nils-herrmann/clean_scirepeval huggingface dataset:
The use of common mitochondrial variants to detect and characterise population structure in the Australian population: implications for genome-wide association studies

There is an increasing recognition of the potential role of variants in mitochondrial DNA and nuclear-encoded mitochondrial proteins in modifying disease risk. This has led to a rise in the number of mitochondrial association studies being undertaken. The unique inheritance pattern of mitochondria makes mitochondrial DNA variation susceptible to having geographical structure. Such a structure may have a dramatic impact on mitochondrial association studies, particularly in heterogeneous populations. By combining self-reported ancestry data and mitochondrial genotype data for a sample of 3839 individuals from 1037 Australian families, population substructure is tested by looking for evidence of differences in mitochondrial haplogroup and single nucleotide polymorphism (SNP) frequencies between different ancestral groups in Australia. In addition, the substructure within ancestral groups is tested by comparing the similarity of mates to randomly drawn pairs of individuals from the same ancestral group. It is shown that there are significant differences in the frequency of variants both between European and non-European groups, and within Europe. This agrees with previous studies of European mitochondrial variation. No evidence was found for structure within ancestral groups. These results have implications for future association studies in the Australian population, and other populations of heterogeneous ancestry.
Remote ischemic preconditioning and endothelial function in patients with acute myocardial infarction and primary PCI.

Remote ischemic preconditioning by transient limb ischemia reduces myocardial ischemia-reperfusion injury in patients undergoing percutaneous coronary intervention. The aim of the study we report here was to assess the effect of remote ischemic preconditioning on endothelial function in patients with acute myocardial infarction who underwent primary percutaneous coronary intervention.



Forty-eight patients with acute myocardial infarction were enrolled. All participants were randomly divided into 2 groups. In Group I (n = 23), remote ischemic preconditioning was performed before primary percutaneous coronary intervention (intermittent arm ischemia-reperfusion through 4 cycles of 5-minute inflation and 5-minute deflation of a blood-pressure cuff to 200 mm Hg). In Group II (n = 25), standard percutaneous coronary intervention without preconditioning was performed. We assessed endothelial function using the flow-mediated dilation test on baseline, then within 1-3 hours after percutaneous coronary intervention, and again on days 2 and 7 after percutaneous coronary intervention.



The brachial artery flow-mediated dilation results were significantly higher on the first day after primary percutaneous coronary intervention in the preconditioning group (Group I) than in the control group (Group II) (12.1% vs 0.0%, P = .03, and 11.1% vs 6.3%, P = .016, respectively), and this difference remained on the seventh day (12.3% vs 7.4%, P = .0005, respectively).



We demonstrated for the first time that remote ischemic preconditioning before primary percutaneous coronary intervention significantly improves endothelial function in patients with acute myocardial infarction, and this effect remains constant for at least a week. We suppose that the improvement of endothelial function may be one of the possible explanations of the effect of remote ischemic preconditioning.
Revalidating the brief jail mental health screen to increase accuracy for women.

Jails need a reliable tool to identify inmates who require further mental health assessment and treatment. This research attempted to revalidate the Brief Jail Mental Health Screen (BJMHS) as such a tool. This research added four items to the original eight-item screen (BJMHS-R), targeting depression and trauma to improve performance of the screen with women.



BJMHS-R data were collected in four jails from 10,258 detainees. A subset of 464 were administered the Structured Clinical Interview for DSM-IV (SCID) for cross-validation.



The original BJMHS outperformed the revised screen. The original correctly classified 80% of males and 72% of females on the basis of SCID diagnoses, compared with classification rates of 72% and 66%, respectively, with the BJMHS-R. Overall, the BJMHS identified 16% of screened detainees as needing referral for further assessment, whereas the BJMHS-R identified 22%.



The original eight-item BJMHS is a practical, efficient tool for intake screening by jail correction officers of male and female detainees.
Barnidipine real-life tolerability in arterial hypertension: results from the BASIC-HT study.

Blood pressure (BP) is generally poorly controlled in hypertensive patients. One cause is poor adherence to drugs, which can be improved by treatments combining good efficacy and tolerability. Barnidipine is a strong lipophilic calcium channel blocker (CCB) with efficacy similar to other dihydropyridines.



BASIC HT is an observational study in a large population of patients with essential hypertension to evaluate the tolerability of barnidipine in a real-life setting.



20479 patients were enrolled in the study. Tolerability and efficacy was assessed at 2 visits during a 3-month period. 20275 patients were included in the analysis.



Adverse events were reported by 10.6% of the patients, leading to treatment discontinuation in 3%. Events were those expected with CCBs. The drop-out rate was 8%. Mean systolic and diastolic pressure decreased from 159.6 to 138.2 and from 92.5 to 81.7 mmHg.



The decrease in BP, is probably due to stimulation of good adherence by barnidipine.
Long Coronary Lesions Treated With Thin Strut Bioresorbable Polymer Drug Eluting Stent: Experience From Multicentre Randomized CENTURY II Study.

To assess performance of new, bioresorbable polymer sirolimus-eluting stent (BP-SES), in patients with long coronary lesions (LL) and to compare it to permanent polymer everolimus-eluting stent (PP-EES).



LL have been associated with worse clinical outcomes in percutaneous coronary interventions (PCI). The impact of lesion length on the outcomes of drug eluting stent (DES) implantations is not as clear.



In the frame of a randomized, multicentre CENTURY II study, out of 1119 patients enrolled, 182 patients had LL (defined as ≥25 mm), and were assigned randomly to treatment with BP-SES (101) or PP-EES (81). Primary endpoint was target lesion failure (TLF, composite of cardiac death, target vessel related myocardial infarction [MI], and target lesion revascularization [TLR]) at 9 months. All data were 100% monitored and adverse events were adjudicated by an independent clinical event committee.



The baseline patient and lesion characteristics were similar in the 2 study arms. At 9-months, the rates of cardiac death (2.0% vs 1.2%; P = 0.70), MI (3.0% vs 4.9%; P = 0.49) and clinically driven TLR (2.0% vs 3.7%; P = 0.48) and TLF (6.9% vs 8.6%; P = 0.67) were similar for BP-SES and PP-EES, respectively. There was no stent thrombosis (ST) in BP-SES group up to 9 months, while 1 case (1.2%) of ST was recorded in PP-EES group (P = 0.44).



Patients with LL showed similar clinical outcomes when treated with Ultimaster BP-SES and Xience PP-EES.
Chemoradiation for anaplastic oligodendrogliomas: clinical outcomes and prognostic value of molecular markers

Combination of procarbazine, lomustine and vincristine (PCV) with radiation therapy (RT) has been associated with longer survival in patients with anaplastic oligodendroglioma (AO) and anaplastic oligoastrocytoma (AOA), especially in those with chromosome 1p/19q codeletion. We report a multicenter retrospective study of 84 consecutive adult patients with AO and AOA treated with RT plus concomitant and adjuvant temozolomide (TMZ) between February 2004 and January 2011. Correlations between chromosome 1p/19q codeletion, isocitrate dehydrogenase1 (IDH1) mutation, and O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation with survival outcomes have been analyzed. For all 84 patients the median overall survival (OS) and progression-free survival rates were 55.6 and 45.2 months, respectively. Grade 3 or 4 hematological toxicity occurred in 17 % of patients. Chromosome 1p/19q codeletion was detected in 57 %, IDH1 mutation in 63 %, and MGMT promoter methylation in 74 % of evaluable patients. In multivariate analysis the presence of chromosome 1p/19q codeletion was associated with significant survival benefit (median OS 34 months in noncodeleted tumors and not reached in codeleted tumors; HR 0.16, 95 % CI 0.03–0.45; P = 0.005). IDH1 mutation was also of prognostic significance for longer survival (P = 0.001; HR 0.20, 95 % 0.06–0.41), whereas MGMT promoter methylation was only of borderline significance. The study indicates that RT with concomitant and adjuvant TMZ is a relatively safe treatment associated with longer survival in patients with 1p/19q codeleted and IDH1 mutated tumors. Results from ongoing randomized studies will be essential to clarify if RT plus TMZ may provide survival as good as or better than RT combined with PCV for patients with AO and AOA.
Measuring spleen stiffness to predict varices in chronic hepatitis B cirrhotic patients with or without receiving non-selective beta-blockers.

we aimed to investigate the accuracy of liver (LSM) spleen stiffness measurement (SSM) with transient elastography (TE) to predict varices in the presence of non-selective beta-blockers (NSBB).



In this cross-sectional study of consecutive patients with chronic hepatitis B (CHB) and cirrhosis, all patients underwent TE and upper endoscopic examinations. LSM and SSM in predicting varices in patients receiving and not receiving NSBB were evaluated.



Altogether 144 CHB patients (29 receiving NSBB; 35 with any varices, 31 and 11 with esophageal and gastric varices, respectively) were recruited. Their mean LSM and SSM were 13.3 ± 9.0 kPa and 32.8 ± 19.2 kPa, respectively. The correlation between LSM and SSM was better in the NSBB subgroup (r = 0.525, P = 0.003) than its counterpart (r = 0.329, P  < 0.001). The area under receiver operating characteristic curve (AUROC) of LSM and SSM for any varices was 0.675 and 0.685 (P = 0.002 and 0.001), respectively. SSM of 18.9 kPa had a negative predictive value of 92.1% and negative likelihood ratio of 0.27 for ruling out any varices; and SSM of 54.9 kPa had a positive predictive value of 56.5% and a positive likelihood ratio of 4.05 to rule in varices. The AUROC of LSM for varices was 0.742 and 0.549 in patients with or without NSBB, respectively; the corresponding AUROC of SSM was 0.572 and 0.603, respectively.



SSM only has modest accuracy to predict varices independent of NSBB use. An SSM cutoff value of 18.9 kPa may be adopted to achieve a high negative predictive value to rule out varices.
Evaluation of the effect of curcumin capsules on glyburide therapy in patients with type-2 diabetes mellitus.

This study aimed to assess the possible beneficial effects of curcumin capsules as lipid-lowering effects and as a permeability glycoprotein (P-gp) inhibitor on the pharmacokinetics and pharmacodynamics of glyburide and as a P-gp substrate with glyburide in patients with type-2 diabetes mellitus. Open-label, randomized control trial was carried out for 11 days on eight type-2 diabetic patients on glyburide therapy. On the first day of the study, following the administration of 5 mg of glyburide, blood samples were collected from the patients at various time intervals ranging from 0.5 to 24 h. Blood sampling was repeated on the 11th day of the study, after treating the patients with curcumin for ten consecutive days. Glyburide concentrations changed at the second hour, Cmax was unchanged, the glucose levels were decreased, Area Under first Movement Curre (AUMC) was increased, and no patient has experienced the hypoglycaemia. The low-density lipoprotein, very-low-density lipoprotein and triglycerides were decreased significantly, and the high-density lipoprotein content increased. The co-administration of curcumin capsules with glyburide may be beneficial to the patients in better glycaemic control. The lipid lowering and antidiabetic properties of the curcumin show as a potential future drug molecule.
Intermittent balneotherapy at the Dead Sea area for patients with knee osteoarthritis.

Balneotherapy, traditionally administered during a continuous stay at the Dead Sea area, has been shown to be effective for patients suffering from knee osteoarthritis.



To evaluate the effectiveness of an intermittent regimen of balneotherapy at the Dead Sea for patients with knee osteoarthritis.



Forty-four patients with knee osteoarthritis were included in a prospective randomized single-blind controlled study. The patients were divided into two groups: a treatment group (n=24), which were treated twice weekly for 6 consecutive weeks in a sulfur pool heated to 35-36 degrees C, and a control group (n=20) treated in a Jacuzzi filled with tap water heated to 35-36 degrees C. Participants were assessed by the Lequesne index of osteoarthritis severity, the WOMAC index, the SF-36 quality of health questionnaire, VAS scales for pain (completed by patients and physicians), and physical examination.



A statistically significant improvement, lasting up to 6 months, was observed in the treatment group for most of the clinical parameters. In the control group the only improvements were in the SF-36 bodily pain scale at 6 months, the Lequesne index at 1 month and the WOMAC pain score at the end of the treatment period. Although the patients in the control group had milder disease, the difference between the two groups was not statistically significant.



Intermittent balneotherapy appears to be effective for patients with knee osteoarthritis.
A phase II trial of autologous transplantation of bone marrow stem cells for critical limb ischemia: results of the Naples and Pietra Ligure Evaluation of Stem Cells study.

Critical limb ischemia (CLI) is a vascular disease affecting lower limbs, which is going to become a demanding challenge because of the aging of the population. Despite advances in endovascular therapies, CLI is associated with high morbidity and mortality. Patients without direct revascularization options have the worst outcomes. To date, 25%-40% of CLI patients are not candidates for surgical or endovascular approaches, ultimately facing the possibility of a major amputation. This study aimed to assess the safety and efficacy of autologous bone marrow (BM) transplantation performed in "no-option" patients, in terms of restoring blood perfusion by collateral flow and limb salvage. A multicenter, prospective, not-controlled phase II study for no-option CLI patients was performed. Patients were subjected to intra-arterial infusion of autologous bone marrow and followed for 12 months after the treatment. Variation of blood perfusion parameters, evaluated by laser Doppler flowmetry or transcutaneous oximetry, was set as the primary endpoint at 12 months after treatment and amputation-free survival as the secondary endpoint. Sixty patients were enrolled and treated with BM transplantation, showing improvement in objective and subjective measures of perfusion. Furthermore, survival analysis demonstrated improved amputation-free survival rates (75.2%) at 12 months after the treatment. This study provides further evidence that autologous bone marrow transplantation is well tolerated by CLI patients without adverse effects, demonstrating trends toward improvement in perfusion and reduced amputation rate, confirming the feasibility and safety of the procedure.
How does robotic anti-reflux surgery compare with traditional open and laparoscopic techniques: a cost and outcomes analysis

Conventional laparoscopic fundoplications (CLF) have been the gold standard for Nissen fundoplications (NFs) for two decades. The advent of a robotic approach for fundoplication procedures creates a potential alternative. Thus, we used a national database to examine perioperative outcomes with respect to open, laparoscopic, and robotic approaches. The University Health System Consortium is an alliance of medical centers, numbering over 115 academic institutions and their 271 affiliated hospitals. We used International Classification of Diseases codes to elicit patients over the age of 18 years who received NF procedures. A total of 12,079 patients of similar demographic background received fundoplication procedures from October 2008 to June 2012. Of those, 2,168 were open fundoplications (OF), 9,572 were CLF, and 339 were robot-assisted laparoscopic fundoplications (RLF). CLF and RLF displayed no significance in mortality (0.1 vs. 0 %; p = 0.5489), morbidity (4.0 vs. 5.6 %; p = 0.1744), length of stay (2.8 ± 3.6 vs. 3.0 ± 3.5; p = 0.3242), and intensive care unit (ICU) cases (8.4 vs. 11.5 %; p = 0.051). However, CLF remained superior, with a lower 30-day re-admission rate (1.8 vs. 3.6 %; p < 0.05) and cost (US$7,968 ± 6,969 vs. US$10,644 ± 6,041; p < 0.05). When RLF was compared with OF, RLF had significantly improved morbidity (5.6 vs. 11 %; p < 0.05), length of stay (6.1 ± 7.2 vs. 3.0 ± 3.5 days; p < 0.05), less ICU admission (11.5 vs. 23.1 %; p <0.05) and less cost (US$10,644 ± 6,041 vs. US$12,766 ± 13,982; p < 0.05). Current data suggests that robot-assisted NF procedures have similar patient outcomes to conventional laparoscopic NF, with the exception of added cost and higher re-admission rate. While the higher costs are expected given the new technology, increasing re-admission rates are concerning and may represent the level of experience of the surgeon as well as the robotic learning curve.
Evaluating surrogate measures of renal dysfunction after cardiac surgery.

Renal insufficiency after cardiac surgery is associated with increased mortality, morbidity, and length of intensive care unit stay. A convenient surrogate measure would facilitate the evaluation of renal-protective therapies. We evaluated two measures: the 72-h change in serum creatinine (Cr) (DeltaCr(72h)) and the percentage 72-h change in calculated (Cockcroft-Gault equation) Cr clearance (%DeltaCrCl(72h)). We randomly selected 2000 individuals who underwent aortocoronary bypass, valve surgery, or both at the Toronto General Hospital between May 1999 and August 2000. The variables were analyzed with frequency histograms and normal probability plots. Their association with dialysis, mortality, and prolonged intensive care unit stay was determined by using receiver operating characteristic (ROC) curves. DeltaCr(72h) was skewed to the right, whereas %DeltaCrCl(72h) was normally distributed. ROC curve areas showed DeltaCr(72h) to be a good predictor of dialysis (0.98), death (0.83), and prolonged hospitalization (0.74). %DeltaCrCl(72h) had similar ROC curve areas for predicting dialysis (0.97), death (0.82), and prolonged hospitalization (0.74). ROC curve areas did not differ significantly with respect to mortality (P = 0.89), dialysis (P = 0.49), or prolonged hospitalization (P = 0.85). Both variables were correlated with patient-relevant outcomes. Mathematical transformation of DeltaCr(72h) to %DeltaCrCl(72h) results in a normal distribution that is amenable to parametric statistical tests. DeltaCr(72h) and %DeltaCrCl(72h) may be used as surrogate outcomes in future trials.



A convenient surrogate measure of renal function is needed for evaluating renal-protective therapies in cardiac surgery. We evaluated the performance of serum creatinine concentration and calculated creatinine clearance for predicting dialysis, mortality, and prolonged hospitalization. Both measures were correlated with clinical outcomes. Creatinine clearance had the advantage of a distribution suitable for parametric statistical tests.
Comment on: Use of parenteral methotrexate significantly reduces the need for biological therapy.

SIR, We read with interest Bharadwaj et al.’s letter  demonstrating encouraging responses to parenteral MTX in a retrospective analysis of 32 patients with RA. We conducted a prospective study to investigate the effectiveness of parenteral MTX in a cohort of patients with RA  for whom oral MTX was ineffective or not tolerated. In addition, we assessed whether the change from oral to parenteral MTX prevented the need for a biologic agent. This study was conceived as an audit of our standard practice in RA management and as such did not require explicit ethical approval. All patients, however, provided informed consent to the use of parenteral MTX. Thirty consecutive patients (26 females, 4 males) with mean disease duration of 15.3 yrs (range 2–46 yrs) were recruited between October 2004 and March 2006 from our rheumatology clinics. They were assessed at baseline, 3 and 6 months after the introduction of subcutaneous (s.c.) MTX. We measured tender joint score (TJC), swollen joint score (SJC), patient’s global assessment of disease activity (PGA), CRP and 28-joint disease activity score (DAS28) at each visit. Oral MTX was discontinued due to lack of efficacy (23) and intolerance (7). Patients were started on s.c. MTX at a mean dose of 14.25mg (range 7.5–17.5mg). At 6 months the mean dose was 19.9mg (range 12.5–25mg). Three patients discontinued treatment at 3 months due to leucopenia (1) and poor compliance (2); a further two stopped s.c. MTX at 6 months due to lack of efficacy (1) and nausea (1). Five reported minor side-effects (nausea in four, an injection site reaction in the other). Compared with baseline, there was a significant improvement in DAS28 at both 3 and 6 months with a mean reduction of 2.34 (mean DAS28 5.2–2.95 7.5%; n1⁄4 27, P< 0.001) at 3 months and 2.09 (mean DAS28 5.2–3.05 8.9%; n1⁄4 25, P< 0.001) at 6 months. At 3 months, 20/27 patients showed a good response (using EULAR response criteria) and 13/25 maintained this at 6 months. Moreover, of the 11 patients who met BSR criteria for anti-TNFtherapy at baseline, 8 had a good response at 3 months. None needed anti-TNFtherapy at 6 months, although two of the three patients who failed to respond at 3 months needed it at 6 months. Our results provide further evidence of the efficacy of parenteral MTX in controlling active RA in patients who fail to respond to, or are intolerant of, oral MTX. In a cohort who fulfilled NICE criteria for treatment with anti-TNFtherapy the majority responded to the switch to parenteral MTX (8/11). Whilst parenteral MTX is an under-utilized therapy in the UK its superiority over oral MTX has recently been demonstrated in a prospective randomized controlled trial comparing oral and s.c. MTX in 375 patients . Whilst it is tempting to suggest that patients should receive a trial of parenteral MTX prior to biologics, the lack of comparative outcome data of biologic agents and parenteral MTX makes this debatable; however, the increasing evidence of the superior efficacy of parenteral MTX over the oral route does support the need for further studies.