Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Triglycerides to High-Density Lipoprotein Cholesterol Ratio Predicts Chronic Renal Disease in Patients without Diabetes Mellitus (STELLA Study)

Background: The triglycerides to high-density lipoprotein cholesterol (TG/HDL-C) ratio has been included in the potential indices for atherosclerosis in chronic kidney disease (CKD). In this study, we addressed the role of the TG/HDL-C ratio on CKD prediction defined by both classified estimated glomerular filtration rate (eGFR) and classified urinary albumin-to-creatinine ratio (UACR) in non-diabetic participants. Methods: One hundred and eighty-three subjects with a mean age 67.3 ± 15.6 years old were included. Our participants were classified in both eGFR and UACR categories according to the Kidney Disease Improving Global Outcomes 2012 criteria. Estimated pulse wave velocity (ePWV) was calculated using an equation from age and mean blood pressure. The TG/HDL-C ratio was calculated. X2 tests and adjusted models were applied using confounders. Results: The TG/HDL-C ratio was inversely associated with eGFR and positively with both UACR and ePWV. We divided our patients in two groups according to the found ROC curve of the TG/HDL-C ratio cut-off point, either with an eGFR of less or more than 60 mL/min/1.73 m2. X2 tests showed significant association between the high TG/HDL-C ratio and classified eGFR, and classified UACR and hypertension (x2 = 24.5, p = 0.001, x2 = 12.5, p = 0.002 and x2 = 12.6, p = 0.001, respectively). The adjusted model showed the high TG/HDL-C ratio to be an independent predictor for both a low eGFR and UACR (OR = 1.5, 1.2–1.9 and OR = 1.22, 1.02–1.47, respectively) in combination with old age and hypertension. Conclusion: The TG/HDL-C ratio was revealed to be a potential predictor for both a low eGFR and micro/macroalbuminuria in non-diabetic patients. The arterial stiffening was included in the main underlying pathophysiological mechanisms

Metabolic acidosis status and mortality in patients on the end stage of renal disease

BACKGROUND AND OBJECTIVES: Uncorrected metabolic acidosis leads to higher death risk in dialysis patients. We observed the relationship between metabolic acidosis status and mortality rate in patients on renal replacement therapy during a median follow up time of 60 months. METHODS: We studied 76 patients on an on-line hemodiafiltration. The dialysis adequacy was defined by Kt/V for urea. The Framingham risk score (FRS) points were used to determine the 10-year risk for coronary heart disease. We examined the impact of high or low serum bicarbonate concentrations on mortality rate and on 10-year risk for coronary heart disease via the Kaplan-Meier method. Cox’s model was used to evaluate a combination of prognostic variables, such as dialysis adequacy defined by Kt/V for urea, age and serum bicarbonate concentrations. RESULTS: We divided the enrolled patients in three groups according to serum bicarbonate concentrations (< 20 mmol/L, 20-22 mmol/L and > 22 mmol/L). Kaplan-Meier survival curve for the impact of serum bicarbonate concentrations on overall mortality was found significant (log-rank = 7.8, P = 0.02). The prevalence of serum bicarbonate less or more than 20 mmol/L on high FRS (> 20%) by Kaplan-Meier curve was also found significant (log-rank = 4.9, P = 0.02). Cox’s model revealed the significant predictive effect of serum bicarbonate on overall mortality (P = 0.006, OR = 1.5, 95% CI = 1.12-1.98) in combination to Kt/V for urea and age. CONCLUSION: Uncorrected severe metabolic acidosis, defined by serum bicarbonate concentrations less than 20 mmol/L, is associated with a 10-year risk for coronary heart disease more than 20% and high overall mortality in patients on renal replacement therapy

Metabolic acidosis status and mortality in patients on the end stage of renal disease.

BACKGROUND AND OBJECTIVES: Uncorrected metabolic acidosis leads to higher death risk in dialysis patients. We observed the relationship between metabolic acidosis status and mortality rate in patients on renal replacement therapy during a median follow up time of 60 months. METHODS: We studied 76 patients on an on-line hemodiafiltration. The dialysis adequacy was defined by Kt/V for urea. The Framingham risk score (FRS) points were used to determine the 10-year risk for coronary heart disease. We examined the impact of high or low serum bicarbonate concentrations on mortality rate and on 10-year risk for coronary heart disease via the Kaplan-Meier method. Cox’s model was used to evaluate a combination of prognostic variables, such as dialysis adequacy defined by Kt/V for urea, age and serum bicarbonate concentrations. RESULTS: We divided the enrolled patients in three groups according to serum bicarbonate concentrations (&lt; 20 mmol/L, 20-22 mmol/L and &gt; 22 mmol/L). Kaplan-Meier survival curve for the impact of serum bicarbonate concentrations on overall mortality was found significant (log-rank = 7.8, P = 0.02). The prevalence of serum bicarbonate less or more than 20 mmol/L on high FRS (&gt; 20%) by Kaplan-Meier curve was also found significant (log-rank = 4.9, P = 0.02). Cox’s model revealed the significant predictive effect of serum bicarbonate on overall mortality (P = 0.006, OR = 1.5, 95% CI = 1.12-1.98) in combination to Kt/V for urea and age. CONCLUSION: Uncorrected severe metabolic acidosis, defined by serum bicarbonate concentrations less than 20 mmol/L, is associated with a 10-year risk for coronary heart disease more than 20% and high overall mortality in patients on renal replacement therapy

Association between Low Serum Bicarbonate Concentrations and Cardiovascular Disease in Patients in the End-Stage of Renal Disease.

BACKGROUND: Metabolic acidosis, a common condition particularly in the end-stage of renal disease patients, results in malnutrition, inflammation and oxidative stress. In this study, we focused on the association between low serum bicarbonate and cardiovascular disease in patients on intermittent dialysis. METHODS: We studied 52 on-line-pre-dilution hemodiafiltration (on-l HDF) patients, 32 males and 20 females, with a mean age of 58.01 ± 15.4 years old. Metabolic acidosis was determined by serum bicarbonate concentrations less than 22 mmol/L. Residual renal function (RRF) was defined by interdialytic urine volume. Kaplan-Meier curves and Cox regression models were performed to predict coronary artery disease (CAD), defined by ejection fraction &lt;50%, or diastolic dysfunction congestive heart failure (CHF) and peripheral vascular disease (PVD). RESULTS: Kaplan-Meier analyses showed that a lower or higher than 22 mmol/L serum bicarbonate metabolic acidosis status was significantly associated with both PVD and diastolic dysfunction (log-rank = 5.07, p = 0.02 and log-rank = 5.84, p = 0.01, respectively). A similar prevalence of serum bicarbonate on CAD or CHF by low ejection fraction was not shown. The RRF was associated with PVD event and serum bicarbonate less than 22 mmol/L (log-rank = 5.49, p = 0.01 and log-rank = 3.9, p = 0.04, respectively). Cox regression analysis revealed that serum bicarbonate and RRF were significant risk factors for PVD after adjustment for confounders. Furthermore, RRF adjusted for covariates was shown to be a significant risk factor for diastolic dysfunction. CONCLUSION: Low serum bicarbonate was associated with peripheral vascular disease and diastolic dysfunction in intermittent dialysis. The residual renal function may impact patients’ outcomes through its relationship with metabolic acidosis status, particularly for peripheral vascular disease manifestation

The Association between Intradialytic Hypertension and Metabolic Disorders in End Stage Renal Disease

Background. Intradialytic hypertension was associated with a high mortality risk. We examined the relationship between intradialytic hypertension and metabolic disorders in hemodialysis treatment patients. Methods. We studied 76 patients in online hemodiafiltration. Dialysis adequacy was defined by Kt/V for urea. Normalized protein catabolic rate (nPCR), as a marker of protein intake, was calculated. Sodium removal was determined as percent sodium removal. Metabolic acidosis was determined by serum bicarbonate less than 22 mmol/L. Interdialytic urine volume more than 100 ml was recorded. Intradialytic hypertension was defined by an increase in systolic blood pressure equal to 10 mmHg from pre- to posthemodialysis. Arterial stiffness was assessed as carotid-femoral pulse wave velocity (c-fPWV) and carotid augmentation index (AIx). Chi-square tests and logistic regression analysis were applied for intradialytic hypertension prediction. Results. Patients with intradialytic hypertension were older and had significantly lower hemoglobin, nPCR, urine output, and serum bicarbonate and significantly higher c-fPWV, though similar Kt/V for urea, than patients without intradialytic hypertension. They also had increased sodium removal and pulse pressure related to less urine output. Serum bicarbonate was inversely associated with c-fPWV (r=-0.377, p=0.001). Chi-square test showed significant association between intradialytic hypertension and serum bicarbonate < 22 mmol/L (x2=5.6, p=0.01), which was supported by an adjusted model. Conclusion. The intradialytic hypertension was significantly associated with metabolic disorders including malnutrition/inflammation and uncontrolled metabolic acidosis in hemodialysis treatment patients. Severe metabolic acidosis may reflect sodium imbalance and hemodynamic instability of these patients resulting in volume overload and increased vascular resistance

Association between Low Serum Bicarbonate Concentrations and Cardiovascular Disease in Patients in the End-Stage of Renal Disease

Background: Metabolic acidosis, a common condition particularly in the end-stage of renal disease patients, results in malnutrition, inflammation and oxidative stress. In this study, we focused on the association between low serum bicarbonate and cardiovascular disease in patients on intermittent dialysis. Methods: We studied 52 on-line-pre-dilution hemodiafiltration (on-l HDF) patients, 32 males and 20 females, with a mean age of 58.01 ± 15.4 years old. Metabolic acidosis was determined by serum bicarbonate concentrations less than 22 mmol/L. Residual renal function (RRF) was defined by interdialytic urine volume. Kaplan–Meier curves and Cox regression models were performed to predict coronary artery disease (CAD), defined by ejection fraction &lt;50%, or diastolic dysfunction congestive heart failure (CHF) and peripheral vascular disease (PVD). Results: Kaplan–Meier analyses showed that a lower or higher than 22 mmol/L serum bicarbonate metabolic acidosis status was significantly associated with both PVD and diastolic dysfunction (log-rank = 5.07, p = 0.02 and log-rank = 5.84, p = 0.01, respectively). A similar prevalence of serum bicarbonate on CAD or CHF by low ejection fraction was not shown. The RRF was associated with PVD event and serum bicarbonate less than 22 mmol/L (log-rank = 5.49, p = 0.01 and log-rank = 3.9, p = 0.04, respectively). Cox regression analysis revealed that serum bicarbonate and RRF were significant risk factors for PVD after adjustment for confounders. Furthermore, RRF adjusted for covariates was shown to be a significant risk factor for diastolic dysfunction. Conclusion: Low serum bicarbonate was associated with peripheral vascular disease and diastolic dysfunction in intermittent dialysis. The residual renal function may impact patients’ outcomes through its relationship with metabolic acidosis status, particularly for peripheral vascular disease manifestation

Glucose Serum Concentrations and Cardiovascular Disease in Patients on the End Stage of Renal Disease without Diabetes Mellitus

Background/Aim: It is still controversial whether tighter glycemic control is associated with better clinical outcomes in patients with kidney failure. We examined the association between glucose serum concentrations and cardiovascular disease in patients on the end stage of renal disease without diabetes mellitus. Methods: We studied 76 patients on on-line hemodiafiltration. Cardiovascular disease was defined by the existence of coronary disease (CD). Arterial stiffness was measured as carotid-femoral pulse wave velocity (c-fPWV) and carotid augmentation index (AIx). The concentrations of beta2-microglobulin (β2M) and insulin were measured by radioimmunoassays and insulin resistance by HOMA-IR. We built a logistic-regression analysis to examine the role of glucose on cardiovascular disease after adjustment for the traditional and specific risk factors for dialysis patients. Results: Serum glucose was positively correlated with beta2M, insulin and HOMA-IR (r = 0.361, p = 0.002, r = 0.581, p = 0.001 and r = 0.753, p = 0.001 respectively). Logistic-regression analysis did not show significant impact of glucose concentrations on cardiovascular disease after adjustment for traditional and specific risk factors. Conclusions: The association between elevated glucose serum concentrations and represented by coronary syndrome cardiovascular disease in patients on the end stage of renal disease without diabetes mellitus was not found significant