cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.cq7nma
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Setophaga pitiayumi)",
 "Country is one of (Afghanistan, Armenia, Azerbaijan, Bahrain, Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, Cyprus, Georgia, Hong Kong, India, Indonesia, Iran (Islamic Republic of), Iraq, Israel, Japan, Jordan, Kazakhstan, Korea (Democratic People’s Republic of), Korea, Republic of, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Lebanon, Macao, Malaysia, Maldives, Mongolia, Myanmar, Nepal, Oman, Pakistan, Palestine, State of, Philippines, Qatar, Saudi Arabia, Singapore, Sri Lanka, Syrian Arab Republic, Tajikistan, Thailand, Timor-Leste, Türkiye, Turkmenistan, United Arab Emirates, Uzbekistan, Viet Nam, Yemen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032002-250802193616735/datasets/export for details.
DOI: 10.15468/dl.yzqkds
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:AAB9335"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032004-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.snv7nb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Setophaga pitiayumi)",
 "Country is one of (American Samoa, Australia, Christmas Island, Cocos (Keeling) Islands, Cook Islands, Fiji, French Polynesia, Guam, Heard Island and McDonald Islands, Kiribati, Marshall Islands, Micronesia (Federated States of), Nauru, New Caledonia, New Zealand, Niue, Norfolk Island, Northern Mariana Islands, Palau, Papua New Guinea, Pitcairn, Samoa, Solomon Islands, Tokelau, Tonga, Tuvalu, United States Minor Outlying Islands, Vanuatu, Wallis and Futuna)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032005-250802193616735/datasets/export for details.
DOI: 10.15468/dl.x38syu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Setophaga pitiayumi)",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032006-250802193616735/datasets/export for details.
DOI: 10.5281/zenodo.16784467
title: Supplementary Materials for "Prognostic Significance of ctDNA Mutations in HER2-Targeted Breast Cancer Therapy: A Meta-analysis"

description: Supplementary Table 1. Summary of included studies evaluating the prognostic value of ctDNA mutation status in HER2-targeted therapy for breast cancer.

This table summarizes the key characteristics of the 12 included studies investigating the association between ctDNA mutation status and PFS in patients receiving anti-HER2 therapies. Data include publication year, country, study type, clinical phase, treatment regimens, ctDNA mutation frequency, and HR comparing PFS between MT and WT ctDNA groups.Abbreviations:ctDNA, circulating tumor DNA; PFS, progression-free survival; HR, hazard ratio; CI, confidence interval; WT, wild type; MT, mutant type; RCT, randomized controlled trial; N/A, not available; Y, yes; N, no.*Note: Median PFS values are reported in months. Where available, HRs and 95% confidence intervals were extracted directly from the original publications. All HRs calculated with wild-type as reference; HR>1 indicates worse prognosis in mutation group. Studies varied in anti-HER2 regimens, including monoclonal antibodies, TKIs, and ADCs, as well as combination with chemotherapy or endocrine therapy.

 

Supplementary Figure 1. Sensitivity analysis of ERBB2 subgroup.Supplementary Figure 2. Funnel plot of ERBB2 subgroup.  Supplementary Figure 3. Sensitivity analysis of PIK3CA subgroup.Supplementary Figure 4. Funnel plot of PIK3CA subgroup.

Supplementary Figure 5. Sensitivity analysis of the TKI subgroup.Supplementary Figure 6. Funnel plot of the TKI subgroup.

Supplementary Figure 7. Sensitivity analysis of the non-TKI subgroup.Supplementary Figure 8. Funnel plot of the non-TKI subgroup.

Supplementary Figure 9. Sensitivity analysis of the pyrotinib subgroup.Supplementary Figure 10. Funnel plot of the pyrotinib subgroup.

Supplementary Figure 11. Sensitivity analysis of the non-pyrotinib subgroup.Supplementary Figure 12. Funnel plot of the non-pyrotinib subgroup.

  Supplementary Figure 13. Sensitivity analysis of monotherapy subgroup.Supplementary Figure 14. Funnel plot of monotherapy subgroup.  Supplementary Figure 15. Sensitivity analysis of combination subgroup.Supplementary Figure 16. Funnel plot of combination subgroup.

Supplementary Figure 17. Sensitivity analysis of capecitabine-based subgroup.Supplementary Figure 18. Funnel plot of capecitabine-based subgroup.

Supplementary Figure 19. Sensitivity analysis of other combination subgroup.Supplementary Figure 20. Funnel plot of other combination subgroup.
DOI: 10.5281/zenodo.16784468
title: Supplementary Materials for "Prognostic Significance of ctDNA Mutations in HER2-Targeted Breast Cancer Therapy: A Meta-analysis"

description: Supplementary Table 1. Summary of included studies evaluating the prognostic value of ctDNA mutation status in HER2-targeted therapy for breast cancer.

This table summarizes the key characteristics of the 12 included studies investigating the association between ctDNA mutation status and PFS in patients receiving anti-HER2 therapies. Data include publication year, country, study type, clinical phase, treatment regimens, ctDNA mutation frequency, and HR comparing PFS between MT and WT ctDNA groups.Abbreviations:ctDNA, circulating tumor DNA; PFS, progression-free survival; HR, hazard ratio; CI, confidence interval; WT, wild type; MT, mutant type; RCT, randomized controlled trial; N/A, not available; Y, yes; N, no.*Note: Median PFS values are reported in months. Where available, HRs and 95% confidence intervals were extracted directly from the original publications. All HRs calculated with wild-type as reference; HR>1 indicates worse prognosis in mutation group. Studies varied in anti-HER2 regimens, including monoclonal antibodies, TKIs, and ADCs, as well as combination with chemotherapy or endocrine therapy.

 

Supplementary Figure 1. Sensitivity analysis of ERBB2 subgroup.Supplementary Figure 2. Funnel plot of ERBB2 subgroup.  Supplementary Figure 3. Sensitivity analysis of PIK3CA subgroup.Supplementary Figure 4. Funnel plot of PIK3CA subgroup.

Supplementary Figure 5. Sensitivity analysis of the TKI subgroup.Supplementary Figure 6. Funnel plot of the TKI subgroup.

Supplementary Figure 7. Sensitivity analysis of the non-TKI subgroup.Supplementary Figure 8. Funnel plot of the non-TKI subgroup.

Supplementary Figure 9. Sensitivity analysis of the pyrotinib subgroup.Supplementary Figure 10. Funnel plot of the pyrotinib subgroup.

Supplementary Figure 11. Sensitivity analysis of the non-pyrotinib subgroup.Supplementary Figure 12. Funnel plot of the non-pyrotinib subgroup.

  Supplementary Figure 13. Sensitivity analysis of monotherapy subgroup.Supplementary Figure 14. Funnel plot of monotherapy subgroup.  Supplementary Figure 15. Sensitivity analysis of combination subgroup.Supplementary Figure 16. Funnel plot of combination subgroup.

Supplementary Figure 17. Sensitivity analysis of capecitabine-based subgroup.Supplementary Figure 18. Funnel plot of capecitabine-based subgroup.

Supplementary Figure 19. Sensitivity analysis of other combination subgroup.Supplementary Figure 20. Funnel plot of other combination subgroup.
DOI: 10.15468/dl.vdgayj
title: Occurrence Download

description: A dataset containing 344 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Norfolkia thomasi"
 ]
}

 The dataset includes 344 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032008-250802193616735/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.29875031
title: Supplementary Material for: Diagnostic value and prognostic effect of miR-7-5p in cirrhosis

description: Objectives:
The purpose of this study was to examine miR-7-5p levels in patients with liver cirrhosis and its correlation with liver function, as well as to evaluate its clinical value as a diagnostic and prognostic biomarker.
Methods: 
miR-7-5p levels in 86 liver cirrhosis patients and 95 healthy volunteers were measured using qRT-PCR. Pearson correlation analysis was employed to calculate the relationship between miR-7-5p and liver function indicators (ALT, AST, PT, INR, TBil and albumin). ROC curve was conducted to evaluate its diagnostic significance. Additionally, Cox regression analysis and the Kaplan-Meier method were utilized to evaluate the prognostic significance of miR-7-5p.
Results: 
The findings revealed that miR-7-5p was upregulated in the serum liver cirrhosis patients. Its levels positively correlated with ALT (r = 0.319, P = 0.003), AST (r = 0.424, P &lt; 0.001), PT (r = 0.357, P &lt; 0.001), INR (r = 0.312, P = 0.003), TBil (r = 0.557, P &lt; 0.001), but negatively correlated with albumin (r = -0.484, P &lt; 0.001). ROC curve analysis indicated that the AUC for miR-7-5p was 0.862, demonstrating high diagnostic value. Furthermore, high miR-7-5p levels were linked to poorer survival rates and was confirmed as an independent prognostic factor for liver cirrhosis (95% CI 1.442-11.811, P = 0.008).
Conclusion: 
miR-7-5p not only demonstrated potential value in the diagnosis of liver cirrhosis but also effectively predicted patient prognosis. As a biomarker, miR-7-5p may provide important evidence for early diagnosis and the formulation of individualized care strategies for patients, thereby promoting improvements in clinical nursing practice.
DOI: 10.6084/m9.figshare.29875031.v1
title: Supplementary Material for: Diagnostic value and prognostic effect of miR-7-5p in cirrhosis

description: Objectives:
The purpose of this study was to examine miR-7-5p levels in patients with liver cirrhosis and its correlation with liver function, as well as to evaluate its clinical value as a diagnostic and prognostic biomarker.
Methods: 
miR-7-5p levels in 86 liver cirrhosis patients and 95 healthy volunteers were measured using qRT-PCR. Pearson correlation analysis was employed to calculate the relationship between miR-7-5p and liver function indicators (ALT, AST, PT, INR, TBil and albumin). ROC curve was conducted to evaluate its diagnostic significance. Additionally, Cox regression analysis and the Kaplan-Meier method were utilized to evaluate the prognostic significance of miR-7-5p.
Results: 
The findings revealed that miR-7-5p was upregulated in the serum liver cirrhosis patients. Its levels positively correlated with ALT (r = 0.319, P = 0.003), AST (r = 0.424, P &lt; 0.001), PT (r = 0.357, P &lt; 0.001), INR (r = 0.312, P = 0.003), TBil (r = 0.557, P &lt; 0.001), but negatively correlated with albumin (r = -0.484, P &lt; 0.001). ROC curve analysis indicated that the AUC for miR-7-5p was 0.862, demonstrating high diagnostic value. Furthermore, high miR-7-5p levels were linked to poorer survival rates and was confirmed as an independent prognostic factor for liver cirrhosis (95% CI 1.442-11.811, P = 0.008).
Conclusion: 
miR-7-5p not only demonstrated potential value in the diagnosis of liver cirrhosis but also effectively predicted patient prognosis. As a biomarker, miR-7-5p may provide important evidence for early diagnosis and the formulation of individualized care strategies for patients, thereby promoting improvements in clinical nursing practice.
DOI: 10.6084/m9.figshare.29875034
title: Supplementary Material for: Comprehensive Bioinformatics Analysis Reveals Associations Between the DNA Damage Response and Osteoarthritis

description: Introduction: DNA damage in chondrocytes has been found to be associated with osteoarthritis (OA) and could be a primary pathological mechanism of the disease. Here, we performed transcriptomic analysis of human chondrocytes using existing RNA-seq data sets to characterize DNA damage repair pathway alterations associated with OA status.
Methods: We collected 9 public RNA-seq datasets of cartilage samples in the Gene Expression Omnibus (GEO) from 57 OA patients and 35 non-OA controls. We identified differentially expressed genes (DEGs), examined enriched pathways, and predicted regulatory networks of the DNA damage response (DDR) in OA by comparing RNA-seq data from OA and non-OA chondrocytes. Furthermore, we evaluated the potential associations between DDR-related gene signatures and OA status.
Results: We identified 490 upregulated and 350 downregulated DEGs in OA. The upregulated DEGs are significantly enriched in DDR pathways, including the Fanconi anemia, mismatch repair and base excision repair pathways. A total of 10 significant DDR downstream pathways were enriched and upregulated in OA, including DNA replication, DNA repair and cell cycle pathways in relation to the DNA damage response. Finally, we identified 9 core genes for DNA damage repair in OA (DDR-OA genes) as potential targets for OA biomarkers. Three of these genes are known to be associated with both DDR processes and OA pathology.
Conclusion: Elevated expression of DDR-related genes and enhanced activity of DDR signaling pathways were observed in conjunction with OA onset and progression. Our computational analysis prioritizes identified DDR-OA genes as high-confidence candidates for further experimental investigation.
DOI: 10.6084/m9.figshare.29875034.v1
title: Supplementary Material for: Comprehensive Bioinformatics Analysis Reveals Associations Between the DNA Damage Response and Osteoarthritis

description: Introduction: DNA damage in chondrocytes has been found to be associated with osteoarthritis (OA) and could be a primary pathological mechanism of the disease. Here, we performed transcriptomic analysis of human chondrocytes using existing RNA-seq data sets to characterize DNA damage repair pathway alterations associated with OA status.
Methods: We collected 9 public RNA-seq datasets of cartilage samples in the Gene Expression Omnibus (GEO) from 57 OA patients and 35 non-OA controls. We identified differentially expressed genes (DEGs), examined enriched pathways, and predicted regulatory networks of the DNA damage response (DDR) in OA by comparing RNA-seq data from OA and non-OA chondrocytes. Furthermore, we evaluated the potential associations between DDR-related gene signatures and OA status.
Results: We identified 490 upregulated and 350 downregulated DEGs in OA. The upregulated DEGs are significantly enriched in DDR pathways, including the Fanconi anemia, mismatch repair and base excision repair pathways. A total of 10 significant DDR downstream pathways were enriched and upregulated in OA, including DNA replication, DNA repair and cell cycle pathways in relation to the DNA damage response. Finally, we identified 9 core genes for DNA damage repair in OA (DDR-OA genes) as potential targets for OA biomarkers. Three of these genes are known to be associated with both DDR processes and OA pathology.
Conclusion: Elevated expression of DDR-related genes and enhanced activity of DDR signaling pathways were observed in conjunction with OA onset and progression. Our computational analysis prioritizes identified DDR-OA genes as high-confidence candidates for further experimental investigation.
DOI: 10.6084/m9.figshare.29875037
title: Supplementary Material for: The effectiveness of lesion detection for IgG4-related kidney diseases by diffusion-weighted imaging

description: Objectives: To compare the efficacy of magnetic resonance imaging (MRI) with that of plain or contrast-enhanced computed tomography (CT) in the detection of renal parenchymal and pelvic lesions of immunoglobulin G4-related kidney disease (IgG4-RKD).
Methods: Patients with IgG4-RKD and controls, who performed plain, contrast-enhanced CT and MRI around the kidney region in our hospital were enrolled. The diagnosis of IgG4-RKD was made by definite cases of IgG4-RKD diagnostic criteria in 2020. Five blinded observers independently assessed image datasets by confidence scores to assess diagnostic accuracy, sensitivity, specificity, areas under the receiver operating characteristic curve (AUROC), and Cronbach's alpha coefficient.
Results: A total of 31 patients were included in the study. 14 (45.2%) had IgG4-RKD. Five patients with IgG4-RKD had parenchymal lesions, five had renal pelvic lesions, and four had both. In the parenchymal lesions, there was no significant difference in diagnostic performance between contrast-enhanced CT and diffusion-weighted imaging (DWI)-b800. The AUROC and sensitivity were higher in DWI-b800 than in plain CT (P &lt; 0.05). Cronbach's alpha coefficient was 0.44 for plain CT and over 0.80 for contrast-enhanced CT and DWI-b800. In the pelvic lesions, there were fewer differences in the performance among each sequence. Cronbach's alpha coefficient was over 0.80 for plain CT, contrast-enhanced CT, and DWI-b800.
Conclusion: Plain MRI, especially in DWI-b800, can effectively detect renal parenchymal lesions in IgG4-RKD. In difficult cases to use a contrast agent of CT, DWI-b800 can be an alternative for the screening of IgG4-RKD.
DOI: 10.6084/m9.figshare.29875037.v1
title: Supplementary Material for: The effectiveness of lesion detection for IgG4-related kidney diseases by diffusion-weighted imaging

description: Objectives: To compare the efficacy of magnetic resonance imaging (MRI) with that of plain or contrast-enhanced computed tomography (CT) in the detection of renal parenchymal and pelvic lesions of immunoglobulin G4-related kidney disease (IgG4-RKD).
Methods: Patients with IgG4-RKD and controls, who performed plain, contrast-enhanced CT and MRI around the kidney region in our hospital were enrolled. The diagnosis of IgG4-RKD was made by definite cases of IgG4-RKD diagnostic criteria in 2020. Five blinded observers independently assessed image datasets by confidence scores to assess diagnostic accuracy, sensitivity, specificity, areas under the receiver operating characteristic curve (AUROC), and Cronbach's alpha coefficient.
Results: A total of 31 patients were included in the study. 14 (45.2%) had IgG4-RKD. Five patients with IgG4-RKD had parenchymal lesions, five had renal pelvic lesions, and four had both. In the parenchymal lesions, there was no significant difference in diagnostic performance between contrast-enhanced CT and diffusion-weighted imaging (DWI)-b800. The AUROC and sensitivity were higher in DWI-b800 than in plain CT (P &lt; 0.05). Cronbach's alpha coefficient was 0.44 for plain CT and over 0.80 for contrast-enhanced CT and DWI-b800. In the pelvic lesions, there were fewer differences in the performance among each sequence. Cronbach's alpha coefficient was over 0.80 for plain CT, contrast-enhanced CT, and DWI-b800.
Conclusion: Plain MRI, especially in DWI-b800, can effectively detect renal parenchymal lesions in IgG4-RKD. In difficult cases to use a contrast agent of CT, DWI-b800 can be an alternative for the screening of IgG4-RKD.
DOI: 10.6084/m9.figshare.29875040
title: Supplementary Material for: Association of a Healthy Lifestyle with Risk of Parkinson’s Disease and Genetic Predisposition

description: Background: Parkinson’s disease (PD) is the second most common neurodegenerative disease with largely unknown etiology. Evaluating the association between a healthy lifestyle with PD and genetic risk is necessary. 
Methods: The study included 438,241 participants from UK Biobank, with lifestyle information collected via baseline questionnaires. Polygenic risk scores (PRS) were divided into quartiles. The healthy lifestyle, including alcohol consumption, BMI, physical activity, sleep duration, sedentary time, social connections, and diet, was categorized into favorable (scoring 6-7), intermediate (scoring 4-5), and unfavorable (scoring≤3) lifestyles.
Results: During an average follow-up of 9.34 years, 2,996 cases were diagnosed with PD. Compared to participants with an unfavorable lifestyle, those with a favorable lifestyle had a significantly lower risk (HR 0.862, 95% CI 0.753-0.986). Regular physical activity, adequate sleep, and appropriate social connection were protective factors for the risk of PD (HR 0.839, 95% CI 0.779-0.905; HR 0.921, 95% CI 0.851- 0.997; HR 0.790, 95% CI 0.698-0.893). Subgroup analysis by PRS showed that adhering to a healthy lifestyle reduced the risk of PD in all subgroups except the low genetic risk (HR 0.673, 95% CI 0.510-0.889; HR 0.774, 95% CI 0.611-0.982; HR 0.769, 95% CI 0.633-0.935). There was an interaction between high genetic risk and lifestyle scores and sleep duration (P=0.015 and P=0.024, respectively), also between sex and sedentary time (P=0.002). 
Conclusion: A healthy lifestyle was associated with a lower risk of PD, and it’s important to identify the effect of genetic risk and sex on PD significantly influenced by lifestyle.