nils-herrmann/clean_scirepeval huggingface dataset:
Validation of the equations for estimating daily sodium excretion from spot urine in patients with chronic kidney disease

Measuring sodium excretion in a 24-h urine collection is the most reliable method of estimating salt intake, but it is not applicable to all patients. As an alternative, equations for estimating Na excretion from Japanese by a spot urine sample were created, but they have not been validated in patients with chronic kidney disease (CKD), which are frequently associated with nocturia and medication. We enrolled 136 patients with CKD and collected both 24-h urine and the first morning urine. Na excretion was estimated from the first morning urine by Kawasaki’s equation, which was originally used for the second morning urine, and Tanaka’s equation, which is applied for spot urine samples taken at any time from 9 am to 7 pm. We evaluated the two equations for bias, RMSE and accuracy within 30 and 50% of the measured Na excretion. Bias, RMSE and accuracy within 30% of the estimated Na excretion were 48 ± 69 and 2 ± 69 mmol/day, 84 and 69 mmol/day, and 35 and 49% using Kawasaki’s equation and Tanaka’s equation, respectively. Na excretion in the first morning urine was accurately estimated by Tanaka’s equation, but it was overestimated by Kawasaki’s equation. Nocturia and medication such as diuretics and ACE inhibitor or angiotensin receptor blocker did not affect the accuracy with which Na excretion was estimated by Tanaka’s equation substantially. Tanaka’s equation for estimating Na excretion from the first morning urine in patients with CKD is accurate enough for use in clinical practice.
Colorectal Cancer Burden and Access to Federally Qualified Health Centers in California

Colorectal cancer burden and access to primary health care, California. A vast majority of Californians (96%) live within a 30-minute drive of a federally qualified health center (FQHC). This is true for areas in both the top and bottom quintiles (96% and 93% respectively) based on the percentage of colorectal cancers (CRC) diagnosed at a late stage. There was no meaningful connection found between geographic access to affordable CRC screening services and late-stage diagnosis percentages. This finding suggests that other barriers besides physical distance to affordable CRC screening need to be examined in order to reduce the geographic disparities in late-stage CRC diagnoses.
Cognitive behavioral therapy, singly and combined with medication, for persistent insomnia: a randomized controlled trial.

Cognitive behavioral therapy (CBT) and hypnotic medications are efficacious for short-term treatment of insomnia, but few patients achieve complete remission with any single treatment. It is unclear whether combined or maintenance therapies would enhance outcome.



To evaluate the added value of medication over CBT alone for acute treatment of insomnia and the effects of maintenance therapies on long-term outcome.



Prospective, randomized controlled trial involving 2-stage therapy for 160 adults with persistent insomnia treated at a university hospital sleep center in Canada between January 2002 and April 2005.



Participants received CBT alone or CBT plus 10 mg/d (taken at bedtime) of zolpidem for an initial 6-week therapy, followed by extended 6-month therapy. Patients initially treated with CBT attended monthly maintenance CBT for 6 months or received no additional treatment and those initially treated with combined therapy (CBT plus 10 mg/d of zolpidem) continued with CBT plus intermittent use of zolpidem or CBT only.



Sleep onset latency, time awake after sleep onset, total sleep time, and sleep efficiency derived from daily diaries (primary outcomes); treatment response and remission rates derived from the Insomnia Severity Index (secondary outcomes).



Cognitive behavioral therapy used singly or in combination with zolpidem produced significant improvements in sleep latency, time awake after sleep onset, and sleep efficiency during initial therapy (all P<.001); a larger increase of sleep time was obtained with the combined approach (P = .04). Both CBT alone and CBT plus zolpidem produced similar rates of treatment responders (60% [45/75] vs 61% [45/74], respectively; P = .84) and treatment remissions (39% [29/75] vs 44% [33/74], respectively; P = .52) with the 6-week acute treatment, but combined therapy produced a higher remission rate compared with CBT alone during the 6-month extended therapy phase and the 6-month follow-up period (56% [43/74 and 32/59] vs 43% [34/75 and 28/68]; P = .05). The best long-term outcome was obtained with patients treated with combined therapy initially, followed by CBT alone, as evidenced by higher remission rates at the 6-month follow-up compared with patients who continued to take zolpidem during extended therapy (68% [20/30] vs 42% [12/29]; P = .04).



In patients with persistent insomnia, the addition of medication to CBT produced added benefits during acute therapy, but long-term outcome was optimized when medication is discontinued during maintenance CBT.
Decreased risk of secondary brain herniation with intracranial pressure monitoring in patients with haemorrhagic stroke

Intracranial-pressure (ICP) monitoring is considered standard care for severe traumatic brain injury and is used frequently, but the efficacy of treatment based on monitoring in patients with hemorrhagic stroke has not been rigorously assessed. In this study, we investigated the clinical value of ICP monitoring in patients with hemorrhagic stroke.



We conducted a randomized, unblinded, controlled trial in which 90 patients with hemorrhagic stroke were randomly assigned to ICP monitoring or a control group. The primary outcome was a composite of incidence rate of hematoma enlargement and secondary brain herniation. The secondary outcome was neurological status assessed using the Glasgow Outcome Scale scores at 6 months post-onset. Characteristics of the patients at baseline and outcome measurements were also compared between the two groups.



There was no significant between-group difference in the incidence of hematoma enlargement (control group, 38.6% vs. ICP monitoring group, 32.6%; P > 0.05). The incidence rate of secondary brain herniation in the ICP monitoring group was significantly lower compared with the control group (10.9% vs. 20.5%, P = 0.04). Six-month mortality was 6.5% in the ICP group and 9.1% in the control group (P < 0.05), and neurological outcome was better in the ICP group compared with the control group (P < 0.05).



The dynamic ICP value may be more sensitive and effective in preventing secondary brain herniation in patients with hemorrhagic stroke compared with guidance directed by clinical signs and radiological indicators.
Changes in lipid and lipoprotein values during a cross-over treatment of doxazosin, moduretic and amlodipine in hypertensive patients.

A cross-over study, comparing the effects of doxazosin, moduretic and amlodipine on plasma lipid and lipoprotein levels in 9 hypertensive Nigerians aged 35 to 65 years is presented. Doxazosin therapy had favourable lipid changes characterized by a statistically significant reduction in total cholesterol (TC) at 6 months. Though consistent reduction was observed in total triglycerides (TG) low density lipoprotein cholesterol (LDL-C), very low density lipoprotein-cholesterol (VLDLC) upto 6 months, no effect was seen on high density lipoprotein cholesterol (HDLC). This is against unfavourable increments in the mean values of TC, VLDLC, LDLC/HDLC and decrease in HDLC/TC during moduretic treatment phase. Amlodipine therapy did not alter the lipid and lipoprotein levels. The non-significant variation in the mean high density lipoprotein-cholesterol (HDLC) level observed with these agents, seem to suggest that HDL-cholesterol metabolism may be maintained during antihypertensive pharmacotherapy.
Four Square Step Test in ambulant persons with multiple sclerosis: validity, reliability, and responsiveness.

The aim of this study was to establish the concurrent validity and relative and absolute reliability, define the minimal detectable change, and evaluate the floor and ceiling effects of the Four Square Step Test (FSST) in ambulant persons with multiple sclerosis (pwMS). Twenty-five pwMS performed the FSST on two occasions, 8.1±4.1 days apart. During the first testing, session participants also reported their fall history, performed the Berg Balance Scale, Dynamic Gait Index, and completed the Activities-Specific Balance Confidence Scale. Performance on the FSST was significantly (P<0.001) and strongly associated with performance on the Berg Balance Scale (rs=-0.84), Dynamic Gait Index (rs=-0.81), and Activities-Specific Balance Confidence Scale (rs=-0.78). Relative reliability of the FSST was excellent (ICC2,1=0.922). The minimal detectable change estimate for the FSST was 4.6 s. The FSST is a valid and reliable measure of dynamic standing balance in ambulant pwMS. However, because a substantial change (43%) is required to demonstrate a real change in individual performance, the FSST is unlikely to be sensitive in detecting longitudinal change in dynamic standing balance.
The AUGMENT precompiler as a tool for the development of special purpose arithmetic packages

We discuss the use of a FORTRAN precompiler in the development of packages for nonstandard arithmetics. In particular, the use of the FORTRAN precompiler, AUGMENT, renders the source code more lucid, reduces the number of lines of code in a nonstandard arithmetic package, facilitates modification, and ameliorates the problems of transporting such a package to another host system.
Prominent streak discovery in sequence data

This paper studies the problem of prominent streak discovery in sequence data. Given a sequence of values, a prominent streak is a long consecutive subsequence consisting of only large (small) values. For finding prominent streaks, we make the observation that prominent streaks are skyline points in two dimensions- streak interval length and minimum value in the interval. Our solution thus hinges upon the idea to separate the two steps in prominent streak discovery' candidate streak generation and skyline operation over candidate streaks. For candidate generation, we propose the concept of local prominent streak (LPS). We prove that prominent streaks are a subset of LPSs and the number of LPSs is less than the length of a data sequence, in comparison with the quadratic number of candidates produced by a brute-force baseline method. We develop efficient algorithms based on the concept of LPS. The non-linear LPS-based method (NLPS) considers a superset of LPSs as candidates, and the linear LPS-based method (LLPS) further guarantees to consider only LPSs. The results of experiments using multiple real datasets verified the effectiveness of the proposed methods and showed orders of magnitude performance improvement against the baseline method.
A double-blind placebo-controlled trial of bupropion sustained-release for smoking cessation in schizophrenia.

The objective of this study was to examine the efficacy of bupropion for smoking cessation in patients with schizophrenia. Adults with schizophrenia who smoked more than 10 cigarettes per day and wished to try to quit smoking were recruited from community mental health centers, enrolled in a 12-week group cognitive behavioral therapy intervention, and randomly assigned to receive either bupropion sustained-release 300 mg/d or identical placebo. Fifty-three adults, 25 on bupropion and 28 on placebo, were randomized, completed at least 1 postbaseline assessment and were included in the analysis. The primary outcome measures were 7-day point prevalence abstinence in the week after the quit date (week 4) and at the end of the intervention (week 12). Subjects in the bupropion group were significantly more likely to be abstinent for the week after the quit date (36% [9/25] vs. 7% [2/28], P = 0.016) and at end of the intervention (16% [4/25] vs. 0%, P = 0.043). Subjects in the bupropion group also had a higher rate of 4-week continuous abstinence (weeks 8-12) (16% [4/25] vs. 0%, P = 0.043) and a longer duration of abstinence (4.2 [3.2] weeks vs. 1.8 [0.96] weeks, t = 2.30, P = 0.037). The effect of bupropion did not persist after discontinuation of treatment. Subjects in the bupropion group had no worsening of clinical symptoms and had a trend toward improvement in depressive and negative symptoms. We conclude that bupropion does not worsen clinical symptoms of schizophrenia and is modestly effective for smoking cessation in patients with schizophrenia. The relapse rate is high after treatment discontinuation.
Trends in Socioeconomic Inequalities in Ischemic Heart Disease Mortality in Small Areas of Nine Spanish Cities from 1996 to 2007 Using Smoothed ANOVA

The aim of this study was to analyze the evolution of socioeconomic inequalities in mortality due to ischemic heart diseases (IHD) in the census tracts of nine Spanish cities between the periods 1996–2001 and 2002–2007. Among women, there are socioeconomic inequalities in IHD mortality in the first period which tended to remain stable or even increase in the second period in most of the cities. Among men, in general, no socioeconomic inequalities have been detected for this cause in either of the periods. These results highlight the importance of intra-urban inequalities in mortality due to IHD and their evolution over time.
Insulin-treated diabetes is not associated with increased mortality in critically ill patients

This was a planned substudy from the European observational Sepsis Occurrence in Acutely ill Patients (SOAP) study to investigate the possible impact of insulin-treated diabetes on morbidity and mortality in ICU patients.



The SOAP study was a cohort, multicenter, observational study which included data from all adult patients admitted to one of 198 participating ICUs from 24 European countries during the study period. For this substudy, patients were classified according to whether or not they had a known diagnosis of insulin-treated diabetes mellitus. Outcome measures included the degree of organ dysfunction/failure as assessed by the sequential organ failure assessment (SOFA) score, the occurrence of sepsis syndromes and organ failure in the ICU, hospital and ICU length of stay, and all cause hospital and ICU mortality.



Of the 3147 patients included in the SOAP study, 226 (7.2%) had previously diagnosed insulin-treated diabetes mellitus. On admission, patients with insulin-treated diabetes were older, sicker, as reflected by higher simplified acute physiology system II (SAPS II) and SOFA scores, and more likely to be receiving hemodialysis than the other patients. During the ICU stay, more patients with insulin-treated diabetes required renal replacement therapy (hemodialysis or hemofiltration) than other patients. There were no significant differences in ICU or hospital lengths of stay or in ICU or hospital mortality between patients with or without insulin-treated diabetes. Using a Cox proportional hazards regression analysis with hospital mortality censored at 28-days as the dependent factor, insulin-treated diabetes was not an independent predictor of mortality.



Even though patients with a history of insulin-treated diabetes are more severely ill and more likely to have renal failure, insulin-treated diabetes is not associated with increased mortality in ICU patients.
Fludarabine, cyclophosphamide and rituximab plus granulocyte macrophage colony-stimulating factor as frontline treatment for patients with chronic lymphocytic leukemia.

Fludarabine, cyclophosphamide and rituximab (FCR), the standard of care for the frontline treatment of patients with chronic lymphocytic leukemia (CLL), is associated with a high rate of neutropenia and infectious complications. Granulocyte macrophage colony-stimulating factor (GM-CSF) reduces myelosuppression and can potentiate rituximab activity. We conducted a clinical trial combining GM-CSF with FCR for frontline treatment of 60 patients with CLL. Eighty-six percent completed all six courses and 18% discontinued GM-CSF for toxicity: grade 3-4 neutropenia was observed in 30% of cycles, and severe infections in 16% of cases. The overall response rate was 100%. Both median event-free survival (EFS) and overall survival (OS) have not been reached. Longer EFS was associated with favorable cytogenetics. GM-CSF led to a lower frequency of infectious complications than in the historical FCR group, albeit similar EFS and OS.
Genetic algorithms applied to multi-class prediction for the analysis of gene expression data

An important challenge in the use of large-scale gene expression data for biological classification occurs when the expression dataset being analyzed involves multiple classes. Key issues that need to be addressed under such circumstances are the efficient selection of good predictive gene groups from datasets that are inherently 'noisy', and the development of new methodologies that can enhance the successful classification of these complex datasets.



We have applied genetic algorithms (GAs) to the problem of multi-class prediction. A GA-based gene selection scheme is described that automatically determines the members of a predictive gene group, as well as the optimal group size, that maximizes classification success using a maximum likelihood (MLHD) classification method.



The GA/MLHD-based approach achieves higher classification accuracies than other published predictive methods on the same multi-class test dataset. It also permits substantial feature reduction in classifier genesets without compromising predictive accuracy. We propose that GA-based algorithms may represent a powerful new tool in the analysis and exploration of complex multi-class gene expression data.


AVAILABILITY
Supplementary information, data sets and source codes are available at http://www.omniarray.com/bioinformatics/GA.
Aml1 gene rearrangements and mutations in radiation-associated acute myeloid leukemia and myelodysplastic syndromes.

Several studies suggested a causal link between AML1 gene rearrangements and both radiation-induced acute myeloid leukaemia (AML) and myelodysplastic syndromes (MDS). Fifty-three AML samples were analyzed for the presence of AML1 abnormalities using fluorescent in-situ hybridization (FISH) and reverse transcription polymerase chain reaction (RT-PCR). Of these patients, 24 had experienced radiation exposure due to the Chernobyl accident, and 29 were non-irradiated spontaneous AML cases and served as controls. AML1/ETO translocations were found in 9 of 29 spontaneous AML but only in 1 of 24 radiation-associated AML cases. This difference between translocation frequencies is statistically significant in the age-unstratified cohorts (p=0.015). Following age stratification, the difference becomes less pronounced but remains on borderline significance (p=0.053). AML1 mutation status was assessed in 5 clean-up workers at Chernobyl NPP with MDS, or AML following MDS, by direct sequencing of genomic DNA from the coding region (exon 3 through 8). In one patient who developed MDS following an acute radiation syndrome, a hexanucleotide duplication of CGGCAT in exon 8 was found, inserted after base position 1502. Our results suggest that AML1 gene translocations are infrequent in radiation-induced leukemogenesis but are consistent with the idea that radiation may contribute to the development of MDS through AML1 gene mutation.
An Internet-Based Diabetes Management Platform Improves Team Care and Outcomes in an Urban Latino Population

To compare usual diabetes care (UDC) to a comprehensive diabetes care intervention condition (IC) involving an Internet-based "diabetes dashboard" management tool used by clinicians.



We used a parallel-group randomized design. Diabetes nurses, diabetes dietitians, and providers used the diabetes dashboard as a clinical decision support system to deliver a five-visit, 6-month intervention to 199 poorly controlled (HbA1c >7.5% [58 mmol/mol]) Latino type 2 diabetic (T2D) patients (mean age 55 years, 60% female) at urban community health centers. We compared this intervention to an established, in-house UDC program (n = 200) for its impact on blood glucose control and psychosocial outcomes.



Recruitment and retention rates were 79.0 and 88.5%, respectively. Compared with UDC, more IC patients reached HbA1c targets of <7% (53 mmol/mol; 15.8 vs. 7.0%, respectively, P < 0.01) and <8% (64 mmol/mol; 45.2 vs. 25.3%, respectively, P < 0.001). In multiple linear regression adjusting for baseline HbA1c, adjusted mean ± SE HbA1c at follow-up was significantly lower in the IC compared with the UDC group (P < 0.001; IC 8.4 ± 0.10%; UDC 9.2 ± 0.10%). The results showed lower diabetes distress at follow-up for IC patients (40.4 ± 2.1) as compared with UDC patients (48.3 ± 2.0) (P < 0.01), and also lower social distress (32.2 ± 1.3 vs. 27.2 ± 1.4, P < 0.01). There was a similar, statistically significant (P < 0.01) improvement for both groups in the proportion of patients moving from depressed status at baseline to nondepressed at follow-up (41.8 vs. 40%; no significance between groups).



The diabetes dashboard intervention significantly improved diabetes-related outcomes among Latinos with poorly controlled T2D compared with a similar diabetes team condition without access to the diabetes dashboard.
Clinical pharmacology of propafenone.

We determined the efficacy, pharmacokinetics, and plasma concentration-response relationships of propafenone, a promising new antiarrhythmic drug. Thirteen patients with frequent and complex ventricular premature beats were studied after receiving four increasing doses, during drug washout and during a randomized double-blind placebo-controlled trial, to evaluate the optimal dose in each patient. A nonlinear relationship was found between propafenone dose and steady-state mean concentration with a 10-fold increase in drug concentration as dose increased threefold from 300 to 900 mg/day. There was great intersubject variability in elimination half-life (mean 6 hr, range 2.4 to 11.8), steady-state mean concentration on 900 mg/day of propafenone (mean 1008 ng/ml, range 482 to 1812), and "therapeutic" plasma concentration (mean 588 ng/ml, range 64 to 1044). The interaction of these three parameters in individual patients determined the duration of the antiarrhythmic action of propafenone during washout (mean 11.5 hr, range 4 to 22). There was a greater than 90% reduction of ventricular premature beats in 10 subjects during dose ranging and in seven during double-blind crossover. Side effects requiring discontinuation of the drug occurred in three patients and included apparent worsening of arrhythmias in two. We conclude that propafenone effectively suppresses ventricular arrhythmias and that nonlinear drug accumulation and intersubject variability in elimination of half-life, steady-state mean plasma concentration, and therapeutic concentration indicate a need for individual therapy.