusion. The red-eared slider genome has a greater proportion of satellite DNA than was previously reported. These satellites demonstrate no specificity for either macrochromosomes or microchromosomes. Differences between in situ and in silico results indicate the challenges of repetitive sequence assembly, as well as discrepancies between chromosome numbering in the current chromosome-level genome assembly and the physical chromosome map.
DOI: 10.6084/m9.figshare.28538768.v1
title: Supplementary Material for: In situ and in silico localization of major satellite DNAs in the genome of the red-eared slider (Trachemys scripta elegans, Emydidae, Testudines)

description: Introduction. Satellite DNA is an important component of the eukaryotic genome. Some satellite DNAs plays an important role in various biological processes. The red-eared slider (Trachemys scripta elegans, 2n=50, C=1.43 pg) belongs to the American freshwater turtle family and is recognised as one of the world's most invasive species. In the T. s. elegans chromosome-level genome assembly, which has been recently published, satellite DNAs comprise only 0.1%. From the repetitive repertoire of the T. elegans genome, only ribosomal DNA genes and telomeric repeats have been localised on the species' chromosomes.
Methods. Using publicly available short-read sequencing data, we conducted de novo identification of the most abundant satellite DNAs in T. s. elegans using TAREAN pipeline. We combined bioinformatics (using blastn) and chromosome mapping by fluorescence in situ hybridization to describe the distribution of major tandem repetitive DNAs. The diversity and distribution of satDNA in the assembled genome of T. s. elegans were explored using the SatXplor pipeline.
Results. Six major satellite sequences occupying approximately 0.8% of the genome were identified in the genome data, all of which were successfully localised both in situ and in silico on T. s. elegans chromosomes and in silico on chromosomal scaffolds. We revealed a complex structural organisation of these sequences: monomers may be moderately or highly variable and they may contain regions homologous to retrotransposons. Cytogenetic mapping showed the accumulation of satellite DNAs in the pericentromeric regions of most chromosomes and in the distal regions of the short arms of submetacentric chromosomes. Comparisons between cytogenetic maps and genome assembly data revealed discrepancies in the number and chromosomal locations of the identified satellite DNA clusters.
Conclusion. The red-eared slider genome has a greater proportion of satellite DNA than was previously reported. These satellites demonstrate no specificity for either macrochromosomes or microchromosomes. Differences between in situ and in silico results indicate the challenges of repetitive sequence assembly, as well as discrepancies between chromosome numbering in the current chromosome-level genome assembly and the physical chromosome map.
DOI: 10.6084/m9.figshare.28538774
title: Supplementary Material for: Toward a Comprehensive Overview of Cytogenomics in the Galliformes: a Focus on Western Capercaillie and Hazel Grouse Karyotypes

description: Introduction: The Phasianidae family belongs to Galliformes, which is basal to other Neognathae. Despite the availability of chromosome-level genome assemblies for many Phasianidae species, the karyotypes for some species remain poorly investigated.
Methods: In this study, we described karyotypes using classical, differential, and molecular cytogenetic (BAC-FISH) methods. To compare chromosome-level genomes of 10 Galliformes species dot-plot analysis was performed.
Results: We provide the first comprehensive description of the karyotype of two Tetraonini species: the western capercaillie (Tetrao urogallus, 2n=78) and the hazel grouse (Tetrastes bonasia, 2n=80). We mapped chicken BAC clones (CHORI-261) with known coordinates to the chromosomes of the western capercaillie and Japanese quail (Coturnix japonica, 2n=78) to anchor physical chromosomes to chromosome-level assemblies. Finally, we performed dot-plot comparisons of ten available chromosome-level genome assemblies to identify inter- and intrachromosomal rearrangements in Galliformes.
Conclusion: We show that the centromeric fusion of orthologs of GGA6 and GGA8 is shared by all analyzed species in the tetraonid clade: T. urogallus, T. bonasia, and Lagopus muta. We identified linage-specific intrachromosomal rearrangements on chromosomes orthologs to chicken Z (Phasianinae and Tetraoninae), 7 and 12 (Phasianinae and Tetraoninae), 5 and 13 (Perdicinae), 22 (Alectoris). Our study shows that analysis of the genomes of several closely related species allows us to identify chromosomal rearrangements characteristic of individual evolutionary lines.
DOI: 10.6084/m9.figshare.28538771
title: Supplementary Material for: 18F-FDG PET/CT predicts the prognosis of patients with hepatocellular carcinoma undergoing liver transplantation

description: Introduction: In addition to radical resection, liver transplantation (LTx) is an effective treatment for hepatocellular carcinoma (HCC). However, tumor recurrence limits the efficacy of LTx in some patients. This study investigated the role of 18F-fludeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) in predicting the prognosis of patients with HCC after LTx.
Methods: A total of 278 consecutive patients with HCC who underwent pre-LTx PET/CT were divided into derivation (n = 178) and temporal validation (n = 100) cohorts and evaluated for PET/CT values, immunohistochemical (IHC) findings, and DNA sequencing of tumor tissues.
Results: Patients with post-LTx recurrence exhibited significantly higher tumor maximum standardized uptake values (SUVmax) in pre-LTx PET/CT scans. Receiver operating characteristic (ROC) curve analyses identified the tumor SUVmax to liver SUVmax ratio (TSUVmax/LSUVmax) as the strongest predictor of post-LTx recurrence, with an optimal cutoff value of 1.43. Kaplan-Meier analyses demonstrated that a TSUVmax/LSUVmax &gt; 1.43 was associated with a shorter time to recurrence (TTR) and overall survival (OS) in both cohorts (p &lt; 0.001 for both). Multivariate Cox regression analyses confirmed that TSUVmax/LSUVmax &gt; 1.43 was an independent risk factor for tumor recurrence in both cohorts. IHC revealed that TSUVmax/LSUVmax &gt; 1.43 correlated with higher Ki-67 and CK19 expression. Next-generation sequencing (NGS) indicated that tumors with TSUVmax/LSUVmax &gt; 1.43 had more mutations and a higher tumor mutational burden (TMB). Furthermore, TSUVmax/LSUVmax &gt; 1.43 was significantly associated with mutations in TP53, EPPK1, MDM4, SLAMF7, SDHC, B4GALT3, RXRG and FCGR family genes, as well as TP53 and PI3K signaling pathway alterations.
Conclusions: The preoperative TSUVmax/LSUVmax is a potential predictor of tumor recurrence in patients with HCC following LTx. Its use improves candidate selection and post-LTx management.
DOI: 10.6084/m9.figshare.28538777
title: Supplementary Material for: Impaired Dietary Decision-Making in Children and Adolescents with Congenital Adrenal Hyperplasia

description: Introduction: Children and adolescents with congenital adrenal hyperplasia (CAH) are at increased risk for obesity and exhibit differences in brain regions associated with food reward and decision-making. We aimed to understand differences in dietary decision-making between youth with CAH compared to controls.
Methods: 37 youth with CAH (12.2 ± 3.1y, 59.5% female) and 100 controls (11.7 ± 2.4y, 57% female) rated 30 low- and 30 high-calorie foods for health, taste, and liking. Participants then chose between 100 food pair trials using a mouse-tracking paradigm; 75 were discordant for health and taste ratings. Self-control success was measured as the percentage of trials in which the healthier food was chosen instead of the tastier food. Area under the curve (AUC) and maximum deviation (MD) are used as real-time indices of decision-making. 
Results: Patients with CAH exhibited higher AUCs (CAH: 9.48 ± 8.08, Control: 6.40 ± 7.33; p &lt; 0.05) and MDs (CAH: 0.20 ± 0.13, Control: 0.15 ± 0.12; p &lt; 0.05) in self-control trials. However, patients with CAH and controls did not differ in their self-control success (CAH: 28.47 ± 24.27%, Control: 35.16 ± 25.01%; p = 0.16). In youth with CAH, testosterone was correlated with AUC (R = 0.46, p &lt; 0.01) and MD (R = 0.38, p = 0.02) during successful self-control trials.
Conclusions: Children and adolescents with CAH exhibit more cognitive conflict when choosing between healthy and tasty foods. Two indicators of disease severity were associated with cognitive conflict during food choice in patients with CAH. Our findings suggest impaired dietary decision-making in CAH could contribute to obesity risk.
DOI: 10.6084/m9.figshare.28538777.v1
title: Supplementary Material for: Impaired Dietary Decision-Making in Children and Adolescents with Congenital Adrenal Hyperplasia

description: Introduction: Children and adolescents with congenital adrenal hyperplasia (CAH) are at increased risk for obesity and exhibit differences in brain regions associated with food reward and decision-making. We aimed to understand differences in dietary decision-making between youth with CAH compared to controls.
Methods: 37 youth with CAH (12.2 ± 3.1y, 59.5% female) and 100 controls (11.7 ± 2.4y, 57% female) rated 30 low- and 30 high-calorie foods for health, taste, and liking. Participants then chose between 100 food pair trials using a mouse-tracking paradigm; 75 were discordant for health and taste ratings. Self-control success was measured as the percentage of trials in which the healthier food was chosen instead of the tastier food. Area under the curve (AUC) and maximum deviation (MD) are used as real-time indices of decision-making. 
Results: Patients with CAH exhibited higher AUCs (CAH: 9.48 ± 8.08, Control: 6.40 ± 7.33; p &lt; 0.05) and MDs (CAH: 0.20 ± 0.13, Control: 0.15 ± 0.12; p &lt; 0.05) in self-control trials. However, patients with CAH and controls did not differ in their self-control success (CAH: 28.47 ± 24.27%, Control: 35.16 ± 25.01%; p = 0.16). In youth with CAH, testosterone was correlated with AUC (R = 0.46, p &lt; 0.01) and MD (R = 0.38, p = 0.02) during successful self-control trials.
Conclusions: Children and adolescents with CAH exhibit more cognitive conflict when choosing between healthy and tasty foods. Two indicators of disease severity were associated with cognitive conflict during food choice in patients with CAH. Our findings suggest impaired dietary decision-making in CAH could contribute to obesity risk.
DOI: 10.15468/dl.tahfen
title: Occurrence Download

description: A dataset containing 13045 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bassia scoparia (L.) A.J.Scott)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 13045 records from 362 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005793-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.925ufj
title: Occurrence Download

description: A dataset containing 50145724 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Occurrence evidence, Human Observation)",
 "Continent is Asia",
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 50145724 records from 213 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005786-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6832bj
title: Occurrence Download

description: A dataset containing 1219 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bauhinia monandra Kurz)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 1219 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005794-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12715657
title: A monthly 5 km Arctic sea ice thickness product from 1995 to 2023 using multiple radar altimetry data

description: Arctic sea ice is of great importance to the regional and global climate change study. Satellite observations have demonstrated that the Arctic sea ice extent has been declined for the last four decades. However, long-term variations of the Arctic sea ice thickness (SIT) are less focused as SIT cannot be measured directly by satellite-based instruments. Here, we presented a monthly Arctic SIT product based on multiple radar altimetry observations from ERS-2, Envisat, and CryoSat-2. To ensure the accuracy of the SIT retrievals, we proposed a novel data processing procedure including leads detection, freeboard conversion to thickness and inter-mission bias correction. Finally, we were able to generate the monthly SIT estimates for the Arctic Ocean from October 1995 to December 2023. The thickness estimates are posted on a 5 km resolution polar stereographic grid. The variations of the Arctic SIT are analyzed in terms of the spatial and temporal distributions. We also compared our SIT estimates with observations from upward looking sonars (ULSs) and airborne laser altimetry from Operation IceBridge (OIB), as well as seven publicly released Arctic SIT products. The validation results demonstrate that our SIT product features equivalent accuracy with existing products. The accuracy of our products is about 0.4 m during Envisat period, and is within 0.2 m during CryoSat-2 period.
DOI: 10.5281/zenodo.13282942
title: A monthly 5 km Arctic sea ice thickness product from 1995 to 2023 using multiple radar altimetry data

description: Arctic sea ice is of great importance to the regional and global climate change study. Satellite observations have demonstrated that the Arctic sea ice extent has been declined for the last four decades. However, long-term variations of the Arctic sea ice thickness (SIT) are less focused as SIT cannot be measured directly by satellite-based instruments. Here, we presented a monthly Arctic SIT product based on multiple radar altimetry observations from ERS-2, Envisat, and CryoSat-2. To ensure the accuracy of the SIT retrievals, we proposed a novel data processing procedure including leads detection, freeboard conversion to thickness and inter-mission bias correction. Finally, we were able to generate the monthly SIT estimates for the Arctic Ocean from October 1995 to December 2023. The thickness estimates are posted on a 5 km resolution polar stereographic grid. The variations of the Arctic SIT are analyzed in terms of the spatial and temporal distributions. We also compared our SIT estimates with observations from upward looking sonars (ULSs) and airborne laser altimetry from Operation IceBridge (OIB), as well as seven publicly released Arctic SIT products. The validation results demonstrate that our SIT product features equivalent accuracy with existing products. The accuracy of our products is about 0.4 m during Envisat period, and is within 0.2 m during CryoSat-2 period.
DOI: 10.5281/zenodo.13377908
title: A monthly 5 km Arctic sea ice thickness product from 1995 to 2023 using multiple radar altimetry data

description: Arctic sea ice is of great importance to the regional and global climate change study. Satellite observations have demonstrated that the Arctic sea ice extent has been declined for the last four decades. However, long-term variations of the Arctic sea ice thickness (SIT) are less focused as SIT cannot be measured directly by satellite-based instruments. Here, we presented a monthly Arctic SIT product based on multiple radar altimetry observations from ERS-2, Envisat, and CryoSat-2. To ensure the accuracy of the SIT retrievals, we proposed a novel data processing procedure including leads detection, freeboard conversion to thickness and inter-mission bias correction. Finally, we were able to generate the monthly SIT estimates for the Arctic Ocean from October 1995 to December 2023. The thickness estimates are posted on a 5 km resolution polar stereographic grid. The variations of the Arctic SIT are analyzed in terms of the spatial and temporal distributions. We also compared our SIT estimates with observations from upward looking sonars (ULSs) and airborne laser altimetry from Operation IceBridge (OIB), as well as seven publicly released Arctic SIT products. The validation results demonstrate that our SIT product features equivalent accuracy with existing products. The accuracy of our products is about 0.4 m during Envisat period, and is within 0.2 m during CryoSat-2 period.
DOI: 10.5281/zenodo.13377969
title: A monthly 5 km Arctic sea ice thickness product from 1995 to 2023 using multiple radar altimetry data

description: Arctic sea ice is of great importance to the regional and global climate change study. Satellite observations have demonstrated that the Arctic sea ice extent has been declined for the last four decades. However, long-term variations of the Arctic sea ice thickness (SIT) are less focused as SIT cannot be measured directly by satellite-based instruments. Here, we presented a monthly Arctic SIT product based on multiple radar altimetry observations from ERS-2, Envisat, and CryoSat-2. To ensure the accuracy of the SIT retrievals, we proposed a novel data processing procedure including leads detection, freeboard conversion to thickness and inter-mission bias correction. Finally, we were able to generate the monthly SIT estimates for the Arctic Ocean from October 1995 to December 2023. The thickness estimates are posted on a 5 km resolution polar stereographic grid. The variations of the Arctic SIT are analyzed in terms of the spatial and temporal distributions. We also compared our SIT estimates with observations from upward looking sonars (ULSs) and airborne laser altimetry from Operation IceBridge (OIB), as well as seven publicly released Arctic SIT products. The validation results demonstrate that our SIT product features equivalent accuracy with existing products. The accuracy of our products is about 0.4 m during Envisat period, and is within 0.2 m during CryoSat-2 period.
DOI: 10.5281/zenodo.13634465
title: A monthly 5 km Arctic sea ice thickness product from 1995 to 2023 using multiple radar altimetry data

description: Arctic sea ice is of great importance to the regional and global climate change study. Satellite observations have demonstrated that the Arctic sea ice extent has been declined for the last four decades. However, long-term variations of the Arctic sea ice thickness (SIT) are less focused as SIT cannot be measured directly by satellite-based instruments. Here, we presented a monthly Arctic SIT product based on multiple radar altimetry observations from ERS-2, Envisat, and CryoSat-2. To ensure the accuracy of the SIT retrievals, we proposed a novel data processing procedure including leads detection, freeboard conversion to thickness and inter-mission bias correction. Finally, we were able to generate the monthly SIT estimates for the Arctic Ocean from October 1995 to December 2023. The thickness estimates are posted on a 5 km resolution polar stereographic grid. The variations of the Arctic SIT are analyzed in terms of the spatial and temporal distributions. We also compared our SIT estimates with observations from upward looking sonars (ULSs) and airborne laser altimetry from Operation IceBridge (OIB), as well as seven publicly released Arctic SIT products. The validation results demonstrate that our SIT product features equivalent accuracy with existing products. The accuracy of our products is about 0.4 m during Envisat period, and is within 0.2 m during CryoSat-2 period.
DOI: 10.5281/zenodo.13699698
title: A monthly 5 km Arctic sea ice thickness product from 1995 to 2023 using multiple radar altimetry data

description: Arctic sea ice is of great importance to the regional and global climate change study. Satellite observations have demonstrated that the Arctic sea ice extent has been declined for the last four decades. However, long-term variations of the Arctic sea ice thickness (SIT) are less focused as SIT cannot be measured directly by satellite-based instruments. Here, we presented a monthly Arctic SIT product based on multiple radar altimetry observations from ERS-2, Envisat, and CryoSat-2. To ensure the accuracy of the SIT retrievals, we proposed a novel data processing procedure including leads detection, freeboard conversion to thickness and inter-mission bias correction. Finally, we were able to generate the monthly SIT estimates for the Arctic Ocean from October 1995 to December 2023. The thickness estimates are posted on a 5 km resolution polar stereographic grid. The variations of the Arctic SIT are analyzed in terms of the spatial and temporal distributions. We also compared our SIT estimates with observations from upward looking sonars (ULSs) and airborne laser altimetry from Operation IceBridge (OIB), as well as seven publicly released Arctic SIT products. The validation results demonstrate that our SIT product features equivalent accuracy with existing products. The accuracy of our products is about 0.4 m during Envisat period, and is within 0.2 m during CryoSat-2 period.