nils-herrmann/clean_scirepeval huggingface dataset:
Potential responders to FOLFOX therapy for colorectal cancer by Random Forests analysis

Molecular characterisation using gene-expression profiling will undoubtedly improve the prediction of treatment responses, and ultimately, the clinical outcome of cancer patients.To establish the procedures to identify responders to FOLFOX therapy, 83 colorectal cancer (CRC) patients including 42 responders and 41 non-responders were divided into training (54 patients) and test (29 patients) sets. Using Random Forests (RF) algorithm in the training set, predictor genes for FOLFOX therapy were identified, which were applied to test samples and sensitivity, specificity, and out-of-bag classification accuracy were calculated.In the training set, 22 of 27 responders (81.4% sensitivity) and 23 of 27 non-responders (85.1% specificity) were correctly classified. To improve the prediction model, we removed the outliers determined by RF, and the model could correctly classify 21 of 23 responders (91.3%) and 22 of 23 non-responders (95.6%) in the training set, and 80.0% sensitivity and 92.8% specificity, with an accuracy of 69.2% in 29 independent test samples.Random Forests on gene-expression data for CRC patients was effectively able to stratify responders to FOLFOX therapy with high accuracy, and use of pharmacogenomics in anticancer therapy is the first step in planning personalised therapy.
Comparing the sensitivity of linear and volumetric MRI measurements to detect changes in the size of vestibular schwannomas in patients with neurofibromatosis type 2 on bevacizumab treatment.

To compare the sensitivity of linear and volumetric measurements on MRI in detecting schwannoma progression in patients with neurofibromatosis type 2 on bevacizumab treatment as well as the extent to which this depends on the size of the tumour.



We compared retrospectively, changes in linear tumour dimensions at a range of thresholds to volumetric tumour measurements performed using Brainlab iPlan(®) software (Feldkirchen, Germany) and classified for tumour progression according to the Response Evaluation in Neurofibromatosis and Schwannomatosis (REiNS) criteria.



Assessment of 61 schwannomas in 46 patients with a median follow-up of 20 months (range 3-43 months) was performed. There was a mean of 7 time points per tumour (range 2-12 time points). Using the volumetric REiNS criteria as the gold standard, a sensitivity of 86% was achieved for linear measurement using a 2-mm threshold to define progression.



We propose that a change in linear measurement by 2 mm (particularly in tumours with starting diameters 20-30 mm, the majority of this cohort) could be used as a filter to identify cases of possible progression requiring volumetric analysis. This pragmatic approach can be used if stabilization of a previously growing schwannoma is sufficient for a patient to continue treatment in such a circumstance.


ADVANCES IN KNOWLEDGE
We demonstrate the real-world limitations of linear vs volumetric measurement in tumour response assessment and identify limited circumstances where linear measurements can be used to determine which patients require the more resource-intensive volumetric measurements.
Stressful events, personality, and mood disturbance: gender differences in alcoholics and problem drinkers.

The present study examined relationships among stressful events, personality characteristics, and affective status in males and females of various alcohol drinking patterns. We examined a total of 154 participants from three distinct alcohol subgroups: alcohol dependent, problem drinker, and light social drinker. These subjects did not meet criteria for any concurrent nonalcohol comorbid psychiatric disorder. The study included an alcohol quantity-frequency interview and self-report questionnaires on stressful life events, depressive symptoms, trait anxiety, and personality characteristics. Results showed female alcoholics reported significantly greater depression, anxiety, and neuroticism compared to their male counterparts (and all other drinking groups). Female problem drinkers reported significantly greater depressive symptoms and health-related stressful events compared to male problem drinkers and the light drinkers. In contrast, male problem drinkers did not show elevations on these dimensions and more closely resembled light drinkers, of whom no gender differences were found. The findings support theories suggesting a "telescoping" of complications, health-related stress, and mood dysfunction in women at a lower threshold level of alcohol consumption compared to their male counterparts.
Validity of self-report for fractures among a multiethnic cohort of postmenopausal women: results from the Women's Health Initiative observational study and clinical trials.

The purpose of this study is to examine the validity of, and factors associated with, the accuracy of self-report (participant-report and proxy-report) for fractures.



Study participants were from the Women's Health Initiative Clinical Trial and Observational Study cohorts. All women were postmenopausal; populations included American Indian, Asian/Pacific Islander, black, Hispanic, and non-Hispanic white. The average length of follow-up was 4.3 years. Self-reported fractures were adjudicated by reviewing medical records. The first adjudicated self-report of fractures for each participant was included in the analysis (n = 6,652).



We found substantial variations in validity of self-report by the fracture site. Agreements between self-reports for single-site fractures and medical records were high for hip (78%) and forearm/wrist (81%) but relatively lower for clinical spine fractures (51%). The average confirmation rate for all single-site fractures was 71%. Misidentification of fracture sites by participants or proxy-reporters seemed to be a cause of unconfirmed self-reports. Higher confirmation rates were observed in participant-reports than in proxy-reports. Results of the multivariate analysis indicated that multiple factors, such as ethnicity, a history of osteoporosis or fractures, body mass index, years since menopause, smoking status, and number of falls in the past year were significantly (P < 0.05) related to the validity of self-report.



The validity of self-reports for fracture varies by fracture sites and many other factors. The assessed validity in this study is likely conservative because some of the unconfirmed self-reports may be due to poor medical record systems. The validity of self-reports for hip and forearm/wrist fractures is high in this study, supporting their use in epidemiological studies among postmenopausal women.
An ultrasonication-assisted extraction and derivatization protocol for GC/TOFMS-based metabolite profiling.

Conventional chemical derivatization of metabolites in biological specimens is time-consuming, which limits the throughput and efficiency of metabolite profiling using a gas chromatography/time-of-flight mass spectrometry (GC/TOFMS) platform. We report an ultrasonication-assisted protocol which reduces the derivatization time from hours to about 30 min and significantly enhances the derivatization efficiency prior to a GC/TOFMS analysis. The protocol was evaluated using 40 compounds representing different classes of human metabolites, and demonstrated good analytical precision and accuracy. In comparison with the conventional method, the new protocol was able to increase the intensity of most of the identified peaks (71.0%) in the GC/TOFMS chromatograms of human serum samples. The detected compounds with increased intensity include most amino acids, keto-containing organic acids, carbonyl-containing carbohydrates, and unsaturated fatty acids. We applied this protocol in a metabolomic study of human serum samples obtained from 34 patients diagnosed with hypertension and 29 age- and gender-matched healthy subjects. Metabolite markers associated with hypertension, including glucosamine, D-sorbitol, 1-stearoylglycerol, and homocysteine, were identified and validated by statistical methods and use of reference standards. Our work highlights the potential of this novel approach for the large-scale metabolite profiling of samples generated from plant, animal, and clinical and epidemiological studies.
Efficacy of short-term adjunctive subantimicrobial dose doxycycline in diabetic patients--randomized study.

To investigate the effectiveness of short-term adjunctive subantimicrobial dose doxycycline (SDD) treatment in patients with diabetes mellitus type 2 and chronic periodontitis (CP).



Thirty-four patients with CP and type 2 diabetes mellitus were included in the placebo-controlled, double-blind study. After scaling and root planing (SRP), patients were randomly assigned to two groups, receiving either SDD or placebo bid for 3 months. The probing depth (PD), clinical attachment level (CAL), bleeding on probing (BOP), approximal plaque index, glycated hemoglobin (HbA1c) level were recorded and gingival crevicular fluid (GCF) samples were collected at baseline and after 3-month therapy for the estimation of matrix metalloproteinase-8 levels.



Clinical attachment level, PD, and BOP improved significantly in both groups after therapy (P < 0.05). The statistically significant difference between the two groups after the therapy was observed only in PD in tooth sites with initial PD ≥ 4 mm (SRP + placebo: 3.41 ± 0.6 mm vs SRP + SDD: 2.92 ± 0.5 mm, P < 0.05). GCF matrix metalloproteinase-8 levels were significantly reduced only in SRP + SDD group (P < 0.01). There were no changes in HbA1c levels after therapy.



The short-term administration of SDD gives significant benefit at tooth sites with moderate disease (PD ≥ 4 mm) when compared to SRP alone in patients with diabetes and CP.
The analgesic effect of morphine on postoperative pain in diabetic patients.

Many clinical and experimental studies have suggested that diabetes or hyperglycemia alter opioid responsiveness. However, little information is available on the effects of diabetes mellitus on opioid requirements in the postoperative period.



Sixty-four patients scheduled for elective, total abdominal hysterectomy were included into this prospective study to evaluate the effect of diabetes mellitus on morphine requirement in the postoperative period. A loading dose of morphine (50 micro g kg(-1)) was administered in the perioperative period. Postoperative analgesia consisted of intravenous morphine-PCA. No analgesic other than morphine was allowed during the study. In cases of inadequate analgesia intravenous 1 mg of morphine was given as a rescue analgesic. Cumulative morphine consumption, pain scores and morphine-related adverse effects were recorded.



A total of 60 patients were evaluated: Group D, 30; and Group ND, 30. Patients in Group D received more morphine than those in Group ND (54.12 +/- 25.09 and 42.66 +/- 20.67, respectively). The difference in cumulative morphine consumption was higher in the first hour (P = 0.037) in diabetic patients and they required significantly more morphine in the last 24 h (P = 0.015). Postoperative pain scores were higher in the diabetic group. More patients in the diabetic group required rescue medication (26 vs. 19) and felt nauseous (25 vs. 14; P = 0.003).



The findings of the study appear to support experimental and clinical impressions that the analgesic effect of morphine is attenuated in hyperglycemic conditions. Therefore, larger doses of morphine may be administered to diabetic patients for effective postoperative analgesia.
A Placebo-Controlled Trial of L-DOPA/Carbidopa in Early Cocaine Abstinence

Thirty patients with primary cocaine dependence who had used cocaine within the past 24 hours and were being admitted to a detoxification ward were rated for signs and symptoms of cocaine abstinence and craving. They then received four doses of either L-dihydroxy-phenylalanine/carbidopa (100 mg/25 mg) or placebo over the next day. Ratings were repeated in the late afternoon of the day of admission and after the final morning dose the next day. No significant differences in abstinence scores were found between the two treatment groups. The lack of drug-placebo differences appeared to be mainly due to rapid clearing of abstinence symptoms in the placebo-treated patients.
Pri-miR-34b/c rs4938723 polymorphism is associated with a decreased risk of gastric cancer.

Previous studies have demonstrated that miR-34 family members are abnormally expressed in gastric cancer. Overexpression of the miR-34 family suppresses gastric carcinogenesis, whereas downregulation of the miR-34 family promotes tumorigenesis. p53 can bind to the promoter region of miR-34b/c, leading to an increase of miR-34b/c expression. Recently, a variant in the promoter region of pri-miR-34b/c (rs4938723) has been discovered, with the function of altering the binding efficiency of transcription factor GATA. The purpose of this study was to examine the role of the miR-34b/c rs4938723 and TP53 Arg72Pro polymorphisms in the susceptibility of gastric cancer. We analyzed the distribution of the two polymorphisms in 197 patients with gastric cancer and 289 age-, gender-, ethnicity-, and living area-matched controls using polymerase chain reaction-restriction fragment length polymorphism and DNA direct sequencing. We found that the CT and CT/CC genotypes of the miR-34b/c rs4938723 were associated with a significantly decreased risk of gastric cancer compared with the TT genotype (CT vs. TT: odds ratio [OR]=0.66; 95% confidence interval [95% CI], 0.45-0.97; and CT/CC vs. TT: OR=0.67; 95% CI, 0.47-0.97, respectively). Combined analysis showed that subjects carrying the miR-34b/c rs4938723 CT/CC and TP53 CG/CC genotypes had a 0.62-fold decreased risk to develop gastric cancer compared with subjects carrying the miR-34b/c rs4938723 TT and TP53 CG/CC genotypes (OR=0.62; 95% CI, 0.40-0.96). These findings suggest that the miR-34b/c rs4938723 may individually and jointly have a protective effect on the risk of gastric risk.
Comparison of high and low intensity contact between secondary and primary care to detect people at ultra-high risk for psychosis: study protocol for a theory-based, cluster randomized controlled trial

The early detection and referral to specialized services of young people at ultra-high risk (UHR) for psychosis may reduce the duration of untreated psychosis and, therefore, improve prognosis. General practitioners (GPs) are usually the healthcare professionals contacted first on the help-seeking pathway of these individuals.



This is a cluster randomized controlled trial (cRCT) of primary care practices in Cambridgeshire and Peterborough, UK. Practices are randomly allocated into two groups in order to establish which is the most effective and cost-effective way to identify people at UHR for psychosis. One group will receive postal information about the local early intervention in psychosis service, including how to identify young people who may be in the early stages of a psychotic illness. The second group will receive the same information plus an additional, ongoing theory-based educational intervention with dedicated liaison practitioners to train clinical staff at each site. The primary outcome of this trial is count data over a 2-year period: the yield - number of UHR for psychosis referrals to a specialist early intervention in psychosis service - per primary care practice.



There is little guidance on the essential components of effective and cost-effective educational interventions in primary mental health care. Furthermore, no study has demonstrated an effect of a theory-based intervention to help GPs identify young people at UHR for psychosis. This study protocol is underpinned by a robust scientific rationale that intends to address these limitations.
Long-Acting Insulin Analogs and the Risk of Diabetic Ketoacidosis in Children and Adolescents With Type 1 Diabetes

To investigate if long-acting insulin analogs decrease the risk of diabetic ketoacidosis (DKA) in young individuals with type 1 diabetes.  Of 48,110 type 1 diabetic patients prospectively studied between 2001 and 2008, the incidence of DKA requiring hospitalization was analyzed in 10,682 individuals aged </=20 years with a diabetes duration of >/=2 years.  The overall rate of DKA was 5.1 (SE +/- 0.2)/100 patient-years. Patients using insulin glargine or detemir (n = 5,317) had a higher DKA incidence than individuals using NPH insulin (n = 5,365, 6.6 +/- 0.4 vs. 3.6 +/- 0.3, P < 0.001). The risk for DKA remained significantly different after adjustment for age at diabetes onset, diabetes duration, A1C, insulin dose, sex, and migration background (P = 0.015, odds ratio 1.357 [1.062-1.734]).  Despite their long-acting pharmacokinetics, the use of insulin glargine or detemir is not associated with a lower incidence of DKA compared with NPH insulin.
Caregiver burden, patients' self-perceived burden, and preference for palliative care among cancer patients and caregivers.

Recently, caregiver burden (CB) has emerged as an important issue in the area of palliative medicine. However, patients' feelings related to being a burden to their families (i.e., self-perceived burden [SPB]) is also a significant issue. We evaluated the relation of CB and SPB as preference for palliative care.



A national, multicenter, cross-sectional survey of 326 patient-caregiver dyads was performed. A set of paired questionnaires evaluating CB and SPB (five domain items assessed on a four-point Likert scale) were independently administered to patients and their caregivers. Among the respondents, only the patients with distant stage cancer and their caregivers were included. Multivariate analyses were conducted to identify the associations between CB and SPB and preference for palliative care.



Caregivers and patients who preferred palliative care to life sustaining treatment reported higher CB and SPB scores, respectively. Caregivers who felt more of a burden were more likely to prefer palliative care over life sustaining treatment for their patients (adjusted odds ratio [aOR] = 1.67, 95% CI: 1.21-2.31). In addition, patients who perceived their caregivers' burden as large tended to prefer palliative care (aOR = 1.61, 95% CI: 1.16-2.22).



Both CB and SPB increased preference for palliative care. This could be interpreted that high CB can lead to preference for palliative care in both patients and their caregivers, potentially threatening patient autonomy. Efforts to relieve CB and SPB are needed.
Radiofrequency ablation of advanced head and neck cancer.

To determine if the application of radiofrequency ablation to advanced head and neck cancer (HNC) would result in local control of the tumor.



Radiofrequency ablation was applied to advanced head and neck malignant tumors in the participants of this nonrandomized controlled trial.



Academic tertiary care medical center.



Twenty-one participants with recurrent and/or unresectable HNC who failed treatment with surgery, radiation, and/or chemotherapy were selected for the trial. Patients deemed appropriate for curative standard radiation or surgery were not accepted as participants.



Radiofrequency ablation was applied to head and neck tumors under general anesthesia and computed tomographic scan guidance.



The primary end point was local control. Computed tomographic scan tumor measurements were used to assess response by standard response evaluation criteria in solid tumors (RECIST) guidelines. Secondary outcome measures included survival and quality of life.



Eight of 13 participants had stable disease after intervention. Median survival was 127 days, and an improvement in University of Washington quality-of-life scores was noted. Adverse outcomes included 1 death due to carotid hemorrhage and 2 strokes.



Radiofrequency ablation is a palliative treatment alternative that shows promise in addressing the challenges of local control and quality of life in patients with incurable HNC who have failed standard curative treatment.
Adherence to antiretroviral therapy during pregnancy and the first year postpartum among HIV-positive women in Ukraine

Poor adherence to antiretroviral therapy (ART) is associated with HIV disease progression and, during pregnancy, increased mother-to-child transmission risk. In Ukraine, access to combination ART is expanding but data on adherence are scarce.



Cross-sectional surveys of HIV-positive women were conducted i) at delivery (on antenatal ART adherence) and ii) during the first year postpartum (on ART adherence in the preceding four weeks). Factors associated with a score ≤ 11 on the self-report Case Adherence Support Evaluation (CASE) index or ≥ 1 self-reported missed dose were assessed using Fisher's exact test.



Of 185 antenatal participants and 102 postnatal participants, median ages were 27.5 and 29.5 years respectively: 28% (50/180) and 27% (26/98) reported an unplanned pregnancy, and 13% (24/179) and 17% (17/98) an illicit drug-use history (excluding marijuana). One quarter (49/180 antenatally, 27/101 postnatally) screened positive for depression. The proportion reporting 'low' ART-related self-efficacy (i.e. unable to do ≥ 1/5 ART-taking activities) was 20% (28/141) antenatally and 17% (11/66) postnatally. Antenatally, 14% (95% CI 10-21%) had a CASE score ≤ 11 and 35% (95% CI 28-42%) reported missing ≥ 1 dose. Factors associated with a CASE score ≤ 11 were unplanned pregnancy (25% (12/48) vs. 11% (13/120) where planned, p = 0.03) and living with extended family (23% (13/57) vs. 10% (12/125) living with partner/alone, p = 0.04). Self-report of ≥ 1 missed dose antenatally was additionally associated with younger age (p = 0.03) and lower self-efficacy (50% (14/28) reported ≥ 1 missed dose vs. 28% (30/108) of those with high self-efficacy, p = 0.04). Of 102 postnatal participants, 8% (95% CI 4-15%) had a CASE score ≤ 11 and 31% (95% CI 22-41%) reported ≥ 1 missed dose. Of 11 women with low self-efficacy, 3 (27%) had a CASE score ≤ 11 compared with 3/55 (5%) of those with high self-efficacy (p = 0.05). Current smokers more commonly reported ≥ 1 missed dose postnatally (50% (13/26) vs. 25% (18/72) of non-smokers, p = 0.03).



Our results highlight unmet needs for counselling and support. We identify some groups at risk of poor ART adherence, including women with markers of social vulnerability and those with low ART-related self-efficacy, who may benefit from targeted interventions.
Clinical outcomes in patients with implantable cardioverter defibrillators and Sprint Fidelis leads.

The performances of implantable cardioverter defibrillators and leads are important issues for healthcare providers and patients. In 2007 Sprint Fidelis leads were found to be associated with an increased failure rate and so the purpose of the study was to evaluate long-term mortality and clinical outcomes in patients implanted with Sprint Fidelis leads compared with Sprint Quattro leads.



508 patients with Sprint Fidelis leads and 468 with Sprint Quattro leads were prospectively followed in 12 Italian cardiology centres.



Information on hospitalisations and other clinical events were collected during scheduled and unscheduled hospital visits. Deaths were identified from medical records or via phone contacts with patients' family members or through the National Office of Vital Statistics.



Over a mean follow-up of 27±18 months 141 deaths occurred in the overall population. No death was observed in patients with diagnosed failing lead. Kaplan-Meier patient survival differed between the two lead groups (80±2% in Fidelis leads vs 70±4% in the Sprint Quattro leads at 4 years, p=0.002). Multivariate analyses showed that mortality was neither associated with lead type nor with diagnosed failed lead. The annual rate of lead failure was 1.8% patient-year for Fidelis leads and 0.2% for the Sprint Quattro leads.



In our multicentre research, the clinical outcomes of patients with Fidelis leads differed from those of patients with Sprint Quattro leads. Nevertheless, neither mortality nor the combined endpoint of mortality and heart failure hospitalisations was associated with the lead type. http://clinicaltrials.gov/ct2/show/NCT01007474.