nils-herrmann/clean_scirepeval huggingface dataset:
Evaluation of the influence of ayurvedic formulation (Ayushman-15) on psychopathology, heart rate variability and stress hormonal level in major depression (Vishada).

Ayurveda (Indian-complimentary and alternative medicine) is still most sought after in India and has promising potential in management of Vishada [major depressive disorder (MDD)]. But, systematic research is lacking. In this study we evaluated of influence of ayurvedic treatment (Panchakarma and Ayushman-15) on psychopathology, heart rate variability (HRV) and endocrinal parameters in patients with major depression.



81 drug naive patients diagnosed as Vishada by ayurvedic physician and MDD according to DSM IV-TR were given ayurvedic Virechana module (therapeutic purgation) and were randomized into two groups. Patients in group A (n=41) received Ayushman-15A while group B (n=40) received Ayushman-15B for two months and Shirodhara (forehead-oil pouring therapy). Patients were assessed with Hamilton Depression Rating Scale (HDRS), Montgomery Asberg Depression Rating Scale (MADRS), Heart Rate Variability (HRV). Cortisol and adrenocorticotropic hormone (ACTH) were estimated at baseline and after ayurvedic therapy. HRV and endocrinal parameters were compared with age and gender matched healthy volunteers.



HRV parameters showed significant sympathetic dominance in patients compared to healthy volunteers. Two months of ayurvedic treatment significantly decreased psychopathology, showed increase in vagal tone, decrease in sympathetic tone and reduced cortisol levels. However, there was no significant difference between groups receiving Ayushman A and B.



This study provides evidence for antidepressant, cardiac (HRV) and beneficial neuroendocrine modulatory influence of Ayurveda therapy in patients of Vishada (MDD). Further studies are needed to confirm these findings. Greater insight into the neurobiology behind this therapy might provide valuable information about newer drug target.
Improving patient care for attention deficit hyperactivity disorder in children by organizational redesign (Tornado program) and enhanced collaboration between psychiatry and general practice: a controlled before and after study

Implementation of clinical guidelines for diagnosis and treatment of attention deficit hyperactivity disorder (ADHD) in children and adolescents is a challenge in practice due to insufficient availability of mental health specialists and lack of effective cooperation with primary care physicians. The Tornado program aims to reduce time between referral and start of treatment in eligible patients. This study aims to assess the effectiveness and efficiency of this program.



This is a non-randomized controlled before-after study involving 90 outpatients (6-18 years old) suspected of uncomplicated ADHD, which were recruited by ten mental health teams. The Tornado program, provided by three teams, combines accelerated-track diagnosis and treatment planning. This is followed by psychoeducation at a mental health center and pharmacological treatment by primary care physicians, who received an online e-learning module for this purpose. The control group consists of patients of seven other teams, who receive care as usual. Primary outcome is the patients' time between referral to the mental health or pediatric center and start of treatment. Secondary outcomes include severity of ADHD symptoms; functional status; health-related quality of life; treatment adherence; indicators of diagnostic procedures and treatments; patient, parent, and professional experiences and satisfaction with care; and an economic evaluation. The study is powered to detect a difference of 36 days.



This study will provide insight into the effectiveness and efficiency of the Tornado program, an accelerated-track program in mental healthcare.
Comparison of the effect of alendronate on lumbar bone mineral density and bone turnover in men and postmenopausal women with osteoporosis

The purpose of the present study was to compare the effect of alendronate treatment on lumbar bone mineral density (BMD) and bone turnover in men and postmenopausal women with osteoporosis. Sixty men with primary or secondary osteoporosis and 318 women with postmenopausal osteoporosis were treated with alendronate. The primary end points were lumbar BMD and urinary cross-linked N-terminal telopeptides of type I collagen (NTX) and serum alkaline phosphatase (ALP) levels. The secondary end point was the incidence of vertebral and nonvertebral fractures. Forty-seven (78.3%) men and 254 (79.9%) women who could complete the 12-month trial were analyzed. The mean ages of men and postmenopausal women were 69.1 and 70.4 years, respectively. Both men and postmenopausal women showed higher levels of urinary NTX as compared with normal range of premenopausal women. Alendronate treatment decreased urinary NTX level by 39.2% in men and 45.4% in postmenopausal women at 3 months and serum ALP level by 17.8 and 21.0%, respectively, at 12 months. Following reduction in bone turnover markers, lumbar BMD increased 5.8 and 7.6% in men and postmenopausal women, respectively, at 12 months. Reduction in urinary NTX level and increase in lumbar BMD were smaller in men than in postmenopausal women. The incidence of vertebral and nonvertebral fractures was 10.6 and 8.5%, respectively, in men and 8.3 and 7.5%, respectively, in postmenopausal women, with no significant difference in these incidences between them. These results suggested that alendronate treatment effectively increased lumbar BMD from baseline in men with primary or secondary osteoporosis following reduction in bone turnover, although its efficacy did not appear to be greater than in postmenopausal women with osteoporosis.
Current ablation techniques for persistent atrial fibrillation: results of the European Heart Rhythm Association Survey.

The aim of this survey was to provide insight into current practice regarding ablation of persistent atrial fibrillation (AF) among members of the European Heart Rhythm Association electrophysiology research network. Thirty centres responded to the survey. The main ablation technique for first-time ablation was stand-alone pulmonary vein isolation (PVI): in 67% of the centres for persistent but not long-standing AF and in 37% of the centres for long-standing persistent AF as well. Other applied techniques were ablation of fractionated electrograms, placement of linear lesions, stepwise approach until AF termination, and substrate mapping and isolation of low-voltage areas. However, the percentage of centres applying these techniques during first ablation did not exceed 25% for any technique. When stand-alone PVI was performed in patients with persistent but not long-standing AF, the majority (80%) of the centres used an irrigated radiofrequency ablation catheter whereas 20% of the respondents used the cryoballoon. Similar results were reported for ablation of long-standing persistent AF (radiofrequency 90%, cryoballoon 10%). Neither rotor mapping nor one-shot ablation tools were used as the main first-time ablation methods. Systematic search for non-pulmonary vein triggers was performed only in 10% of the centres. Most common 1-year success rate off antiarrhythmic drugs was 50-60%. Only 27% of the centres knew their 5-year results. In conclusion, patients with persistent AF represent a significant proportion of AF patients undergoing ablation. There is a shift towards stand-alone PVI being the primary choice in many centres for first-time ablation in these patients. The wide variation in the use of additional techniques and in the choice of endpoints reflects the uncertainties and lack of guidance regarding the most optimal approach. Procedural success rates are modest and long-term outcomes are unknown in most centres.
Dietary antioxidant capacity of the patients with cardiovascular disease in a cross-sectional study

The purpose of this study was to establish sources and patterns of antioxidant, polyphenol and flavonoid intakes in men and women with cardiovascular disease (CVD).



The subjects with CVD and healthy controls (HC) were participants of the Polish National Multicenter Health Survey (WOBASZ). Food intakes were measured with the 1-day 24-hour recall method. A self-developed database was used to calculate dietary total antioxidant capacity (DTAC), dietary total polyphenol content (DTPC) and dietary total flavonoid content (DTFC).



DTAC did not differ between the men with CVD and HC men (6442 vs. 6066 μmol trolox equivalents - TE), but in the women with CVD it was significantly higher than in the HC women (6182 vs. 5500 μmol TE). The main sources of antioxidants in the males with CVD were: tea, coffee, apples, and nuts and seeds, and tea, coffee and apples in HC. In the females they were: tea, coffee, apples and strawberries, both in the women with CVD and HC. DTPC in the men with CVD did not differ from HC (1198 vs. 1114 mg gallic acid equivalents, GAE). In the females, DTPC was significantly higher in the subjects with CVD as compared to HC (1075 vs. 981 mg GAE). Predominant sources of polyphenols were: tea, coffee, cabbage, potatoes, apples and white bread in the men with CVD, and tea, coffee, potatoes, white bread and apples in HC, while in the women (both with CVD and HC): tea, coffee, apples, potatoes and cabbage. No differences in DTFC have been found between the males with CVD and HC (212 vs. 202 mg quercetine equivalents, QE). In the women with CVD, DTFC was significantly higher than in HC (200 vs. 177 mg QE). Main sources of flavonoids in all participants (men and women, CVD and HC) were tea, apples, cabbage and coffee.



Polish men and women faced with CVD beneficially modify their dietary practices by enhancing intakes of foods that are sources of antioxidants, polyphenols and flavonoids. Different sources and patterns of antioxidant, polyphenol and flavonoid intakes, however, between male and female patients with CVD were observed.
Possible association between screening BV at the prenatal visit and reduced cervical cerclage: multi-center questionnaire in Hokkaido, Japan.

To study the screening frequency for cervical cancer, Chlamydia trachomatis (CT) infection, and bacterial vaginosis (BV) among pregnant women, and to study the association between administration of these three screening tests and performance of cervical cerclage (CC) in Hokkaido during 2004.



Questionnaires were mailed to 70 clinics providing prenatal care only and to 113 hospitals providing prenatal care and performing deliveries. Responses were obtained anonymously.



A total of 6744 pregnant women received prenatal care at the 36 responding clinics and 24 050 deliveries were performed at the 56 hospitals. The percentage of clinics that screened all pregnant women for cervical cancer, CT infection or BV was 66.7%, 69.4% and 33.3%, respectively, and the corresponding percentages among the hospitals were 87.5%, 87.5% and 57.1%, respectively. Pregnant women found to have CT infection or BV, were all treated. Screening for cervical cancer or CT infection was not associated with the frequency of CC. On the other hand, screening for BV was significantly associated with the frequency of CC (P = 0.0006). The frequency of emergency CC was 0.8% among women who received prenatal care at hospitals that did not perform BV screening, while it was only 0.2 or 0.3% among women who received prenatal care at hospitals that performed BV screening on all pregnant women or on those women who were suspected of having BV, respectively.



Our results suggest that the frequency of emergency CC may be reduced in women who receive BV screening and subsequent treatment of positive cases during pregnancy.
A tandem simulation framework for predicting mapping quality

Read alignment is the first step in most sequencing data analyses. Because a read’s point of origin can be ambiguous, aligners report a mapping quality, which is the probability that the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality. I describe a framework for predicting mapping qualities that works by simulating a set of tandem reads. These are like the input reads in important ways, but the true point of origin is known. I implement this method in an accurate and low-overhead tool called Qtip, which is compatible with popular aligners.
Aged garlic extract supplemented with B vitamins, folic acid and L-arginine retards the progression of subclinical atherosclerosis: a randomized clinical trial.

Previous studies demonstrated that aged garlic extract reduces multiple cardiovascular risk factors. This study was designed to assess whether aged garlic extract therapy with supplements (AGE+S) favorably affects inflammatory and oxidation biomarkers, vascular function and progression of atherosclerosis as compared to placebo.



In this placebo-controlled, double-blind, randomized trial (conducted 2005-2007), 65 intermediate risk patients (age 60+/-9 years, 79% male) were treated with a placebo capsule or a capsule containing aged garlic extract (250 mg) plus Vitamin B12 (100 microg), folic acid (300 microg), Vitamin B6 (12.5 mg) and l-arginine (100 mg) given daily for a 1 year. All patients underwent coronary artery calcium scanning (CAC), temperature rebound (TR) as an index of vascular reactivity using Digital Thermal Monitoring (DTM), and measurement of lipid profile, autoantibodies to malondialdehyde (MDA)-LDL, apoB-immune complexes, oxidized phospholipids (OxPL) on apolipoprotein B-100 (OxPL/apoB), lipoprotein (a) [Lp (a)], C-reactive protein (CRP), homocysteine were measured at baseline and 12 months. CAC progression was defined as an increase in CAC>15% per year and an increase in TR above baseline was considered a favorable response.



At 1 year, CAC progression was significantly lower and TR significantly higher in the AGE+S compared to the placebo group after adjustment of cardiovascular risk factors (p<0.05). Total cholesterol, LDL-C, homocysteine, IgG and IgM autoantibodies to MDA-LDL and apoB-immune complexes were decreased, whereas HDL, OxPL/apoB, and Lp (a) were significantly increased in AGE+S to placebo.



AGE+S is associated with a favorable improvement in oxidative biomarkers, vascular function, and reduced progression of atherosclerosis.
Bone fragility fractures in hemodialysis patients: Croatian surveys.

Disturbances of bone mineral metabolism are common complications of chronic kidney disease with bone fractures as one of the most important consequences. The aim of this study was to estimate prevalence of bone fractures among Croatian hemodialysis patients and to determine the possible fracture risk. The study was carried out in 767 hemodialysis patients from nine Croatian hemodialysis centers. Demographic, laboratory and bone fracture data were collected from medical records as well as therapy with vitamin D analogs. Fragility fractures were defined according to the World Health Organization definition. In 31 patient a total of 36 fractures were recorded. The prevalence of patients with bone fractures was 4.0%. The mean age of patients with fractures was 68.6 years. There were 9 male and 22 female patients with frac- tures. The mean hemodialysis duration was 63.3 months. Among all fractures the most common were hip fractures (39%) followed by forearm fractures (22%). This is the first study regarding epidemiology of bone fractures in Croatian hemodialysis patients. The prevalence of patients with bone fractures in our group of hemodialysis patients is high. Fractures were more frequent among women and older patients, patients who have been longer on dialysis and in patients with higher concentration of PTH.
Patient-controlled analgesia with oral methadone in cancer pain: preliminary report.

Methadone is a very useful drug in cancer pain because of its low cost, lack of active metabolites, high oral availability, and the rapid onset of its analgesic effect. It seems to be well tolerated in patients with difficult pain syndromes who are receiving high doses of opioids, and it may deter the development of tolerance, but a high individual variation in terminal elimination half-life can result in different rates and extents of drug accumulation. For this reason, oral patient-controlled analgesia with methadone was used in 24 advanced-disease patients with pain.



A regimen of self-administered oral methadone at fixed doses and flexible patient-controlled dosage intervals to achieve adequate analgesia, while avoiding toxic effects of methadone accumulation, was used in 24 patients requiring opioid therapy. After a priming period of three days with fixed doses of 3-5 mg three times a day for naïve patients and 50% of the morphine equivalent of methadone in patients switched from morphine, patients and relatives were instructed to maintain the night-time dose and to administer a second dose when the pain recurred. When more than four doses of methadone a day were used, an increase of the dosage was prescribed. Continuous pain assessment and monitoring of symptoms were offered.



The majority of patients achieved good pain relief until death, and three were switched to very low doses of subcutaneous morphine in their final days. The methadone escalation index was about 2% a day, with a mean dosage increase of 0.3 mg a day for an average of 60 days of treatment at doses ranging from 9 to 80 mg. The plasma concentration in 14 patients ranged from 0.013 to 0.273 mcg/ml with dosages of 20-80 mg during chronic treatment. A mean of 2.4 doses a day was reported, including the fixed night-time dose. The extent of side effects was considered acceptable.



Patient-administered analgesia with oral methadone appears to be a simple, cheap and relatively safe technique for controlling cancer pain, permitting individualization by the patient him- or herself and avoiding the risk of accumulation. Continuous assessment is necessary.
Epirubicin and docetaxel with or without capecitabine as neoadjuvant treatment for early breast cancer: final results of a randomized phase III study (ABCSG-24).

This randomized phase III trial compared pathologic complete response (pCR) rates of early breast cancer (EBC) following neoadjuvant epirubicin-docetaxel (ED)±capecitabine (C), and evaluated the addition of trastuzumab in HER2-positive tumors.



Patients with invasive breast cancer (except T4d) were randomly assigned to receive six 3-weekly cycles of ED (both 75 mg/m2)±C (1000 mg/m2, twice daily, days 1-14). Patients with HER2-positive disease were further randomized to receive trastuzumab (8 mg/kg, then 6 mg/kg every 3 weeks) or not.  pCR rate at the time of surgery.



Five hundred thirty-six patients were randomized to ED (n=266) or EDC (n=270); 93 patients were further randomized to trastuzumab (n=44) or not (n=49). pCR rate was significantly increased with EDC (23.0% versus 15.4% ED, P=0.027), and nonsignificantly further increased with trastuzumab (38.6% EDC versus 26.5% ED, P=0.212). Rates of axillary node involvement at surgery and breast conservation were improved with EDC versus ED, but not significantly; the addition of trastuzumab had no further impact. Hormone receptor status, tumor size, grade, and C (all P≤0.035) were independent prognostic factors for pCR. Trastuzumab added to ED±C significantly increased the number of serious adverse events (35 versus 18; P=0.020), mainly due to infusion-related reactions.



These findings show that the integration of C into a neoadjuvant taxane-/anthracycline-based regimen is a feasible, safe, and effective treatment option, with incorporation of trastuzumab in HER2-positive disease.
Methylphenidate in the management of asthenia in breast cancer patients treated with docetaxel: results of a pilot study

The objectives of this pilot study were to evaluate the safety and efficacy of the central nervous system stimulant methylphenidate in the management of asthenia in breast cancer patients treated with docetaxel.  Patients with early breast cancer who presented asthenia >3 on the Visual Analogue Scale (VAS) after the first cycle of docetaxel-based chemotherapy were included. Patients received two additional cycles of chemotherapy, one with methylphenidate (10 mg bid) and the other without methylphenidate. Asthenia was evaluated using VAS and the Functional Assessment of Cancer Therapy-Fatigue (FACT-F) scale. Distress was assessed using the Hospital Anxiety and Depression Scale (HADS), and quality of life using FACT-F.  Ten patients were included and evaluated for efficacy and safety. Overall, cycles with methylphenidate were better tolerated than those without methylphenidate in terms of asthenia (VAS, p = 0.004; FACT-F, p = 0.027) and quality of life (FACT-F, p = 0.047). No significant differences were observed in terms of distress (HADS, p = 0.297). Six (60%) patients continued with methylphenidate after study end. Main adverse events during study were palpitations and insomnia (30% of patients each).  This pilot study suggests that methylphenidate may reduce asthenia and improve quality of life in breast cancer patients treated with docetaxel.
An aggregate score to predict the risk of large pleural effusion after pulmonary lobectomy.

The volume of pleural effusion is one of the determinants of chest drain removal following pulmonary resection. Recent research suggests that values up to 400 ml/day are safe. The objective of this study was to develop an aggregate risk score to identify patients at higher risk of developing a large pleural effusion (LPE) (>400 ml/day) on postoperative day 2 (POD2) after pulmonary lobectomy.



An observational study on 229 consecutive patients was conducted prospectively in two European centres (June 2012-September 2013). All patients underwent pulmonary lobectomy for lung cancer (thoracotomy: 131, video-assisted thoracic surgery: 98) and managed by single chest tube connected to an electronic-regulated suction device. Exclusion criteria were chest wall or diaphragm resection and postoperative-assisted mechanical ventilation. To build the aggregate score, variables were initially screened by univariable analysis, and then used in stepwise logistic regression analysis (validated by bootstrap). The scoring system was developed by proportional weighing of the significant predictor estimates, and patients were grouped in classes of incremental risk according to their total score.



The incidence of LPE on POD2 was 23% (53 of 229 patients). The independent risk factors associated with LPE on POD2 were age greater than 70 years (P = 0.01, bootstrap frequency 71%), a lower lobectomy (P = 0.03, bootstrap frequency 59%) and presence of COPD (P = 0.02, bootstrap frequency 63%). Each predictor received a weighted score of 1, and patients were grouped into three risk classes showing an incremental risk of LPE (P < 0.001): Class A (Score 0) 5 LPE in 66 patients, 7.5%; Class B (Score 1) 19 LPE in 88 patients, 22%; Class C (Score >1) 29 LPE in 75 patients, 39%.



The aggregate score is a reliable tool for identifying high-risk patients for LPE and assists in the selection of patients that can safely proceed to chest drain removal early after surgery.