nils-herrmann/clean_scirepeval huggingface dataset:
Comparison of a rule-based algorithm with a phenotype-based algorithm for the interpretation of HIV genotypes in guiding salvage regimens in HIV-infected patients by a randomized clinical trial: the mutations and salvage study.

There is still considerable uncertainty as to the best algorithm for interpreting human immunodeficiency virus (HIV) genotyping results.



A total of 318 subjects with HIV RNA levels of >1000 copies/mL were enrolled in 41 centers throughout Italy from 2001 through 2003, stratified on the basis of their drug history, randomized (1:1) to 2 arms to have their treatments modified on the basis of the results of HIV genotyping (as interpreted by virtual phenotype analysis or with use of a rule-based interpretation system), and followed up for 48 weeks. At least 1 nucleoside reverse-transcriptase inhibitor and 1 protease inhibitor had to be included in any new regimen; nonnucleoside reverse-transcriptase inhibitor-naive patients were also prescribed a nonnucleoside reverse-transcriptase inhibitor. Only drugs licensed in Italy were allowed. The primary end point was a decrease in HIV RNA level to <400 copies/mL by week 12 according to on-treatment analysis.



The mean (+/- standard deviation) values at baseline were as follows: HIV RNA level, 4.1+/-0.74 log(10) copies/mL; CD4(+) T lymphocyte count, 410+/-262 cells/microL; reverse-transcriptase mutations, 4.8+/-2.9; and protease mutations, 2.8+/-2.5. There were 133 patients (41.8%) who were nonnucleoside reverse-transcriptase inhibitor naive and protease inhibitor experienced, 63 patients (19.8%) who were nonnucleoside reverse-transcriptase inhibitor experienced and protease inhibitor naive, and 122 patients (38.4%) who were 3-class experienced. A total of 192 patients completed 12 weeks of the treatment regimen assigned at baseline; at 12 weeks, 66.3% of patients in the virtual phenotype arm and 71.3% of patients in the rule-based interpretation arm had HIV RNA levels of <400 copies/mL (P = .46). No statistically significant difference between arms was observed by intention-to-treat analysis.



Both the virtual phenotype and rule-based interpretation methods of HIV genotyping can guide the selection of effective antiretroviral drugs for a salvage regimen.
Comparing pain control and ability to eat and drink with standard therapy vs Gelclair: a preliminary, double centre, randomised controlled trial on patients with radiotherapy-induced oral mucositis

Oral mucositis (OM) is a functionally destructive complication of aggressive head and neck cancer therapy, often resulting in intense pain, an inability to eat and drink and secondary malnutrition and dehydration. The barrier-forming properties of Gelclair have shown promise in relieving such symptoms. The aim of this randomised-controlled trial was to evaluate the efficacy of Gelclair, as compared to standard therapy, as a means of short-term symptom control for patients suffering from radiotherapy-induced OM. Twenty patients, with radiotherapy-induced OM seen in two oncology centres in Devon, were randomised to either standard therapy (Sucralfate and Mucaine) or Gelclair and assessed over 24 h. Both treatments were taken four times during the 24-h period, 30 min before meals. No significant difference was found between the Gelclair and standard therapy arms in terms of general pain (F = 1.512, df = 1, 17, ns). There did appear to be a trend towards pain improvement initially after the use of Gelclair, but this did not last for the full 24-h assessment period. There was no significant reduction in pain on speaking (F = 0.261, df = 1, 17, ns) nor an improvement in capacity to eat and drink, although the effects of standard therapy did appear to last longer than the Gelclair. This study indicates that Gelclair is no more effective than current standard practice in relieving the pain associated with radiotherapy-induced OM. Nevertheless, observations from this preliminary study warrant further investigation, with a view to shaping the way forward for head and neck cancer practice on a national level.
A double-blind randomized study comparing the effects of continuing or not continuing rosiglitazone + metformin therapy when starting insulin therapy in people with Type 2 diabetes1

To compare the efficacy and safety of either continuing or discontinuing rosiglitazone + metformin fixed-dose combination when starting insulin therapy in people with Type 2 diabetes inadequately controlled on oral therapy.



In this 24-week double-blind study, 324 individuals with Type 2 diabetes inadequately controlled on maximum dose rosiglitazone + metformin therapy were randomly assigned to twice-daily premix insulin therapy (target pre-breakfast and pre-evening meal glucose < or = 6.5 mmol/l) in addition to either rosiglitazone + metformin (8/2000 mg) or placebo.



Insulin dose at week 24 was significantly lower with rosiglitazone + metformin (33.5 +/- 1.5 U/day, mean +/- se) compared with placebo [59.0 +/- 3.0 U/day; model-adjusted difference -26.6 (95% CI -37.7, -15,5) U/day, P < 0.001]. Despite this, there was greater improvement in glycaemic control [HbA(1c) rosiglitazone + metformin vs. placebo 6.8 +/- 0.1 vs. 7.5 +/- 0.1%; difference -0.7 (-0.8, -0.5)%, P < 0.001] and more individuals achieved glycaemic targets (HbA(1c) < 7.0% 70 vs. 34%, P < 0.001). The proportion of individuals reporting at least one hypoglycaemic event during the last 12 weeks of treatment was similar in the two groups (rosiglitazone + metformin vs. placebo 25 vs. 27%). People receiving rosiglitazone + metformin in addition to insulin reported greater treatment satisfaction than those receiving insulin alone. Both treatment regimens were well tolerated but more participants had oedema [12 (7%) vs. 4 (3%)] and there was more weight gain [3.7 vs. 2.6 kg; difference 1.1 (0.2, 2.1) kg, P = 0.02] with rosiglitazone + metformin.



Addition of insulin to rosiglitazone + metformin enabled more people to reach glycaemic targets with less insulin, and was generally well tolerated.
Moment feature based forensic detection of resampled digital images

Forensic detection of resampled digital images has become an important technology among many others to establish the integrity of digital visual content. This paper proposes a moment feature based method to detect resampled digital images. Rather than concentrating on the positions of characteristic resampling peaks, we utilize a moment feature to exploit the periodic interpolation characteristics in the frequency domain. Not only the positions of resampling peaks but also the amplitude distribution is taken into consideration. With the extracted moment feature, a trained SVM classifier is used to detect resampled digital images. Extensive experimental results show the validity and efficiency of the proposed method.
Relative effects of bronchial drainage and exercise for in-hospital care of patients with cystic fibrosis.

Bronchial hygiene therapy is a standard part of the treatment of patients with cystic fibrosis (CF). Coughing alone promotes sputum expectoration and is probably the primary effective component of standard bronchial hygiene therapy. The purpose of this study was to determine whether substituting regular exercise, which also promotes coughing, for two of three daily bronchial hygiene treatments would affect the expected improvements in pulmonary function and exercise response in hospitalized patients with CF. Seventeen patients with CF hospitalized (means length of stay = 13.0 +/- 2.6 days) for an acute exacerbation of their pulmonary disease participated in the study. The patients were randomly assigned to either a group that participated in two cycle ergometer exercise sessions and one bronchial hygiene treatment session per day (EX Group [n = 9]) or a group that participated in three bronchial hygiene treatment sessions per day (PD Group [n = 8]). Pulmonary functions and responses to a progressive, incremental cycle ergometer exercise test were measured on admission and before discharge. Bronchial hygiene therapy consisted of postural drainage, in six positions, with chest percussion and vibration. Therapeutic exercise was of moderate intensity and was individually adjusted based on the patient's heart rate and arterial oxygen saturation response to the admission exercise test. Coughing was encouraged during and after all treatments. Pulmonary function and exercise response were significantly improved over the period of hospitalization in both groups; the improvements were the same in the two groups. These results indicate that, in some hospitalized patients with CF, exercise therapy may be substituted for at least part of the standard protocol of bronchial hygiene therapy.
Predictors of physician referral for patient recruitment to Alzheimer disease clinical trials.

Inadequate recruitment into Alzheimer disease clinical trials is an important threat to the validity and generalizability of the studies. The majority of dementia patients are first evaluated by community-based physicians; however, physician perceptions of clinical research are largely unknown.



A survey was distributed to 3123 physicians in 3 states; 370 were returned. Survey items assessed attitudes, perceived benefits of and barriers to referral to clinical research, and physicians use of the internet for medical information.



The mean age of the respondents was 50.6+/-10.8 years; 70% were male, 78% white, 61% were primary care providers; 63% used the internet > or =3 times/week. No demographic or medical specialty differences existed between those who were likely (n=193) and unlikely (n=162) to refer patients to clinical trials. Differences were discovered in perceived benefits reported by physicians who were more likely to refer, whereas differences in perceived barriers existed in primary care compared with specialists. Referral to clinical trials is predicted by close proximity to a research center [odds ratio (OR): 4.0; 95% confidence interval (CI), 1.1-15.6] and availability of internet information regarding diagnostic evaluation (OR: 2.3; 95% CI, 1.1-4.7). Primary barriers included concerns about exposure of patients to uncomfortable procedures (OR: 4.7; 95% CI, 1.2-18.7) and lack of time to discuss research participation (OR: 6.8; 95% CI, 1.4-32.3).



Proximity to a research center and availability of diagnostic clinical tools are strong predictors of clinical trial referral. Concern over risks to patients and lack of time are strong barriers. These results suggest that dementia outreach education targeted to physicians should emphasize the importance of clinical trials with a focus on discussing research participation in a time-efficient manner and increasing awareness of risk reduction and the safety of research protocols. Providing easy access to up-to-date, user-friendly educational materials on dementia diagnosis and research via the internet are likely to improve referrals of patients to Alzheimer disease clinical trials from community physicians.
Use of lipid-modulating drugs in complicated course of coronary heart disease

We present the results of the study of lipid-modulating drugs (pravastatin, atorvastatin, simvastatin, and fibrate gemfibrozil) in complicated coronary heart disease (acute coronary syndrome without ST elevation, chronic heart failure. In acute coronary syndrome statins produced a positive effect on some studied parameters, while in heart failure only the safety of short-term therapy with statins was demonstrated.
The relationship between suicide ideation and late-life depression.

To describe the course of suicide ideation (SI) in primary-care based late-life depression treatment, identify predictors of SI, characterize the dynamic relationship between depression and SI, and test the hypothesis that collaborative care decreases the likelihood of reporting SI by decreasing the severity of depressive symptoms.



This was a secondary analysis of a randomized controlled trial comparing collaborative care to usual care for late-life depression. Participants were 1,801 adults age 60 and older from eight diverse primary-care systems. Depression was measured using the Hopkins Symptoms Checklist (HSCL-20). SI was operationalized using one item from the HSCL-20. Predictors of incident SI were identified by a series of univariate analyses followed by multiple logistic regression. A mediator analysis was conducted to test the hypothesis that the effect of collaborative care on SI can be ascribed to the intervention's effect on depressive symptoms.



The prevalence of SI was 14% (N = 253); the cumulative incidence over 24 months was 21% (385). The likelihood that SI emerged after baseline was highly dependent on change in depression (odds ratio: 5.38, 95% confidence interval: 3.93-7.36, df = 81, t = 10.66, p <0.0001). As hypothesized, the effect of collaborative care on SI was mediated by the treatment's effect on depression.



SI is not uncommon in depressed older adults being treated in primary care. The likelihood that depressed older adults will report SI is strongly determined by the course of their depression symptoms. Providers should monitor SI throughout the course of depression treatment.
The effect of prior breast biopsy method and concurrent definitive breast procedure on success and accuracy of sentinel lymph node biopsy

It has been suggested that sentinel lymph node (SLN) biopsy for breast cancer may be less accurate after excisional biopsy of the primary tumor compared with core needle biopsy. Furthermore, some have suggested an improved ability to identify the SLN when total mastectomy is performed compared with lumpectomy. This analysis was performed to determine the impact of the type of breast biopsy (needle vs. excisional) or definitive surgical procedure (lumpectomy vs. mastectomy) on the accuracy of SLN biopsy. The University of Louisville Breast Cancer Sentinel Lymph Node Study is a prospective multi-institutional study. Patients with clinical stage T1–2, N0 breast cancer were eligible. All patients underwent SLN biopsy and completion level I/II axillary dissection. Statistical comparison was performed by χ2 analysis. A total of 2206 patients were enrolled in the study. There were no statistically significant differences in SLN identification rate or false-negative rate between patients undergoing excisional versus needle biopsy. The SLN identification and false-negative rates also were not statistically different between patients who had total mastectomy compared with those who had a lumpectomy. Excisional biopsy does not significantly affect the accuracy of SLN biopsy, nor does the type of definitive surgical procedure.
The patient-specific functional scale is more responsive than the Roland Morris disability questionnaire when activity limitation is low

The primary objective of this study was to determine which questionnaire, the Roland Morris disability questionnaire (RMDQ) or the patient-specific functional scale (PSFS), was better at detecting change in activity limitation in a large cohort of patients with low back pain undergoing rehabilitation. A secondary aim was to determine if the responsiveness of the questionnaires was influenced by the patient’s level of activity limitation at baseline. Responsiveness statistics, including effect size statistics, Pearson’s r correlations and receiver operative characteristic (ROC) curve analysis were used to determine ability to detect change in activity limitation on 831 patients with low back pain. Data were analysed at two time points; directly after treatment (termed short-term) and several weeks post-treatment (termed mid-term). The data were subsequently re-analysed on sub-sets of the full cohort according to the level of activity limitation from RMDQ baseline scores. In the total cohort we found that the PSFS was more responsive than the RMDQ; however, in the subgroup with high activity limitation this pattern was not observed. This is true for time points up to 6 months post-treatment. In conclusion, the RMDQ and PSFS both demonstrate good responsiveness according to the definitions given in previous guidelines. The PSFS is more responsive than the RMDQ for patients with low levels of activity limitation but not for patients with high levels of activity limitation.
Cognitive Stimulation Modulates Platelet Total Phospholipases A2 Activity in Subjects with Mild Cognitive Impairment

We evaluated the effect of cognitive stimulation (CS) on platelet total phospholipases A2 activity (tPLA2A) in patients with mild cognitive impairment (MCI_P). At baseline, tPLA2A negatively correlated with Mini-Mental State Examination score (MMSE_s): patients with MMSE_s <26 (Subgroup 1) had significantly higher activity than those with MMSE_s ≥26 (Subgroup 2), who had values similar to the healthy elderly. Regarding CS effect, Subgroup 1 had a significant tPLA2A reduction, whereas Subgroup 2 did not significantly changes after training. Our results showed for the first time that tPLA2A correlates with the cognitive conditions of MCI_P, and that CS acts selectively on subjects with a dysregulated tPLA2A.
The effect of metoprolol on plasma lipids.

Fifteen hypertensive patients entered a single-blind study to examine the effects of metoprolol (100 mg twice daily) on fasting plasma lipids. In 12 patients who completed the study, non-esterified fatty acid concentrations fell, but cholesterol and triglyceride levels were unchanged after 12 weeks' treatment. These results conflict with earlier reports of the effect of metoprolol on plasma triglyceride concentrations.
Who needs direct-acting antivirals for HCV? Challenges faced in advancing HCV therapy for HIV-HCV-coinfected individuals.

The recent availability of new direct-acting antivirals (DAAs) for HCV treatment, which significantly increase sustained virological response rates for genotype 1 HCV infection, has brought new optimism with respect to curative HCV treatment for HIV-HCV-coinfected patients. We describe the characteristics of coinfected patients who could be eligible for DAAs to determine potential challenges facing clinicians and patients hoping to take advantage of these new therapies.



We evaluated the sociodemographic and clinical characteristics of the genotype 1 HCV-HIV-infected participants in a Canadian prospective multicentre cohort study at their most recent visit to assess potential eligibility for combination HCV treatment with boceprevir or telaprevir.



Of the 1,020 coinfected participants enrolled in the cohort, 707 (85%) had evidence of chronic HCV infection (HCV-RNA-positive), of whom 497 (70%) were infected with genotype 1; 375 (75%) were naive to HCV treatment and 122 (25%) had previously received therapy and failed. Only 143 (38%) of HCV treatment-naive and 39 (32%) of treatment-experienced participants had no absolute contraindications for treatment. Alcohol abuse, active depression and decompensated liver disease were the most frequent reasons for treatment ineligibility. The majority would require alterations in antiretroviral regimens to avoid important drug-drug interactions.



Although the need for curative HCV therapy in HIV-HCV coinfection is great, the actual number of patients who could be eligible for DAAs at the present time may be quite low. There remains an urgent need to develop safe, simple and interferon-sparing treatments for coinfected individuals.
Performance of the ASSIGN cardiovascular disease risk score on a UK cohort of patients from general practice.

To evaluate the performance of ASSIGN against the Framingham equations for predicting 10 year risk of cardiovascular disease in a UK cohort of patients from general practice and to make the evaluation comparable to an independent evaluation of QRISK on the same cohort.



Prospective open cohort study. Setting 288 practices from England and Wales contributing to The Health Improvement Network (THIN) database.



Patients registered with 288 UK practices for some period between January 1995 and March 2006. The number of records available was 1,787,169.



First diagnosis of myocardial infarction, coronary heart disease, stroke and transient ischaemic attacks recorded.  We implemented the Anderson Framingham Coronary Heart Disease and Stroke models, ASSIGN, and a more recent Framingham Cox proportional-hazards model and analysed their calibration and discrimination.



Calibration showed that all models tested over-estimated risk particularly for men. ASSIGN showed better discrimination with higher AUROC (0.756/0.792 for men/women), D statistic (1.35/1.58 for men/women), and R²(30.47%/37.39% for men/women). The performance of ASSIGN was comparable to that of QRISK on the same cohort. Models agreed on 93-97% of categorical (high/lower) risk assessments and when they disagreed, ASSIGN was often closer to the estimated Kaplan-Meier incidence. ASSIGN also provided a steeper gradient of deprivation and discriminated between those with and without recorded family history of CVD. The estimated incidence was twice/three times as high for women/men with a recorded family history of CVD.



For systematic CVD risk assessment all models could usefully be applied, but ASSIGN improved on the gradient of deprivation and accounted for recorded family history whereas the Framingham equations did not. However, all models display relatively low specificity and sensitivity. An additional conclusion is that the recording of family history of CVD in primary care databases needs to improve given its importance in risk assessment.
Effects of combination of insulin and acarbose compared with insulin and gliclazide in type 2 diabetic patients

In this prospective study we aimed to compare insulin plus acarbose with insulin plus gliclazide with respect to their effect on insulin requirement, lipid profiles and body mass index (BMI) while achieving good glycemic control. Forty patients with type 2 diabetes mellitus who were on conventional insulin therapy (subcutaneous insulin therapy consisting of regular and NPH insulin, two times a day) were included in the study. They were randomized to double blind treatment with insulin in combination with gliclazide or acarbose for 6 months. For both groups, acceptable glycemic control was achieved at the end of study period. The mean HbA1c levels decreased from 8.32±0.26 to 7.13±0.18% in acarbose group and 8.6±0.15 to 7.48±0.21% in the gliclazide group. The difference between groups was not significant (P 0.29). In the acarbose group, total cholesterol and LDL concentration decreased significantly while other parameters did not change. In the gliclazide group, HDL levels decreased significantly from 46.6±2.48 mg/dl to 41.3±2.09 mg/dl (P 0.001) BMI increased significantly from 27.60±1.21 kg/m2 to 28.69±1.26 kg/m2. (P 0.003) Total daily insulin dose was not changed in the acarbose group significantly, but increased from 42.6±2.73 to 49.27±3.58 U/day, which was significant in gliclazide group of (P 0.016). In the acarbose group, there were no significant differences between responders and nonresponders with respect to fasting and stimulated C-peptide, HbA1c levels and baseline BMI values. But in the gliclazide group, baseline BMI values were significantly higher in the nonresponding group compared to responders (P 0.02). In conclusion, combination of insulin with acarbose can be a good alternative for type 2 diabetic patients on insulin therapy; seems more beneficial than combination with gliclazide; may have advantage of achieving good glycemic control without increasing insulin dose and BMI; also may have the advantage of providing a decrease in LDL level, which are all important to prevent atherosclerosis.