cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25573/data.16828294.v1
title: (high-temp) No 8. Metadata Analysis (16S rRNA/ITS) Output

description: <strong>Output files from the 8. Metadata Analysis Workflow</strong> page of the SWELTR high-temp study. In this workflow, we compared environmental metadata with microbial communities. The workflow is split into two parts.<br> <br> <strong>metadata_ssu18_wf.rdata</strong>: Part 1 contains all variables and objects for the 16S rRNA analysis. To see the Objects, in R run <em>load("metadata_ssu18_wf.rdata", verbose=TRUE)</em><br> <br> <strong>metadata_its18_wf.rdata</strong>: Part 2 contains all variables and objects for the ITS analysis. To see the Objects, in R run <em>load("metadata_its18_wf.rdata", verbose=TRUE)</em><br> Additional files:<br> <br> In both workflows, we run the following steps:<br> <br> <strong>1</strong>) Metadata Normality Tests: Shapiro-Wilk Normality Test to test whether each matadata parameter is normally distributed.<br> <strong>2</strong>) Normalize Parameters: R package bestNormalize to find and execute the best normalizing transformation.<br> <strong>3</strong>) Split Metadata parameters into groups: a) Environmental and edaphic properties, b) Microbial functional responses, and c) Temperature adaptation properties.<br> <strong>4</strong>) Autocorrelation Tests: Test all possible pair-wise comparisons, on both normalized and non-normalized data sets, for each group.<br> <strong>5</strong>) Remove autocorrelated parameters from each group.<br> <strong>6</strong>) Dissimilarity Correlation Tests: Use Mantel Tests to see if any on the metadata groups are significantly correlated with the community data.<br> <strong>7</strong>) Best Subset of Variables: Determine which of the metadata parameters from each group are the most strongly correlated with the community data. For this we use the bioenv function from the vegan package.<br> <strong>8</strong>) Distance-based Redundancy Analysis: Ordination analysis of samples and metadata vector overlays using capscale, also from the vegan package.<br> <br> Source code for the workflow can be found here:<br> https://github.com/sweltr/high-temp/blob/master/metadata.Rmd<br> <br> <br>
DOI: 10.6084/m9.figshare.19964229
title: High prevalence of biochemical disturbances of chronic kidney disease - mineral and bone disorders (CKD-MBD) in a nation-wide peritoneal dialysis cohort: are guideline goals too hard to achieve?

description: Abstract Introduction: Chronic kidney disease - mineral and bone disorders (CKD-MBD) are common in dialysis patients. Definition of targets for calcium (Ca), phosphorus (P), parathormone (iPTH), and alkaline phosphatase (ALP) and their treatment recommendations, are provided by international guidelines. There are few studies analyzing CKD-MBD in peritoneal dialysis (PD) patients and the impact of guidelines on mineral metabolism control. The aim of our study was to describe the prevalence of biomarkers for CKD-MBD in a large cohort of PD patients in Brazil. Methods: Data from the nation-wide prospective observational cohort BRAZPD II was used. Incident patients were followed between December 2004 and January 2011. According to KDOQI recommendations, reference ranges for total Ca were 8.4 to 9.5 mg/dL, for P, 3.5 to 5.5 mg/dL, for iPTH, 150-300 pg/mL, and for ALP, 120 U/L. Results: Mean age was 59.8 ± 16 years, 48% were male, and 43% had diabetes. In the beginning, Ca was 8.9 ± 0.9 mg/dL, and 48.3% were on the KODQI target. After 1 year, Ca increased to 9.1 ± 0.9 mg/dL and 50.4% were in the KDOQI preferred range. P at baseline was 5.2 ± 1.6 mg/dL, with 52.8% on target, declining to 4.9 ± 1.5 mg/dL after one year, when 54.7% were on target. Median iPTH at baseline was 238 (P25% 110 - P75% 426 pg/mL) and it remained stable throughout the first year; patients within target ranged from 26 to 28.5%. At the end of the study, 80% was in 3.5 meq/L Ca dialysate concentration, 66.9% of patients was taking any phosphate binder, and 25% was taking activated vitamin D. Conclusions: We observed a significant prevalence of biochemical disorders related to CKD-MBD in this dialysis population.
DOI: 10.6084/m9.figshare.19964229.v1
title: High prevalence of biochemical disturbances of chronic kidney disease - mineral and bone disorders (CKD-MBD) in a nation-wide peritoneal dialysis cohort: are guideline goals too hard to achieve?

description: Abstract Introduction: Chronic kidney disease - mineral and bone disorders (CKD-MBD) are common in dialysis patients. Definition of targets for calcium (Ca), phosphorus (P), parathormone (iPTH), and alkaline phosphatase (ALP) and their treatment recommendations, are provided by international guidelines. There are few studies analyzing CKD-MBD in peritoneal dialysis (PD) patients and the impact of guidelines on mineral metabolism control. The aim of our study was to describe the prevalence of biomarkers for CKD-MBD in a large cohort of PD patients in Brazil. Methods: Data from the nation-wide prospective observational cohort BRAZPD II was used. Incident patients were followed between December 2004 and January 2011. According to KDOQI recommendations, reference ranges for total Ca were 8.4 to 9.5 mg/dL, for P, 3.5 to 5.5 mg/dL, for iPTH, 150-300 pg/mL, and for ALP, 120 U/L. Results: Mean age was 59.8 ± 16 years, 48% were male, and 43% had diabetes. In the beginning, Ca was 8.9 ± 0.9 mg/dL, and 48.3% were on the KODQI target. After 1 year, Ca increased to 9.1 ± 0.9 mg/dL and 50.4% were in the KDOQI preferred range. P at baseline was 5.2 ± 1.6 mg/dL, with 52.8% on target, declining to 4.9 ± 1.5 mg/dL after one year, when 54.7% were on target. Median iPTH at baseline was 238 (P25% 110 - P75% 426 pg/mL) and it remained stable throughout the first year; patients within target ranged from 26 to 28.5%. At the end of the study, 80% was in 3.5 meq/L Ca dialysate concentration, 66.9% of patients was taking any phosphate binder, and 25% was taking activated vitamin D. Conclusions: We observed a significant prevalence of biochemical disorders related to CKD-MBD in this dialysis population.
DOI: 10.6084/m9.figshare.19964236.v1
title: Rice bran modulates renal disease risk factors in animals submitted to high sugar-fat diet

description: Abstract Introduction: Obesity, diabetes, and hypertension are common risk factors for chronic kidney disease (CKD). CKD arises due to many pathological insults, including inflammation and oxidative stress, which affect renal function and destroy nephrons. Rice bran (RB) is rich in vitamins and minerals, and contains signiﬁcant amount of antioxidants. The aim of this study was to evaluate the preventive effect of RB on renal disease risk factors. Methods: Male Wistar rats (±325 g) were divided into two experimental groups to received a high sugar-fat diet (HSF, n = 8) or high sugar-fat diet with rice bran (HSF + RB, n = 8) for 20 weeks. At the end, renal function, body composition, metabolic parameters, renal inflammatory and oxidative stress markers were analyzed. Results: RB prevented obesity [AI (HSF= 9.92 ± 1.19 vs HSF + RB= 6.62 ± 0.78)], insulin resistance [HOMA (HSF= 83 ± 8 vs. HSF + RB= 42 ± 11)], dyslipidemia [TG (HSF= 167 ± 41 vs. HSF + RB=92 ± 40)], inflammation [TNF-α (HSF= 80 ± 12 vs. HSF + RB=57 ± 14), IL-6 (903 ± 274 vs. HSF + RB=535 ± 277)], oxidative stress [protein carbonylation (HSF= 3.38 ± 0.18 vs. HSF + RB=2.68 ± 0.29), RAGE (HSF=702 ± 36 vs. RSF + RB=570 ± 190)], and renal disease [protein/creatinine ratio (HSF=1.10 ± 0.38 vs. HSF + RB=0.49 ± 0.16)]. Conclusion: In conclusion, rice bran prevented renal disease by modulating risk factors.
DOI: 10.6084/m9.figshare.19964236
title: Rice bran modulates renal disease risk factors in animals submitted to high sugar-fat diet

description: Abstract Introduction: Obesity, diabetes, and hypertension are common risk factors for chronic kidney disease (CKD). CKD arises due to many pathological insults, including inflammation and oxidative stress, which affect renal function and destroy nephrons. Rice bran (RB) is rich in vitamins and minerals, and contains signiﬁcant amount of antioxidants. The aim of this study was to evaluate the preventive effect of RB on renal disease risk factors. Methods: Male Wistar rats (±325 g) were divided into two experimental groups to received a high sugar-fat diet (HSF, n = 8) or high sugar-fat diet with rice bran (HSF + RB, n = 8) for 20 weeks. At the end, renal function, body composition, metabolic parameters, renal inflammatory and oxidative stress markers were analyzed. Results: RB prevented obesity [AI (HSF= 9.92 ± 1.19 vs HSF + RB= 6.62 ± 0.78)], insulin resistance [HOMA (HSF= 83 ± 8 vs. HSF + RB= 42 ± 11)], dyslipidemia [TG (HSF= 167 ± 41 vs. HSF + RB=92 ± 40)], inflammation [TNF-α (HSF= 80 ± 12 vs. HSF + RB=57 ± 14), IL-6 (903 ± 274 vs. HSF + RB=535 ± 277)], oxidative stress [protein carbonylation (HSF= 3.38 ± 0.18 vs. HSF + RB=2.68 ± 0.29), RAGE (HSF=702 ± 36 vs. RSF + RB=570 ± 190)], and renal disease [protein/creatinine ratio (HSF=1.10 ± 0.38 vs. HSF + RB=0.49 ± 0.16)]. Conclusion: In conclusion, rice bran prevented renal disease by modulating risk factors.
DOI: 10.6084/m9.figshare.19964238
title: Cardiovascular mortality in peritoneal dialysis: the impact of mineral disorders

description: Abstract Introduction: Mineral and bone disorders (MBD) are associated with higher mortality in dialysis patients. The main guidelines related to the subject, Kidney Disease Outcomes Quality Initiative (KDOQI) and Kidney Disease: Improving Global Outcomes (KDIGO), were elaborated based on published information from hemodialysis participants. The aim of our study was to evaluate the impact of calcium (Ca), phosphorus (P), and parathyroid hormone (PTH) (according to guideline ranges from KDOQI and KDIGO) on the cardiovascular mortality of peritoneal dialysis (PD) patients. Methods: We used the BRAZPDII database, an observational multi-centric prospective study, which assessed participants on PD between December 2004 and January 2011. Amongst 9,905 participants included in this database, we analyzed 4424 participants who were on PD for at least 6 months. The appropriate confounding variables were entered into the model. Serum levels of Ca, P, and PTH were the variables of interest for the purposes of the current study. Results: We found a significant association between high P serum levels, categorized by KDOQI and KDIGO (P above 5.5 mg/dL), and cardiovascular survival (p &lt; 0.01). Likewise, a compelling association was found between lower levels of PTH, categorized by guidelines (KDOQI and KDIGO - PTH less than 150 pg/mL, p &lt; 0.01), and cardiovascular survival. Conclusion: In conclusion, levels of P above and PTH below the values proposed by KDOQI and KDIGO were associated with cardiovascular mortality in PD patients.
DOI: 10.6084/m9.figshare.19964238.v1
title: Cardiovascular mortality in peritoneal dialysis: the impact of mineral disorders

description: Abstract Introduction: Mineral and bone disorders (MBD) are associated with higher mortality in dialysis patients. The main guidelines related to the subject, Kidney Disease Outcomes Quality Initiative (KDOQI) and Kidney Disease: Improving Global Outcomes (KDIGO), were elaborated based on published information from hemodialysis participants. The aim of our study was to evaluate the impact of calcium (Ca), phosphorus (P), and parathyroid hormone (PTH) (according to guideline ranges from KDOQI and KDIGO) on the cardiovascular mortality of peritoneal dialysis (PD) patients. Methods: We used the BRAZPDII database, an observational multi-centric prospective study, which assessed participants on PD between December 2004 and January 2011. Amongst 9,905 participants included in this database, we analyzed 4424 participants who were on PD for at least 6 months. The appropriate confounding variables were entered into the model. Serum levels of Ca, P, and PTH were the variables of interest for the purposes of the current study. Results: We found a significant association between high P serum levels, categorized by KDOQI and KDIGO (P above 5.5 mg/dL), and cardiovascular survival (p &lt; 0.01). Likewise, a compelling association was found between lower levels of PTH, categorized by guidelines (KDOQI and KDIGO - PTH less than 150 pg/mL, p &lt; 0.01), and cardiovascular survival. Conclusion: In conclusion, levels of P above and PTH below the values proposed by KDOQI and KDIGO were associated with cardiovascular mortality in PD patients.
DOI: 10.6084/m9.figshare.19964239
title: AGEs accumulation is related to muscle degeneration and vascular calcification in peritoneal dialysis patients

description: Abstract Background: Patients with chronic kidney disease (CKD) are affected by dynapenia, sarcopenia, and vascular calcification. Advanced glycation end products (AGEs) may accumulate in peritoneal dialysis (PD) patients and favor sarcopenia via changes in collagen cross-linking, muscle protein breakdown, and the calcification of arterial smooth muscle cells via p38-MAPK activation. The aim of this study is to explore the relationships between AGEs, muscle degeneration, and coronary artery calcification. Methods: This was a clinical observational study in patients with CKD undergoing PD, in which serum and skin AGEs (AGEs-sAF), cumulative glucose load, muscle strength and functional tests, muscle ultrasounds with elastography, coronary artery calcium (CAC) quantification, and muscle density by multislice computed tomography were measured. Results: 27 patients aged 48±16 years, dialysis vintage of 27±17 months, had AGEs-sAF levels of 3.09±0.65 AU (elevated in 13 [87%] patients), grip strength levels of 26.2±9.2 kg (11 [42%] patients with dynapenia), gait speed of 1.04±0.3 m/s (abnormal in 14 [58%] patients) and "timed-up-and-go test" (TUG) of 10.5±2.2s (abnormal in 7 [26%] patients). Correlations between AGEs-sAF levels and femoral rectus elastography (R=-0.74; p=0.02), anterior-tibialis elastography (R= -0.68; p=0.04) and CAC (R=0.64; p=0.04) were detected. Cumulative glucose load correlated with femoral rectal elastography (R=-0.6; p=0.02), and serum glycated hemoglobin concentrations correlated with psoas muscle density (R= -0.58; p=0.04) and CAC correlated with psoas muscle density (R=0.57; p=0.01) and lumbar square muscle density (R=-0.63; p=0.005). Conclusions: The study revealed associations between AGEs accumulation and lower muscle stiffness/density. Associations that linked muscle degeneration parameters with vascular calcification were observed.
DOI: 10.6084/m9.figshare.19964239.v1
title: AGEs accumulation is related to muscle degeneration and vascular calcification in peritoneal dialysis patients

description: Abstract Background: Patients with chronic kidney disease (CKD) are affected by dynapenia, sarcopenia, and vascular calcification. Advanced glycation end products (AGEs) may accumulate in peritoneal dialysis (PD) patients and favor sarcopenia via changes in collagen cross-linking, muscle protein breakdown, and the calcification of arterial smooth muscle cells via p38-MAPK activation. The aim of this study is to explore the relationships between AGEs, muscle degeneration, and coronary artery calcification. Methods: This was a clinical observational study in patients with CKD undergoing PD, in which serum and skin AGEs (AGEs-sAF), cumulative glucose load, muscle strength and functional tests, muscle ultrasounds with elastography, coronary artery calcium (CAC) quantification, and muscle density by multislice computed tomography were measured. Results: 27 patients aged 48±16 years, dialysis vintage of 27±17 months, had AGEs-sAF levels of 3.09±0.65 AU (elevated in 13 [87%] patients), grip strength levels of 26.2±9.2 kg (11 [42%] patients with dynapenia), gait speed of 1.04±0.3 m/s (abnormal in 14 [58%] patients) and "timed-up-and-go test" (TUG) of 10.5±2.2s (abnormal in 7 [26%] patients). Correlations between AGEs-sAF levels and femoral rectus elastography (R=-0.74; p=0.02), anterior-tibialis elastography (R= -0.68; p=0.04) and CAC (R=0.64; p=0.04) were detected. Cumulative glucose load correlated with femoral rectal elastography (R=-0.6; p=0.02), and serum glycated hemoglobin concentrations correlated with psoas muscle density (R= -0.58; p=0.04) and CAC correlated with psoas muscle density (R=0.57; p=0.01) and lumbar square muscle density (R=-0.63; p=0.005). Conclusions: The study revealed associations between AGEs accumulation and lower muscle stiffness/density. Associations that linked muscle degeneration parameters with vascular calcification were observed.
DOI: 10.6084/m9.figshare.19964242
title: Blood pressure control of hypertensive patients followed in a high complexity clinic and associated variables

description: Abstract Introduction: Arterial hypertension is a disease that has a high impact on cardiovascular mortality and morbidity; however, it is still insufficiently controlled. Objectives: To assess hypertension control in patients seen at a specialized clinic and to identify associated variables. Method: Cross-sectional study involving the analysis of medical records from 782 patients treated in a highly complex outpatient clinic. Inclusion criteria: age ≥18 years, diagnosed with hypertension, in treatment ≥6 months. Patients with secondary hypertension (104) and incomplete data (64) were excluded. The main outcome was blood pressure control (systolic &lt;140 and diastolic &lt;90 mmHg). The independent variables studied were: sociodemographic and clinical characteristics (use of drugs, comorbidities and laboratory tests). Pearson's χ2 tests, Fisher's test, Student's t and Wilcoxon-Mann-Whitney tests were performed in the bivariate analysis and logistic regression in the multiple analyses, adopting p≤0.05. Results: The prevalence of hypertensive control was 51.1%. It was associated with a lack of control: body mass index (OR = 1.038; 95% CI = 1.008 - 1.071), history of stroke (OR = 0.453; 95% CI = 0.245 - 0.821), left ventricular hypertrophy (OR = 1.765; 95% CI = 1.052 - 3.011), and number of medications (OR = 1.082; 95% CI = 1.033 - 1.136). Conclusion: About half of the hypertensive patients had their blood pressure controlled; clinical variables and target organ damage were associated with the control.
DOI: 10.6084/m9.figshare.19964242.v1
title: Blood pressure control of hypertensive patients followed in a high complexity clinic and associated variables

description: Abstract Introduction: Arterial hypertension is a disease that has a high impact on cardiovascular mortality and morbidity; however, it is still insufficiently controlled. Objectives: To assess hypertension control in patients seen at a specialized clinic and to identify associated variables. Method: Cross-sectional study involving the analysis of medical records from 782 patients treated in a highly complex outpatient clinic. Inclusion criteria: age ≥18 years, diagnosed with hypertension, in treatment ≥6 months. Patients with secondary hypertension (104) and incomplete data (64) were excluded. The main outcome was blood pressure control (systolic &lt;140 and diastolic &lt;90 mmHg). The independent variables studied were: sociodemographic and clinical characteristics (use of drugs, comorbidities and laboratory tests). Pearson's χ2 tests, Fisher's test, Student's t and Wilcoxon-Mann-Whitney tests were performed in the bivariate analysis and logistic regression in the multiple analyses, adopting p≤0.05. Results: The prevalence of hypertensive control was 51.1%. It was associated with a lack of control: body mass index (OR = 1.038; 95% CI = 1.008 - 1.071), history of stroke (OR = 0.453; 95% CI = 0.245 - 0.821), left ventricular hypertrophy (OR = 1.765; 95% CI = 1.052 - 3.011), and number of medications (OR = 1.082; 95% CI = 1.033 - 1.136). Conclusion: About half of the hypertensive patients had their blood pressure controlled; clinical variables and target organ damage were associated with the control.
DOI: 10.6084/m9.figshare.19964241
title: Metabolic assessment in pure struvite stones formers: is it necessary?

description: Abstract Background and objective: Magnesium ammonium phosphate stones (MAP), also known as struvite stones, are associated with urinary infection and impairment of renal unit. The aim of this study is to evaluate the urinary metabolic risk factors for recurrence of renal calculi in patients submitted to nephrectomy due to MAP stones. Methods: We retrospectively reviewed the charts of patients &gt; 18 years old submitted to total nephrectomy due to pure MAP stones and pure calcium oxalate (CaOx) stones from July 2006 to July 2016. Urinary metabolic parameters were assessed through 24-hour urine exams ≥ 3 months after nephrectomy. Urinary metabolic parameters and new event related to lithiasis were compared. Results: Twenty-eight and 39 patients were included in MAP and CaOx group, respectively. Abnormalities in 24-hour urine samples were similar between groups. Hypercalciuria occurred in 7.1 and 10.3% of patients in MAP and CaOx group, respectively (p = 0.66), whereas hypocitraturia was present in 65.2 and 59.0% of patients with MAP and CaOx group, respectively (p = 0.41). No significant difference in new events was found between MAP and CaOx groups (17.9 vs. 23.1%, respectively; p = 0.60). Conclusion: A 24-hour urine evaluation should be offered to patients submitted to nephrectomy due to pure MAP stones in order to detect metabolic risk, improve treatment, and prevent stone recurrence.
DOI: 10.6084/m9.figshare.19964241.v1
title: Metabolic assessment in pure struvite stones formers: is it necessary?

description: Abstract Background and objective: Magnesium ammonium phosphate stones (MAP), also known as struvite stones, are associated with urinary infection and impairment of renal unit. The aim of this study is to evaluate the urinary metabolic risk factors for recurrence of renal calculi in patients submitted to nephrectomy due to MAP stones. Methods: We retrospectively reviewed the charts of patients &gt; 18 years old submitted to total nephrectomy due to pure MAP stones and pure calcium oxalate (CaOx) stones from July 2006 to July 2016. Urinary metabolic parameters were assessed through 24-hour urine exams ≥ 3 months after nephrectomy. Urinary metabolic parameters and new event related to lithiasis were compared. Results: Twenty-eight and 39 patients were included in MAP and CaOx group, respectively. Abnormalities in 24-hour urine samples were similar between groups. Hypercalciuria occurred in 7.1 and 10.3% of patients in MAP and CaOx group, respectively (p = 0.66), whereas hypocitraturia was present in 65.2 and 59.0% of patients with MAP and CaOx group, respectively (p = 0.41). No significant difference in new events was found between MAP and CaOx groups (17.9 vs. 23.1%, respectively; p = 0.60). Conclusion: A 24-hour urine evaluation should be offered to patients submitted to nephrectomy due to pure MAP stones in order to detect metabolic risk, improve treatment, and prevent stone recurrence.