nils-herrmann/clean_scirepeval huggingface dataset:
Clinical Value of Prognosis Gene Expression Signatures in Colorectal Cancer: A Systematic Review

The traditional staging system is inadequate to identify those patients with stage II colorectal cancer (CRC) at high risk of recurrence or with stage III CRC at low risk. A number of gene expression signatures to predict CRC prognosis have been proposed, but none is routinely used in the clinic. The aim of this work was to assess the prediction ability and potential clinical usefulness of these signatures in a series of independent datasets.



A literature review identified 31 gene expression signatures that used gene expression data to predict prognosis in CRC tissue. The search was based on the PubMed database and was restricted to papers published from January 2004 to December 2011. Eleven CRC gene expression datasets with outcome information were identified and downloaded from public repositories. Random Forest classifier was used to build predictors from the gene lists. Matthews correlation coefficient was chosen as a measure of classification accuracy and its associated p-value was used to assess association with prognosis. For clinical usefulness evaluation, positive and negative post-tests probabilities were computed in stage II and III samples.



Five gene signatures showed significant association with prognosis and provided reasonable prediction accuracy in their own training datasets. Nevertheless, all signatures showed low reproducibility in independent data. Stratified analyses by stage or microsatellite instability status showed significant association but limited discrimination ability, especially in stage II tumors. From a clinical perspective, the most predictive signatures showed a minor but significant improvement over the classical staging system.



The published signatures show low prediction accuracy but moderate clinical usefulness. Although gene expression data may inform prognosis, better strategies for signature validation are needed to encourage their widespread use in the clinic.
Exploring gene-environment interactions in Parkinson’s disease

The objective of this study was to explore combined effects of four candidate susceptibility genes and two exposures on Parkinson’s disease (PD) risk; namely, α-synuclein (SNCA) promoter polymorphism REP1, microtubule-associated protein tau (MAPT) H1/H2 haplotypes, apolipoprotein E (APOE) ε2/ε3/ε4 polymorphism, ubiquitin carboxy-terminal esterase L1 (UCHL1) S18Y variant, cigarette smoking and caffeinated coffee consumption. 932 PD patients and 664 control subjects from the NeuroGenetics Research Consortium, with complete data on all six factors, were studied. Uniform protocols were used for diagnosis, recruitment, data collection and genotyping. A logistic regression model which included gene-exposure interactions was applied. Likelihood ratio tests (LRTs) were used for significance testing and Bayesian inference was used to estimate odds ratios (ORs). MAPT (P = 0.007), SNCA REP1 (P = 0.012), smoking (P = 0.001), and coffee (P = 0.011) were associated with PD risk. Two novel interactions were detected: APOE with coffee (P = 0.005), and REP1 with smoking (P = 0.021). While the individual main effects were modest, each yielding OR < 1.6, the effects were cumulative, with some combinations reaching OR = 12.6 (95% CI: 5.9–26.8). This study provides evidence for the long-held notion that PD risk is modulated by cumulative and interactive effects of genes and exposures. Furthermore, the study demonstrates that while interaction studies are useful for exploring risk relationships that might otherwise go undetected, results should be interpreted with caution because of the inherent loss of power due to multiple testing. The novel findings of this study that warrant replication are the evidence for interaction of coffee with APOE, and of smoking with REP1 on PD risk.
Poor numeracy skills are associated with glycaemic control in Type 1 diabetes.

To assess the numeracy and literacy skills of individuals with Type 1 diabetes and determine if there is a relationship with achieved glycaemic control independent of their duration of diabetes, diabetes education, demographic and socio-economic factors.



One hundred and twelve patients completed the study (mean current age 43.8 ± 12.5 years, 47% male, mean duration of diabetes 22.0 ± 13.2 years) out of 650 randomly selected patients from the Bournemouth Diabetes and Endocrine Centre's diabetes register. The Skills for Life Initial Assessments were used to measure numeracy and literacy. These indicate skills levels up to level 2, equivalent to the national General Certificate of Secondary Education grades A*-C. HbA(1c) was also measured. Pearson's correlation was used to measure the correlation of numeracy and literacy scores with HbA(1c.) To compare mean HbA(1c) between those with or without level 2 skills, t-tests were used, and multiple linear regression was used to investigate whether any differences were independent of duration of diabetes, diabetes education, demographic and socio-economic factors.



Literacy was not associated with achieved HbA(1c). In contrast, participants with numeracy skills at level 2 or above achieved an HbA(1c) lower than those with numeracy skills below level 2 (P = 0.027). Although higher socio-economic status was associated with lower mean HbA(1c) , the relationship between numeracy and HbA(1c) appeared to be independent of socio-economic factors.



Low numeracy skills were adversely associated with diabetes control. Assessment of numeracy skills may be relevant to the structure of diabetes education programmes.
The effect of food on the bioavailability and pharmacodynamics of tolbutamide in diabetic patients

The effect of food on the rate and extent of absorption of tolbutamide in diabetic patients was studied by varying the time of drug administration in relation to the ingestion of a standard meal. Serum levels of tolbutamide, insulin and glucose and related bioavailability parameters were compared following the administration of a single dose of tolbutamide 0.5 g to diabetic patients 30 min prior to and immediately before a standardized meal. A placebo dosage form was also administered to determine baseline glucose and insulin response to the meal. The 700 calorie standard meal was composed of 41% carbohydrate, 18% protein, and 41% fat. Administration of the drug with the meal resulted in a 6% (statistically significant) decrease in the extent of absorption, as determined by measurement of the area under the tolbutamide serum level-time curve from zero to infinity. Serum levels of tolbutamide were also significantly higher 0.5 h after drug administration when the drug was taken with the meal. Except for these two minor effects, no other differences between the drug treatments were observed in any other parameters of tolbutamide absorption or in the postprandial glucose and insulin serum levels. Therefore, the small differences found were judged to be clinically meaningless. These findings demonstrate that administration of tolbutamide 0.5 g tablets 30 min prior to or with a standard meal results in equivalent therapeutic actions.
N-acetylcysteine does not prevent renal dysfunction after off-pump coronary artery bypass surgery.

Coronary artery bypass graft surgery in high-risk patients may be associated with postoperative renal dysfunction. N-Acetylcysteine is a powerful antioxidant and has been used to prevent contrast-induced renal dysfunction. The efficacy of N-acetylcysteine in preventing postoperative renal dysfunction following off-pump coronary artery bypass graft surgery was studied.



A prospective, randomized, controlled study was conducted in patients undergoing off-pump coronary artery bypass graft. The study group (37 patients) received N-acetylcysteine in the perioperative period, whereas the control group (37 patients) did not. The data obtained were analysed using the independent sample t-test (Student's t-test) and χ-test.



There was no significant difference in the incidence of renal dysfunction between the two groups. Three patients (8.6%) in the N-acetylcysteine group and four (11.4%) in the control group developed renal dysfunction (P value was 1.00).



N-Acetylcysteine does not have any beneficial effect on renal function in high-risk patients undergoing off-pump coronary artery bypass graft.
Postural support by a standing aid alleviating subjective discomfort among cooks in a forward-bent posture during food preparation.

In this study, we evaluated the effects on subjective discomfort among cooks during food preparation through use of a standing aid that we developed to alleviate the workload on the low back in the forward-bent posture. Twelve female cooks who worked in a kitchen in a nursing home were asked to prepare foods in 2 working postures: (a) supported by the standing aid (Aid) and (b) without the aid (No aid). They were instructed to evaluate discomfort in 13-body regions during food preparation and the degree of fatigue at the day's end and to enter their ratings after the end of the workday. Since a significant correlation was observed between body height and the improvement effect of discomfort through use of the standing aid, cooks were divided into two groups according to the height, and ratings were analyzed in each group. Among the tall cooks, subjective discomfort in the low back and the front and back of thighs was significantly less with the Aid posture than with the No aid posture. However, in short cooks these values tended to increase in the Aid posture compared with the No aid posture. The results suggest that the standing aid was effective in alleviating tall cooks' workload on the low back in the forward-bent posture.
A comparison of patient characteristics and 30-day mortality outcomes after transcatheter aortic valve implantation and surgical aortic valve replacement for the treatment of aortic stenosis: a two-centre study.

It is unclear whether transcatheter aortic valve implantation (TAVI) addresses an unmet clinical need for those currently rejected for surgical aortic valve replacement (SAVR) and whether there is a subgroup of high-risk patients benefiting more from TAVI compared to SAVR. In this two-centre, prospective cohort study, we compared baseline characteristics and 30-day mortality between TAVI and SAVR in consecutive patients undergoing invasive treatment for aortic stenosis.



We pre-specified different adjustment methods to examine the effect of TAVI as compared with SAVR on overall 30-day mortality: crude univariable logistic regression analysis, multivariable analysis adjusted for baseline characteristics, analysis adjusted for propensity scores, propensity score matched analysis, and weighted analysis using the inverse probability of treatment (IPT) as weights. A total of 1,122 patients were included in the study: 114 undergoing TAVI and 1,008 patients undergoing SAVR. The crude mortality rate was greater in the TAVI group (9.6% vs. 2.3%) yielding an odds ratio [OR] of 4.57 (95%-CI 2.17-9.65). Compared to patients undergoing SAVR, patients with TAVI were older, more likely to be in NYHA class III and IV, and had a considerably higher logistic EuroSCORE and more comorbid conditions. Adjusted OR depended on the method used to control for confounding and ranged from 0.60 (0.11-3.36) to 7.57 (0.91-63.0). We examined the distribution of propensity scores and found scores to overlap sufficiently only in a narrow range. In patients with sufficient overlap of propensity scores, adjusted OR ranged from 0.35 (0.04-2.72) to 3.17 (0.31 to 31.9). In patients with insufficient overlap, we consistently found increased odds of death associated with TAVI compared with SAVR irrespective of the method used to control confounding, with adjusted OR ranging from 5.88 (0.67-51.8) to 25.7 (0.88-750). Approximately one third of patients undergoing TAVI were found to be potentially eligible for a randomised comparison of TAVI versus SAVR.



Both measured and unmeasured confounding limit the conclusions that can be drawn from observational comparisons of TAVI versus SAVR. Our study indicates that TAVI could be associated with either substantial benefits or harms. Randomised comparisons of TAVI versus SAVR are warranted.
Adjuvant chemotherapy in Dukes' B and C colorectal cancer has only a minor influence on psychological distress

The object of this cross-sectional study on psychological distress was to reveal such distress among patients treated for colorectal cancer (CRC). Between 1993 and 1996, 95 patients in northern Norway were included in the national study randomising Dukes' B and C CRC patients between adjuvant chemotherapy (ACT : 5-fluorouracil and levamisole) or follow-up following radical surgery. In April 1996, all 82 survivors were mailed the Impact-of-Event Scale (IES), to which 64 patients responded (78%). Less than one-third of the patients reported a moderate to high level of psychological distress. Scores predicting significant stress response syndrome were revealed in 14% of the patients. The mean score on the intrusion and avoidance scales were 6.1 and 7.7, respectively. Such variables as age, sex, tumour location (rectum/colon), Dukes' stage B/C and time of follow up did not significantly influence the scores. Patients receiving ACT reported only a slightly raised level on the intrusion (6.97 vs 5.17) and avoidance (8.48 vs 6.80) scales. This study indicates that ACT in CRC Dukes' B and C is not a stressful happening. All advantages in survival achieved by ACT have to be weighed against the "cost" in terms of physical and psychological side effects. This study indicates the weighting in terms of psychological distress may be minimal.
Non-contrast-enhanced computerized tomography and analgesic-related kidney disease: report of the national analgesic nephropathy study.

Previous studies suggested that the non-contrast-enhanced computerized tomography (CT) scan is a highly reliable tool for the diagnosis of analgesic-associated renal disease. However, this issue has not been addressed in the US population. A total of 221 incident patients with ESRD from different regions of the United States underwent a helical CT scan and detailed questioning about drug history. Specific renal anatomic criteria were developed to determine whether a constellation of CT findings (small indented calcified kidneys [SICK]) is linked to analgesic ingestion. For approximating use before the onset of renal disease, only analgesic ingestion at least 9 yr before starting dialysis was considered relevant. Fifteen patients met the criteria for SICK. This represented 7% of the enrolled patients and approximately 1% of the total ESRD population. There was a significant increase in the estimated risk among patients with a history of heavy aspirin ingestion (odds ratio [OR] 7.4 [95% confidence interval (CI) 1.2 to 43] for > or =1 kg lifetime; OR 8.8 [95% CI 1.2 to 66] for > or =0.3 kg/yr). Total analgesic ingestion of > or =0.3 kg/yr also was significantly associated with SICK (OR 8.2; 95% CI 1.5 to 45). These findings were accounted for largely by combination products that contained aspirin and phenacetin (used by three patients with SICK), which are no longer available. In addition, the CT finding of SICK was present only in a minority of heavy analgesic users, yielding a sensitivity of 5 to 26%. Findings of SICK are infrequent in the US ESRD population and do not occur among a sufficient proportion of heavy analgesic users to render the non-contrast-enhanced CT scan a sensitive tool to detect analgesic-associated kidney injury.
Neuronal and glial markers are differently associated with computed tomography findings and outcome in patients with severe traumatic brain injury: a case control study

Authors of several studies have studied biomarkers and computed tomography (CT) findings in the acute phase after severe traumatic brain injury (TBI). However, the correlation between structural damage as assessed by neuroimaging and biomarkers has not been elucidated. The aim of this study was to investigate the relationships among neuronal (Ubiquitin carboxy-terminal hydrolase L1 [UCH-L1]) and glial (glial fibrillary acidic protein [GFAP]) biomarker levels in serum, neuroradiological findings and outcomes after severe TBI.



The study recruited patients from four neurotrauma centers. Serum samples for UCH-L1 and GFAP were obtained at the time of hospital admission and every 6 hours thereafter. CT scans of the brain were obtained within 24hrs of injury. Outcome was assessed by Glasgow Outcome Scale (GOS) at discharge and at 6 months.



81 severe TBI patients and 167 controls were enrolled. The mean serum levels of UCH-L1 and GFAP were higher (p < 0.001) in TBI patients compared to controls. UCH-L1 and GFAP serum levels correlated significantly with Glasgow Coma Scale (GCS) and CT findings. GFAP levels were higher in patients with mass lesions than in those with diffuse injury (2.95 ± 0.48 ng/ml versus 0.74 ± 0.11 ng/ml) while UCH-L1 levels were higher in patients with diffuse injury (1.55 ± 0.18 ng/ml versus 1.21 ± 0.15 ng/ml, p = 0.0031 and 0.0103, respectively). A multivariate logistic regression showed that UCH-L1 was the only independent predictor of death at discharge [adjusted odds ratios 2.95; 95% confidence interval, 1.46-5.97], but both UCH-L1 and GFAP levels strongly predicted death 6 months post-injury.



Relationships between structural changes detected by neuroimaging and biomarkers indicate each biomarker may reflect a different injury pathway. These results suggest that protein biomarkers could provide better characterization of subjects at risk for specific types of cellular damage than that obtained with neuroimaging alone, as well as provide valuable information about injury severity and outcome after severe TBI.
Comparing methods for assessing bronchial responsiveness in children: single step cold air challenge, multiple step cold air challenge, and histamine provocation.

Cold air challenge (CACh) can be applied by either a single step (SSCACh) or a multiple step (MSCACh) protocol. The interrelationship of the responses of the different protocols has not yet been studied. Furthermore, there is contradictory information on the correlation of cold air challenge responses to the outcome of pharmacological provocations. A single and a multiple step cold air challenge and a histamine provocation were performed in random order on three consecutive days on 28 children and adolescents with bronchial asthma, who were currently symptom- and medication-free. Single step cold air challenge consisted of a 4 min isocapnic hyperventilation of dry, -10 degrees C air; the subjects's response was quantified by the induced change in forced expiratory volume in one second (FEV1). Multiple step cold air challenge consisted of a series of 3 min, cold dry air hyperventilation steps from 20 to 80% of maximal voluntary ventilation (MVV); response was expressed as the provocative dose causing a 10% fall in FEV1 (PD10). Histamine provocation consisted of a series of 2 min inhalations of stepwise increasing histamine concentrations from 0.03 to 8.0 mg.mL-1; response was expressed as the provocative concentration of histamine causing a 20% fall in FEV1 (PC20). Change in FEV1 (delta FEV1) (SSCACh) correlated closely with PD10 (MSCACh); scatter around the regression line was minimal. With one exception, both types of CACh identified the same subjects as hyper- and normoresponsive. delta FEV1 (SSCACh) correlated significantly to PC20 (histamine), but scatter around the regression line was substantial. The correlation of PD10 (MSCACh) to PC20 (histamine) failed to reach statistical significance. These results indicate that the stimulus applied and the bronchoconstrictor mechanism activated, and not the challenge protocol, determine the outcome of a cold air challenge. In clinical practice, a brief single step cold air challenge can substitute for a more time-consuming multiple step cold air challenge. As nonpharmacological challenges seem to measure a different type of bronchial responsiveness, neither a single step nor a multiple step cold air challenge can substitute for a pharmacological provocation.
Prognostic value of late gadolinium enhancement on cardiac magnetic resonance imaging in Japanese hypertrophic cardiomyopathy patients.

The prognostic value of late gadolinium enhancement (LGE) on contrast-enhanced cardiovascular magnetic resonance (CMR) in Japanese hypertrophic cardiomyopathy (HCM) patients in a large, single-center cohort was investigated.


A total of 345 HCM patients (mean age, 59±17 years; 214 male) underwent CMR with gadolinium enhancement, and were followed (mean duration, 21.8 months) for cardiovascular events. Patients were divided into event-positive and event-negative groups. The clinical and CMR characteristics were compared between the 2 groups, and predictors of cardiovascular events assessed on multivariate analysis. LGE was positive in 252 patients (73%). The annual cardiovascular events rate was significantly higher in patients with LGE than in those without (6.2%/year vs. 0.6%/year, P=0.003). On multivariate analysis, LGE (hazard ratio [HR], 7.436; 95% confidence interval [CI]: 1.001-55.228, P=0.050), increased myocardial mass index (HR, 1.013; 95% CI: 1.002-1.023, P=0.018), reduced left ventricular ejection fraction (HR, 0.965; 95% CI: 0.945-0.985, P=0.001), and atrial fibrillation (HR, 2.257; 95% CI: 1.024-4.976, P=0.043) were significantly associated with cardiovascular events.


The presence of LGE, increased myocardial mass index, reduced left ventricular ejection fraction and atrial fibrillation were independent predictors of adverse prognosis in Japanese HCM patients.
[The development and effects of an integrated symptom management program for prevention of recurrent cardiac events after percutaneous coronary intervention].

This study was conducted to develop and to determine the effects of an integrated symptom management program for prevention of recurrent cardiac events after percutaneous coronary intervention.



Subjects consisted of 58 CAD patients (experimental group: 30, control group: 28). The experimental group participated in an integrated symptom management program for 6 months which was composed of tailored education, stress management, exercise, diet, deep breathing, music therapy, periodical telephone monitoring and a daily log. The control group received the usual care.



The experimental group significantly decreased symptom experiences and the level of LDL compared to the control group. The experimental group significantly increased self care activity and quality of life compared to the control group. Although no significant difference was found in cardiac recurrence, the experimental group had fewer recurrences.



These results suggest that an integrated symptom management program for prevention of recurrent cardiac events after percutaneous coronary intervention can improve symptom aggravation, recurrent rate, self care activity and quality of life. Nursing interventions are needed to maintain and further enhance the quality of life of these patients and the interventions should be implemented in the overall transition period.