nils-herrmann/clean_scirepeval huggingface dataset:
Role of conventional angiography in evaluation of patients with carotid artery stenosis demonstrated by Doppler ultrasound in general practice.

Previous studies have suggested that patients with carotid stenosis who are candidates for endarterectomy can be effectively identified on the basis of carotid Doppler ultrasound alone. Before widespread acceptance of this policy, the accuracy of carotid Doppler ultrasound outside selected centers and clinical trials needs to be evaluated. We performed a 12-month prospective study to evaluate the accuracy of Doppler ultrasound in identifying patients for carotid intervention in general practice settings.



Each patient referred to our endovascular service for diagnostic angiography to evaluate for carotid stenosis was interviewed and examined by a neurologist. Subjects consisted of symptomatic patients with >/=50% stenosis and asymptomatic patients with >/=60% stenosis by Doppler ultrasound. Information pertaining to demographic and cerebrovascular risk factors and the results of the carotid Doppler ultrasound were recorded. The severity of stenosis on angiograms was measured with North American Symptomatic Carotid Endarterectomy Trial criteria by a blinded observer. The results of both studies were compared to determine the relative accuracy of ultrasound results.



Of 130 patients (mean age, 69+/-8.8 years) who met Doppler ultrasound criteria, 22 (17%) and 8 patients (6%) were found to have 30% to 49% or <30% stenosis by angiography, respectively. The positive predictive value of carotid Doppler ultrasound for identifying appropriate symptomatic candidates for carotid intervention (angiographic stenosis >/=50%) was 80%, with a false-positive value of 20%. The positive predictive value of carotid Doppler ultrasound for identifying appropriate asymptomatic candidates for carotid intervention (angiographic stenosis >/=60%) was 59%, with a false-positive value of 41%. Carotid endarterectomy or angioplasty and stent placement were undertaken subsequently in 60 (46%) of the patients. In 94 patients who underwent cerebral angiography alone, no complications were observed.



The present accuracy of carotid Doppler ultrasound in general practice does not justify its use as the sole basis of selecting appropriate patients for carotid intervention. Given the relatively low rate of associated morbidity with present day techniques, additional confirmatory studies such as angiography should be performed in every patient before a decision regarding intervention is made.
Cellular HIV-1 DNA quantification and short-term and long-term response to antiretroviral therapy.

The aim of our study was to determine whether HIV-1 DNA level before antiretroviral therapy (ART) was associated with short- and long-term virological and immunological responses.



Patients starting first-line protease inhibitor-containing regimens were enrolled in a prospective multicentre cohort in 1998-99. HIV-1 DNA was quantified using real-time PCR at baseline and after 1 year of ART. The association between HIV-1 DNA and virological and immunological responses after 1 and 7 years on ART was studied in multivariate regression models along with other biological and clinical variables. Virological failure (VF) at month 12 (M12) was defined as a plasma HIV-1 RNA >500 copies/mL. Time to death or two plasma HIV-1 RNA >500 copies/mL between M12 and M84 was studied for long-term VF.



HIV-1 DNA levels were measured in 148 patients. The median baseline peripheral blood mononuclear cell (PBMC) HIV-1 DNA was 3.7 log(10) copies/10(6) PBMCs. At M12, the median PBMC HIV-1 DNA was 2.99 log(10) copies/10(6) PBMCs. The median decrease in PBMC HIV-1 DNA between M0 and M12 was -0.7 log(10) copies/10(6) PBMCs. Higher baseline PBMC HIV-1 DNA and plasma HIV-1 RNA were independently associated with a higher risk of VF at M12. Only the baseline plasma HIV-1 RNA was independently associated with long-term virological response. The baseline CD4 cell count was the only parameter associated with short- and long-term immunological responses.



HIV-1 DNA impacted the virological response in our cohort. Further research is warranted to study the impact of HIV-1 DNA with currently recommended first-line cART.
Factors influencing adherence among Irish haemodialysis patients.

Adherence to dietary and fluid restrictions among haemodialysis patients with end stage renal failure (ESRD) is a multi-factorial concept. This study seeks to assess the predictive value of demographic and psychological variables in non-adherence.



A multi-centre cross sectional design assessed 50 haemodialysis patients on self reported adherence, attitudes towards dietary restrictions, quality of life, depression and anxiety. Adherence to fluid and dietary restrictions was measured objectively using potassium (K), phosphorus (PO4) and inter-dialytic weight gain (IDWG) parameters.



62% of patients were non-adherent with at least one aspect of the treatment regime. Regression analysis revealed age as significantly associated with adherence, in particular IDWG, with younger patients displaying poorer adherence.



Younger patients may experience greater difficulty integrating complex treatment demands into their lifestyles, and non-adherence may be a consequence of the severe lifestyle limitations imposed by the haemodialysis treatment regime.



Individualised interventions may be more effective than traditional methods of adherence monitoring in reducing the non-adherent behaviour.
Thyroid axis function after in-patient treatment of acute psychosis with antipsychotics: a naturalistic study

Endocrine function in psychiatric patients may be affected by mental disorder itself as well as by antipsychotic medications.The aim of this naturalistic observational study was to determine if treatment of acute psychotic episode with antipsychotic medication affects thyroid axis hormone concentrations and if such changes are associated with symptomatic improvement.



Eighty six adult acute psychotic patients, consecutively admitted to a mental hospital, were recruited for the study. All patients were physically healthy and without thyroid disease. During the hospitalization period all study patients received treatment with antipsychotic medication according to clinical need. Severity of the psychotic episode was evaluated using the Brief Psychiatric Rating Scale (BPRS) and venous blood samples were drawn for analysis of free triiodothyronine (FT3), free thyroxine (FT4), and thyroid stimulating hormone (TSH) concentrations on the day of admission and on the day of discharge from the hospital.



Antipsychotic drug treatment was associated with decrease of mean FT3 (p < 0.001) and FT4 (p = 0.002) concentrations; and with increase of mean TSH (p = 0.016) concentrations. Changes in thyroid hormone concentrations were mostly predicted by baseline hormone concentrations. Individual changes were not limited to decrease in high hormone concentrations; in patients who had low FT3 or FT4 concentrations, treatment resulted in increase in concentrations. Such an increase was established in one-quarter of patients for FT3 concentrations and in one-third of patients for FT4 concentrations. Fall in FT4 concentrations negatively correlated with the improvement in the BPRS score (r = -0.235, p = 0.023).



The study indicates that antipsychotic treatment resulted in a decrease in mean FT3 concentrations and in an increase in mean TSH concentrations after recovery from acute psychosis. Symptomatic improvement was less evident in patients who experienced a decrease in FT4 concentrations.
Myocardial proinflammatory cytokine expression and left ventricular remodeling in patients with chronic mitral regurgitation.

In an animal model, stretch was shown to induce myocardial tumor necrosis factor-alpha (TNF-alpha) expression. The purposes of this study were to determine whether the left ventricular (LV) volume overload that occurs in patients with chronic mitral regurgitation (MR) can induce myocardial and systemic TNF-alpha expression and whether there is a relationship between TNF-alpha expression and LV remodeling.



Plasma TNF-alpha and its receptors were measured before mitral valve (MV) repair surgery in 26 MR patients and 23+/-12 months after MV repair surgery in 9 MR patients. Myocardial mRNA copies of TNF-alpha were determined in 11 MR and 10 donor hearts using quantitative RT-PCR. Compared with 15 control subjects, pre-MV repair plasma TNF-alpha (3.59+/-1.81 versus 2.03+/-1.02 pg/mL, P<0.005) and its receptor levels were elevated in MR patients. Myocardial TNF-alpha mRNA copies (corrected for beta-actin mRNA expression) in MR patients and donor hearts were 38.96+/-42.74x10(6) and 0.88+/-0.75x10(6), respectively (P=0.01). After MV surgery, there was a decrease in the plasma levels of TNF-alpha (2.79+/-1.14 versus 3.51+/-1.34 pg/mL, P=0.02) and its receptors. There was a correlation between myocardial TNF-alpha expression and preoperative LV end-diastolic and end-systolic volumes. Moreover, there was an inverse correlation between myocardial TNF-alpha expression and regression in LV end-diastolic (r=-0.76, P=0.007) and end-systolic (r=-0.73, P=0.01) volumes after MV surgery.



TNF-alpha is expressed in the myocardium and plasma of MR patients. Correction of the LV volume overload with MV surgery results in reversal of TNF-alpha expression. There is a relationship between TNF-alpha expression and parameters of LV remodeling, suggesting that TNF-alpha may play a role in the pathogenesis of the LV remodeling that occurs in MR.
Estimation of serum osteocalcin and telopeptide-C in postmenopausal osteoporotic females

A negative correlation of serum C-terminal telopeptide of type I collagen (telopeptide-C) was observed with bone mass density (BMD) in postmenopausal control (r = −0.70, p < 0.05) and osteoporotic females (r = −0.46, p < 0.05) indicating increased bone resorption in these subjects. Since telopeptide-C is a significant determinant of bone loss, it can be used, in combination with bone mass measurement, for the assessment of postmenopausal females. The aim of this study was to find out the significance of serum osteocalcin, a marker of bone formation, and C-terminal telopeptide of type I collagen, a marker of bone resorption, in evaluating osteoporotic patients and to find out their relationship with bone mass density. One hundred and fifty (150) females; 50 premenopausal (age=31.13 ± 1.29), 50 postmenopausal (age = 54.36 ± 0.81) and 50 postmenopausal osteoporotic patients (age = 58.6 ± 0.701) were included in this study. The postmenopusal subjects, with and without osteoporosis, were selected from different osteoporotic clinics and healthy premenopausal females were selected from general population. Height, weight, BMI, waist/hip ratio, age at menarche, years since menopause in case of postmenopausal women, history of disease, and fracture, if any, were recorded. BMD assessment was done on calcaneous by peripheral ultrasound bone densitometery on Sahara Clinical Bone Sonometer and T-scores were calculated. Serum levels of osteocalcin and C-terminal telopeptide of type I collagen and calcium were measured. A lower BMD in postmenopausal subjects, with and without osteoporosis (p < 0.001), indicating increased bone loss with aging and menopause, was observed. A negative correlation was found between age and BMD (r = −0.67, p < 0.05). No correlation was found between osteocalcin and BMD among these groups, suggesting heterogeneity of osteocalcin fragments in serum that limits its significance in the evaluation of osteoporosis. A positive correlation was found between osteocalcin and telopeptide-C (r = 0.26, p < 0.05). A positive correlation of telopeptide-C with age (r = 0.45, p < 0.05) and a negative correlation with BMD (r = −0.46, p < 0.05) was observed indicating increased bone resorption in postmenopausal control and postmenopausal osteoporotic patients. C-terminal telopeptide of type I collagen appears to be a significant determinant of bone loss and may be used as a valuable tool in the assessment of postmenopausal osteoporotic patients.
Non-invasive therapy to reduce the body burden of aluminium in Alzheimer's disease.

There are unexplained links between human exposure to aluminium and the incidence, progression and aetiology of Alzheimer's disease. The null hypothesis which underlies any link is that there would be no Alzheimer's disease in the effective absence of a body burden of aluminium. To test this the latter would have to be reduced to and retained at a level that was commensurate with an Alzheimer's disease-free population. In the absence of recent human interference in the biogeochemical cycle of aluminium the reaction of silicic acid with aluminium has acted as a geochemical control of the biological availability of aluminium. This same mechanism might now be applied to both the removal of aluminium from the body and the reduced entry of aluminium into the body while ensuring that essential metals, such as iron, are unaffected. Based upon the premise that urinary aluminium is the best non-invasive estimate of body burden of aluminium patients with Alzheimer's disease were asked to drink 1.5 L of a silicic acid-rich mineral water each day for five days and, by comparison of their urinary excretion of aluminium pre-and post this simple procedure, the influence upon their body burden of aluminium was determined. Drinking the mineral water increased significantly (P<0.001) their urinary excretion of silicic acid (34.3 +/- 15.2 to 55.7 +/- 14.2 micromol/mmol creatinine) and concomitantly reduced significantly P=0.037) their urinary excretion of aluminium (86.0 +/- 24.3 to 62.2 +/- 23.2 nmol/mmol creatinine). The latter was achieved without any significant (P>0.05) influence upon the urinary excretion of iron (20.7 +/- 9.5 to 21.7 +/- 13.8 nmol/mmol creatinine). The reduction in urinary aluminium supported the future longer-term use of silicic acid as non-invasive therapy for reducing the body burden of aluminium in Alzheimer's disease.
Diagnostic leukapheresis enables reliable detection of circulating tumor cells of nonmetastatic cancer patients.

Circulating tumor cells (CTCs) are promising biomarkers for diagnosis and therapy in systemic cancer. However, their infrequent and unreliable detection, especially in nonmetastatic cancer, currently impedes the clinical use of CTCs. Because leukapheresis (LA) targets peripheral blood mononuclear cells, which have a similar density to CTCs, and usually involves processing the whole circulating blood, we tested whether LA could substantially increase CTC detection in operable cancer patients. Therefore, we screened LA products generated from up to 25 L of blood per patient in two independent studies, and found that CTCs can be detected in more than 90% of nonmetastatic breast cancer patients. Interestingly, complete white blood cell sampling enabled determining an upper level for total CTC numbers of about 100,000 cells (median, 7,500 CTCs) per patient and identified a correlation of CTC numbers with anatomic disease spread. We further show that diagnostic leukapheresis can be easily combined with the US Food and Drug Administration-approved CellSearch system for standardized enumeration of CTCs. Direct comparison with 7.5 mL of blood revealed a significantly higher CTC frequency in matched LA samples. Finally, genomic single-cell profiling disclosed highly aberrant CTCs as therapy-escaping variants in breast cancer. In conclusion, LA is a clinically safe method that enabled a reliable detection of CTCs at high frequency even in nonmetastatic cancer patients, and might facilitate the routine clinical use of CTCs as in the sense of a liquid biopsy. Combined with technologies for single-cell molecular genetics or cell biology, it may significantly improve prediction of therapy response and monitoring of early systemic cancer.
Assessment of optimum stent deployment by stent boost imaging: comparison with intravascular ultrasound

Stent boost (SB) imaging is an enhancement of the radiologic edge of the stent by digital management of regular X-ray images. The purpose of the present study was to validate SB imaging by comparison with the anatomical standard using intravascular ultrasound (IVUS). We investigated SB and IVUS after stent implantation in 68 arteries in 60 patients. Based on those findings, we added high-pressure dilatation in four patients and another stent implantation in four patients. We defined the SB criteria for adequate stent deployment as: complete stent expansion, stent minimum diameter ≥70% of reference diameter, and stent minimum diameter ≥2.0 mm; and IVUS criteria for adequate stent deployment as: minimal stent area ≥5.0 mm2. If the reference vessel was <2.8 mm, adequate stent deployment was defined as minimum stent area ≥4.5 mm2. IVUS findings indicated inadequate stent deployment in 21/72 observations (29%). Seven SB images showed inadequate stent expansion. SB predicted inadequate findings of IVUS with 100% specificity, 33% sensitivity, and 81% agreement. Although the sensitivity of SB image for adequate stent deployment is low, the specificity is sufficiently high for it to be the first-line for monitoring just after stent implantation in centers where IVUS is not used routinely.
Validation and assessment of variant calling pipelines for next-generation sequencing

The processing and analysis of the large scale data generated by next-generation sequencing (NGS) experiments is challenging and is a burgeoning area of new methods development. Several new bioinformatics tools have been developed for calling sequence variants from NGS data. Here, we validate the variant calling of these tools and compare their relative accuracy to determine which data processing pipeline is optimal. We developed a unified pipeline for processing NGS data that encompasses four modules: mapping, filtering, realignment and recalibration, and variant calling. We processed 130 subjects from an ongoing whole exome sequencing study through this pipeline. To evaluate the accuracy of each module, we conducted a series of comparisons between the single nucleotide variant (SNV) calls from the NGS data and either gold-standard Sanger sequencing on a total of 700 variants or array genotyping data on a total of 9,935 single-nucleotide polymorphisms. A head to head comparison showed that Genome Analysis Toolkit (GATK) provided more accurate calls than SAMtools (positive predictive value of 92.55% vs. 80.35%, respectively). Realignment of mapped reads and recalibration of base quality scores before SNV calling proved to be crucial to accurate variant calling. GATK HaplotypeCaller algorithm for variant calling outperformed the UnifiedGenotype algorithm. We also showed a relationship between mapping quality, read depth and allele balance, and SNV call accuracy. However, if best practices are used in data processing, then additional filtering based on these metrics provides little gains and accuracies of >99% are achievable. Our findings will help to determine the best approach for processing NGS data to confidently call variants for downstream analyses. To enable others to implement and replicate our results, all of our codes are freely available at http://metamoodics.org/wes .
The GoodNEWS (Genes, Nutrition, Exercise, Wellness, and Spiritual Growth) Trial: a community-based participatory research (CBPR) trial with African-American church congregations for reducing cardiovascular disease risk factors--recruitment, measurement, and randomization.

Although cardiovascular diseases (CVD) are the leading cause of death among Americans, significant disparities persist in CVD prevalence, morbidity, and mortality based on race and ethnicity. However, few studies have examined risk factor reduction among the poor and ethnic minorities.



Community-based participatory research (CBPR) study using a cluster randomized design--African-American church congregations are the units of randomization and individuals within the congregations are the units of analysis. Outcome variables include dietary change (Diet History Questionnaire), level of physical activity (7-Day Physical Activity Recall), lipoprotein levels, blood pressure, fasting glucose, and hemoglobin A1c.



Eighteen (18) church congregations were randomized to either a health maintenance intervention or a control condition. Complete data were obtained on 392 African-American individuals, 18 to 70 years of age, predominantly employed women with more than a high school diploma. Treatment and intervention groups were similar at baseline on saturated fat intake, metabolic equivalent of tasks (METS) per day, and other risk factors for CVD.



The GoodNEWS trial successfully recruited and evaluated CVD-related risk among African-American participants using a CBPR approach. Several logistical challenges resulted in extending the recruitment, preliminary training, and measurement periods. The challenges were overcome with the assistance of a local community consultant and a professional event planner. Our experience supports the need for incorporating non-traditional community-based staff into the design and operational plan of CBPR trials.
A randomized, controlled trial of linopirdine in the treatment of Alzheimer's disease.

We tested the efficacy and safety of linopirdine, a novel phenylindolinone, in the treatment of Alzheimer's disease.



A multicentre, randomized, double-blind, parallel group, placebo-controlled trial of linopirdine (30 mg three times per day or placebo). Patients (n = 382, 55% male, 98% Caucasian, age range 51-95 years) with mild or moderate Alzheimer's disease, of whom 375 received at least one treatment dose were analysed. There were no important differences between the groups at baseline.



No difference was seen in Clinical Global Impression scores between patients receiving placebo and those receiving linopirdine (n = 189). Small differences in the Alzheimer's Disease Assessment Scale-Cognitive Subscale (ADAS-Cog) scores were seen throughout the study favouring linopirdine; at 6 months the ADAS-Cog scores were 20.2 (linopirdine) and 22.1 (placebo) p = 0.01.



This trial did not detect clinically meaningful differences in patients receiving linopirdine for 6 months, despite evidence of a small degree of improved cognitive function. Further studies may benefit from more sensitive tests of treatment effects in Alzheimer's disease.