cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29097512
title: Supplementary Material for: Association between Salivary pH and estimated glomerular filtration rate status in a community-dwelling population: A Cross-sectional Study

description: Introduction: Globally, chronic kidney disease (CKD) is a common condition, associated with several complications and high mortality. Early detection and monitoring of CKD is important for prolonging healthy life expectancy. Salivary pH is reported to increase in patients with chronic renal failure; however, the association between salivary pH and the estimated glomerular filtration rate (eGFR) status, which is usually considered to assess kidney function at clinical settings, has not been adequately studied. Therefore, this study aimed to examine the association between salivary pH and eGFR through multivariate analysis.
Methods: We conducted a cross-sectional study using the data from a community-based cohort study conducted between 2017 and 2019 in Japan. We aimed to develop a prediction model to determine the eGFR status using salivary pH, instead of blood urea nitrogen (BUN), in combination with self-reported information (age, sex, body mass index, disease history, medication, and lifestyle) in 1,056 subjects (433 men and 623 women) who participated in the study in 2017. We first identified the logistic model including several explanatory variables in addition to BUN (BUN model) and also developed the logistic model that replaced BUN with salivary pH (pH model). We examined the predictive accuracy of the two developed models using the validation data of 298 subjects (116 men and 182 women) who participated in the study in 2019.
Results: BUN and salivary pH were significantly associated with the eGFR status (odds ratio (ORs): 1.24, 95% confidence interval (CI): 1.17–1.32, P &lt; 0.001 for BUN; ORs: 0.96, 95% CI: 0.94–0.98, P &lt; 0.001 for salivary pH, respectively). The developed pH model included age, kidney disease history, diabetes history, habitual medication for hypertension, habitual alcohol consumption status, and habitual exercise status in addition to salivary pH. The pH model showed accuracy comparable to that of BUN model in determining the eGFR status (area under the curve for the pH and BUN models was 0.796 and 0.799, respectively; P = 0.933).
Conclusion: This study clarified the association between salivary pH and the eGFR status.
DOI: 10.6084/m9.figshare.29097512.v1
title: Supplementary Material for: Association between Salivary pH and estimated glomerular filtration rate status in a community-dwelling population: A Cross-sectional Study

description: Introduction: Globally, chronic kidney disease (CKD) is a common condition, associated with several complications and high mortality. Early detection and monitoring of CKD is important for prolonging healthy life expectancy. Salivary pH is reported to increase in patients with chronic renal failure; however, the association between salivary pH and the estimated glomerular filtration rate (eGFR) status, which is usually considered to assess kidney function at clinical settings, has not been adequately studied. Therefore, this study aimed to examine the association between salivary pH and eGFR through multivariate analysis.
Methods: We conducted a cross-sectional study using the data from a community-based cohort study conducted between 2017 and 2019 in Japan. We aimed to develop a prediction model to determine the eGFR status using salivary pH, instead of blood urea nitrogen (BUN), in combination with self-reported information (age, sex, body mass index, disease history, medication, and lifestyle) in 1,056 subjects (433 men and 623 women) who participated in the study in 2017. We first identified the logistic model including several explanatory variables in addition to BUN (BUN model) and also developed the logistic model that replaced BUN with salivary pH (pH model). We examined the predictive accuracy of the two developed models using the validation data of 298 subjects (116 men and 182 women) who participated in the study in 2019.
Results: BUN and salivary pH were significantly associated with the eGFR status (odds ratio (ORs): 1.24, 95% confidence interval (CI): 1.17–1.32, P &lt; 0.001 for BUN; ORs: 0.96, 95% CI: 0.94–0.98, P &lt; 0.001 for salivary pH, respectively). The developed pH model included age, kidney disease history, diabetes history, habitual medication for hypertension, habitual alcohol consumption status, and habitual exercise status in addition to salivary pH. The pH model showed accuracy comparable to that of BUN model in determining the eGFR status (area under the curve for the pH and BUN models was 0.796 and 0.799, respectively; P = 0.933).
Conclusion: This study clarified the association between salivary pH and the eGFR status.
DOI: 10.6084/m9.figshare.29097515
title: Supplementary Material for: The association between number of retrieved lymph nodes and survival in gastric cancer surgery: a Dutch population-based study

description: Background:
This study aimed to evaluate whether the retrieval of 15 or more lymph nodes (LN) during gastrectomy for cancer is associated with better survival and more accurate pathological staging.

Methods:
Patients that underwent gastrectomy between 2011 and 2016 were reviewed from the Dutch Upper Gastrointestinal Cancer Audit. Patients with &lt;15 and ≥15 LN retrieved were compared after propensity-score matching based on patient and tumor characteristics. The primary endpoint was 3-year overall survival. 

Results:
A total of 2047 patients were included in the study. After propensity score matching, 522 patients with ≥15 LNs were matched to 522 patients with &lt;15 LNs. There was no statistically significant difference in overall survival between both groups, with 3-year survival rates of 56% versus 59%, respectively. Patients with ≥15 LNs had a more advanced pN-category. While median survival was higher for patients with ≥15 LNs versus &lt;15 LNs in the subgroups pN2, pN3a, and pN3b, no statistically significant differences were found. Similar results were found in the propensity score matched cohort using 23 LNs as cut-off.

Conclusions:
≥15 LNs retrieved during gastrectomy for cancer was associated with higher pN-stage, likely as a result of stage migration. Three-year overall survival was comparable for patients with ≥15 LNs and patients with &lt;15 LNs retrieved.
DOI: 10.6084/m9.figshare.29097515.v1
title: Supplementary Material for: The association between number of retrieved lymph nodes and survival in gastric cancer surgery: a Dutch population-based study

description: Background:
This study aimed to evaluate whether the retrieval of 15 or more lymph nodes (LN) during gastrectomy for cancer is associated with better survival and more accurate pathological staging.

Methods:
Patients that underwent gastrectomy between 2011 and 2016 were reviewed from the Dutch Upper Gastrointestinal Cancer Audit. Patients with &lt;15 and ≥15 LN retrieved were compared after propensity-score matching based on patient and tumor characteristics. The primary endpoint was 3-year overall survival. 

Results:
A total of 2047 patients were included in the study. After propensity score matching, 522 patients with ≥15 LNs were matched to 522 patients with &lt;15 LNs. There was no statistically significant difference in overall survival between both groups, with 3-year survival rates of 56% versus 59%, respectively. Patients with ≥15 LNs had a more advanced pN-category. While median survival was higher for patients with ≥15 LNs versus &lt;15 LNs in the subgroups pN2, pN3a, and pN3b, no statistically significant differences were found. Similar results were found in the propensity score matched cohort using 23 LNs as cut-off.

Conclusions:
≥15 LNs retrieved during gastrectomy for cancer was associated with higher pN-stage, likely as a result of stage migration. Three-year overall survival was comparable for patients with ≥15 LNs and patients with &lt;15 LNs retrieved.
DOI: 10.6084/m9.figshare.29097518
title: Supplementary Material for: High ultra-processed food consumption is associated with clinical exacerbation in patients with Crohn's disease in remission - a prospective cohort study

description: Introduction: Diet can impact the clinical course of Crohn’s disease (CD). However, the importance of food processing level is uncertain. We aimed to evaluate whether ultra-processed foods (UPFs) are associated with an increased risk of relapse amongst patients with CD in clinical remission. 
Methods: In this prospective cohort study, adult patients with CD in clinical remission, were followed for one year or until clinical relapse, as assessed by the Harvey Bradshaw index. Dietary intake was assessed using a food frequency questionnaire and a dedicated validated processed food questionnaire to evaluate UPFs consumption. Multivariable Cox proportional hazard models were used to estimate the adjusted hazard ratio of disease relapse according to high or low UPFs consumption. 
Results: A total of 111 patients with CD (mean age 37.9±14.0 years) in clinical remission were followed. Over a median period of 12 months [interquartile range, 8-12], 24 patients (21.6%) experienced clinical relapse. Fecal calprotectin levels were increased at relapse visit compared to baseline (193.0 μg/g [114.0-807.0], 79.0 μg/g [17.0-274.5], respectively, P=0.002). A higher intake of UPFs was associated with an increased risk of CD relapse (HR=3.86, 95% CI 1.30-11.47). Ultra-processed breads and pastries, as well as oils and spreads, were the UPF subgroups with the strongest positive associations (HR=3.27, 95% CI 1.26-8.45; HR=2.76, 95% CI 1.02-7.45, respectively).
Conclusion: UPFs consumption is associated with an increased risk of relapse in patients with CD in remission. This study, along with future research, can contribute to establishing nutritional guidelines aimed to reduce UPFs consumption in this population.
DOI: 10.6084/m9.figshare.29097518.v1
title: Supplementary Material for: High ultra-processed food consumption is associated with clinical exacerbation in patients with Crohn's disease in remission - a prospective cohort study

description: Introduction: Diet can impact the clinical course of Crohn’s disease (CD). However, the importance of food processing level is uncertain. We aimed to evaluate whether ultra-processed foods (UPFs) are associated with an increased risk of relapse amongst patients with CD in clinical remission. 
Methods: In this prospective cohort study, adult patients with CD in clinical remission, were followed for one year or until clinical relapse, as assessed by the Harvey Bradshaw index. Dietary intake was assessed using a food frequency questionnaire and a dedicated validated processed food questionnaire to evaluate UPFs consumption. Multivariable Cox proportional hazard models were used to estimate the adjusted hazard ratio of disease relapse according to high or low UPFs consumption. 
Results: A total of 111 patients with CD (mean age 37.9±14.0 years) in clinical remission were followed. Over a median period of 12 months [interquartile range, 8-12], 24 patients (21.6%) experienced clinical relapse. Fecal calprotectin levels were increased at relapse visit compared to baseline (193.0 μg/g [114.0-807.0], 79.0 μg/g [17.0-274.5], respectively, P=0.002). A higher intake of UPFs was associated with an increased risk of CD relapse (HR=3.86, 95% CI 1.30-11.47). Ultra-processed breads and pastries, as well as oils and spreads, were the UPF subgroups with the strongest positive associations (HR=3.27, 95% CI 1.26-8.45; HR=2.76, 95% CI 1.02-7.45, respectively).
Conclusion: UPFs consumption is associated with an increased risk of relapse in patients with CD in remission. This study, along with future research, can contribute to establishing nutritional guidelines aimed to reduce UPFs consumption in this population.
DOI: 10.6084/m9.figshare.29097521
title: Supplementary Material for: Chronic allograft injury by recurrent crystalline nephropathy of Adenine Phosphoribosyl transferase Deficiency, even after early initiation of XOR inhibitor

description: Introduction: Adenine phosphoribosyl　transferase (APRT) deficiency is a rare genetic disorder of purine metabolism that results in excessive renal excretion of poorly soluble 2,8-dihydroxyadenine (DHA), leading to urolithiasis, crystalline nephropathy, and renal failure. Recurrence after renal transplantation usually occurs in the early post-transplantation period and is sometimes the initial indication for the disease. Allograft survival is poor without adequate treatment with xanthine oxidase (XOR) inhibitors to reduce DHA levels. Case presentation: A 49-year-old Japanese man with a history of recurrent renal stones presented with mild renal dysfunction three months after renal transplantation. Allograft biopsy revealed numerous brown crystals within the tubules and active interstitial inflammation. Febuxostat, a high-dose XOR inhibitor, was immediately prescribed. APRT deficiency was confirmed through urine metabolome analysis. The patient’s renal function improved, and the febuxostat dose was subsequently reduced. One-year allograft biopsy demonstrated markedly reduced inflammation and crystals; however, an expanded scarred area with focal active inflammation and a few small crystals were observed. Conclusion: XOR inhibitors effectively reduce the crystals of recurrent APRT deficiency; however, they cannot prevent chronic injury. Diagnosing recurrent crystalline nephropathy and initiating XOR inhibitors as early as possible is essential for improving allograft survival.
DOI: 10.6084/m9.figshare.29097521.v1
title: Supplementary Material for: Chronic allograft injury by recurrent crystalline nephropathy of Adenine Phosphoribosyl transferase Deficiency, even after early initiation of XOR inhibitor

description: Introduction: Adenine phosphoribosyl　transferase (APRT) deficiency is a rare genetic disorder of purine metabolism that results in excessive renal excretion of poorly soluble 2,8-dihydroxyadenine (DHA), leading to urolithiasis, crystalline nephropathy, and renal failure. Recurrence after renal transplantation usually occurs in the early post-transplantation period and is sometimes the initial indication for the disease. Allograft survival is poor without adequate treatment with xanthine oxidase (XOR) inhibitors to reduce DHA levels. Case presentation: A 49-year-old Japanese man with a history of recurrent renal stones presented with mild renal dysfunction three months after renal transplantation. Allograft biopsy revealed numerous brown crystals within the tubules and active interstitial inflammation. Febuxostat, a high-dose XOR inhibitor, was immediately prescribed. APRT deficiency was confirmed through urine metabolome analysis. The patient’s renal function improved, and the febuxostat dose was subsequently reduced. One-year allograft biopsy demonstrated markedly reduced inflammation and crystals; however, an expanded scarred area with focal active inflammation and a few small crystals were observed. Conclusion: XOR inhibitors effectively reduce the crystals of recurrent APRT deficiency; however, they cannot prevent chronic injury. Diagnosing recurrent crystalline nephropathy and initiating XOR inhibitors as early as possible is essential for improving allograft survival.
DOI: 10.15468/dl.bbvnfy
title: Occurrence Download

description: A dataset containing 2526 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.5_1",
 "TaxonKey is Myotis yumanensis (H.Allen, 1864)"
 ]
}

 The dataset includes 2526 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006552-250515123054153/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.29097524
title: Supplementary Material for: Exploring the Heterogeneity of Pediatric Neuroendocrine Tumors: Single-Center Experience

description: Introduction: Neuroendocrine tumors (NETs) are rare, slow-growing tumors with distinct clinical manifestations that can be challenging to diagnose and treat, particularly in children. This retrospective study aimed to improve diagnosis and treatment of NETs by evaluating their clinical course, hormonal activity, and long-term effects in children.
Methods: A retrospective study was conducted on 26 pediatric patients diagnosed with NETs between 2000 and 2024. The cohort included patients with pheochromocytoma and paraganglioma (PPGL), gastroenteropancreatic neuroendocrine tumors (GEP-NETs) medullary thyroid carcinoma (MTC), C cell hyperplasia. The data included demographic, clinical, laboratory, and imaging results.
Results: The study cohort included 26 patients (57.6% male). The median age for diagnosis of NETs was 8.8 (range: 1.0–16.6) years. Among the NETs, 15.4% were GEP-NETs, 15.4% were PPGL, 15.4% were C cell hyperplasia and 53.8% were MTC. The median follow-up was 5 (range: 1–14) years. Among the patients in the study cohort, only one patient died due to MTC. Genetic analysis revealed mutations in the RET gene in 69.2% of patients, mutations in the VHL gene in 3.8%, and no mutations in 3.8%. 23% of the patients did not undergo genetic testing.
Conclusion: Early diagnosis, genetic screening, and long-term follow-up are crucial in managing pediatric NETs to reduce morbidity and mortality. Genetic testing is essential for identifying comorbidities and screening family members at risk.
DOI: 10.6084/m9.figshare.29097524.v1
title: Supplementary Material for: Exploring the Heterogeneity of Pediatric Neuroendocrine Tumors: Single-Center Experience

description: Introduction: Neuroendocrine tumors (NETs) are rare, slow-growing tumors with distinct clinical manifestations that can be challenging to diagnose and treat, particularly in children. This retrospective study aimed to improve diagnosis and treatment of NETs by evaluating their clinical course, hormonal activity, and long-term effects in children.
Methods: A retrospective study was conducted on 26 pediatric patients diagnosed with NETs between 2000 and 2024. The cohort included patients with pheochromocytoma and paraganglioma (PPGL), gastroenteropancreatic neuroendocrine tumors (GEP-NETs) medullary thyroid carcinoma (MTC), C cell hyperplasia. The data included demographic, clinical, laboratory, and imaging results.
Results: The study cohort included 26 patients (57.6% male). The median age for diagnosis of NETs was 8.8 (range: 1.0–16.6) years. Among the NETs, 15.4% were GEP-NETs, 15.4% were PPGL, 15.4% were C cell hyperplasia and 53.8% were MTC. The median follow-up was 5 (range: 1–14) years. Among the patients in the study cohort, only one patient died due to MTC. Genetic analysis revealed mutations in the RET gene in 69.2% of patients, mutations in the VHL gene in 3.8%, and no mutations in 3.8%. 23% of the patients did not undergo genetic testing.
Conclusion: Early diagnosis, genetic screening, and long-term follow-up are crucial in managing pediatric NETs to reduce morbidity and mortality. Genetic testing is essential for identifying comorbidities and screening family members at risk.
DOI: 10.5281/zenodo.15430547
title: INDmet: A High-Resolution (0.05º) Daily Precipitation and Temperature Dataset for India

description: High-resolution meteorological data are essential for managing risks, planning resources, and modelling water systems. However, detailed daily meteorological datasets at a fine scale (0.05°) have been unavailable for India. To address this gap, we created INDmet, a daily dataset covering 1981-2024 for precipitation, maximum temperature, and minimum temperature. INDmet was developed using India Meteorological Department (IMD) observations (0.25° resolution), higher-resolution CHIRPS, and ERA5-Land data. Validation against ground station data shows INDmet effectively captures local climate patterns and extremes such as heatwaves, droughts, and heavy rainfall, supporting improved planning and risk management.
DOI: 10.5281/zenodo.15430548
title: INDmet: A High-Resolution (0.05º) Daily Precipitation and Temperature Dataset for India

description: High-resolution meteorological data are essential for managing risks, planning resources, and modelling water systems. However, detailed daily meteorological datasets at a fine scale (0.05°) have been unavailable for India. To address this gap, we created INDmet, a daily dataset covering 1981-2024 for precipitation, maximum temperature, and minimum temperature. INDmet was developed using India Meteorological Department (IMD) observations (0.25° resolution), higher-resolution CHIRPS, and ERA5-Land data. Validation against ground station data shows INDmet effectively captures local climate patterns and extremes such as heatwaves, droughts, and heavy rainfall, supporting improved planning and risk management.
DOI: 10.15468/dl.gduzzq
title: Occurrence Download

description: A dataset containing 1764 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Meryta J.R.Forst. & G.Forst."
 ]
}

 The dataset includes 1764 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006553-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdfcbr
title: Occurrence Download

description: A dataset containing 284 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((123.77682 49.5703,78.57991 34.50466,98.03034 1.0005,144.12667 16.96556,152.22164 44.84823,123.77682 49.5703))",
 "TaxonKey is Cyclobalanopsis Oerst."
 ]
}

 The dataset includes 284 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006554-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.