nils-herrmann/clean_scirepeval huggingface dataset:
Associations of plasma 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D concentrations with death and progression to maintenance dialysis in patients with advanced kidney disease.

Low vitamin D concentrations are prevalent in patients with chronic kidney disease (CKD). We investigated the relationship between plasma 25-hydroxyvitamin D (25[OH]D) or 1,25-dihydroxyvitamin D (1,25[OH](2)D) concentrations with death, cardiovascular events, and dialysis therapy initiation in patients with advanced CKD.



The HOST (Homocysteinemia in Kidney and End Stage Renal Disease) Study was a randomized double-blind trial evaluating the effects of high doses of folic acid on death and long-term dialysis therapy initiation in patients with advanced CKD (stages 4 and 5 not yet on dialysis therapy). 25(OH)D and 1,25(OH)(2)D were measured in stored plasma samples obtained 3 months after trial initiation and evaluated at clinically defined cutoffs (<10, 10-30, and >30 ng/mL) and tertiles (<15, 15-22, and >22 pg/mL), respectively. Cox proportional hazard models were used to examine the association between vitamin D concentrations and clinical outcomes.



1,099 patients with advanced CKD from 36 Veteran Affairs Medical Centers.



25(OH)D and 1,25(OH)(2)D concentrations.



Death, cardiovascular events, and time to initiation of long-term dialysis therapy.



After a median follow-up of 2.9 years, 41% (n = 453) died, whereas 56% (n = 615) initiated dialysis therapy. Mean 25(OH)D and 1,25(OH)(2)D concentrations were 21 ± 10 ng/mL and 20 ± 11 pg/mL, respectively. After adjustment for potential confounders, the lowest tertile of 1,25(OH)(2)D was associated with death (HR, 1.33; 95% CI, 1.01-1.74) and initiation of long-term dialysis therapy (HR, 1.78; 95% CI, 1.40-2.26) compared with the highest tertile. The association with death and initiation of dialysis therapy was moderately attenuated after adjustment for plasma fibroblast growth factor 23 (FGF-23) concentrations (HRs of lower tertiles of 1.20 [95% CI, 0.91-1.58] and 1.56 [95% CI, 1.23-1.99], respectively, compared with highest tertile). There was no association between 25(OH)D concentrations and outcomes.



Participants were mostly men.



Low plasma 1,25(OH)(2)D concentrations are associated with death and initiation of long-term dialysis therapy in patients with advanced CKD. FGF-23 level may attentuate this relationship.
Effects of insufficient sleep on blood pressure in hypertensive patients: a 24-h study.

The influence of acute sleep deprivation during the first part of the night on 24-h blood pressure monitoring (ABPM) was studied in 36 never-treated mild to moderate hypertensive patients. According to a crossover design, they were randomized to have either sleep deprivation or a full night's sleep 1 week apart, during which they were monitored with ABPM. Urine samples for analysis of nocturnal urinary excretion of norepinephrine were collected. During the sleep-deprivation day, both mean 24-h blood pressure and mean 24-h heart rate were higher in comparison with those recorded during the routine workday, the difference being more pronounced during the nighttime (P < .01). Urinary excretion of norepinephrine showed a significant increase at night during sleep deprivation (P < .05). Blood pressure and heart rate significantly increased in the morning after a sleep-insufficient night (P < .05). These data suggest that lack of sleep in hypertensive patients may increase sympathetic nervous activity during the night and the following morning, leading to increased blood pressure and heart rate. This situation might represent an increased risk for both target organ damage and acute cardiovascular diseases.
ACTuDB, a new database for the integrated analysis of array-CGH and clinical data for tumors

In recent years, an increasing number of projects have investigated tumor genome structure, using microarray-based techniques like array comparative genomic hybridization (array-CGH) or single nucleotide polymorphism (SNP) arrays. The forthcoming studies have to integrate these former results and compare their findings to the existing sets of copy number data for validation. These sets also form the basis from which many comparative retrospective analyses can be carried out. Nevertheless, exploitation of this mass of data relies on a homogeneous preparation of copy number data, which will make it possible to compare them together, and their integration into a unified bioinformatics environment with ad hoc analysis tools and interfaces. To our knowledge, no such data integration has been proposed yet. Therefore the biologists and clinicians involved in cancer research urgently need such an integrative tool, which motivated us to undertake the construction of a database for array-CGH and other DNA copy number data for tumors (ACTuDB). When available, the associated clinical, transcriptome and loss of heterozygosity data were also integrated into ACTuDB. ACTuDB contains currently about 1500 genomic profiles for tumors and cell lines for the bladder, brain, breast, colon, liver, lymphoma, neuroblastoma, mouth and pancreas, together with data for replication timing experiments. The CGH array data were processed, using ad hoc algorithms (probe mapping, breakpoint detection, gain or loss status assignment and visualization) developed at Institut Curie. The database is available from http://bioinfo.curie.fr/actudb/ and can be browsed with a user-friendly interface. This database will be a useful resource for the genomic profiling of tumors, a field of highly active research. We invite research groups involved in tumor genome profiling to submit their data to ACTuDB.
Low validity of the Sensewear Pro3 activity monitor compared to indirect calorimetry during simulated free living in patients with osteoarthritis of the hip

To validate physical activity estimates by the Sensewear Pro3 activity monitor compared with indirect calorimetry during simulated free living in patients diagnosed with osteoarthritis of the hip pre or post total hip arthroplasty.



Twenty patients diagnosed with hip osteoarthritis (10 pre- and 10 post total hip arthroplasty; 40% female; age: 63.3 ± 9.0; BMI: 23.7 ± 3.7). All patients completed a 2 hour protocol of simulated free living with 8 different typical physical activity types. Energy consumption (kcal/min) was estimated by the Sense Wear pro3 Armband activity monitor and validated against indirect calorimetry (criterion method) by means of a portable unit (Cosmed ). Bias and variance was analyzed using functional ANOVA.



Mean bias during all activities was 1.5 Kcal/min 95%CI [1.3; 1.8] corresponding to 72% (overestimation). Normal gait speed showed an overestimation of 2.8 Kcal/min, 95%CI [2.3; 3.3] (93%) while an underestimation of -1.1 Kcal/min, 95%CI [-1.8; -0.3] (-25%) was recorded during stair climb. Activities dominated by upper body movements showed large overestimation with 4.37 Kcal/min, 95%CI [3.8; 5.1] (170%) being recorded during gardening. Both bias and variance appeared to be dependent on activity type.



The activity monitor generally overestimated the energy consumption during common activities of low to medium intensity in the patient group. The size and direction of the bias was highly dependent on the activity type which indicates the activity monitor is of limited value in patients with hip osteoarthritis and that the results do not express the real energy expenditure.
Nurse versus doctor management of HIV-infected patients receiving antiretroviral therapy (CIPRA-SA): a randomised non-inferiority trial

Expanded access to combination antiretroviral therapy (ART) in resource-poor settings is dependent on task shifting from doctors to other health-care providers. We compared outcomes of nurse versus doctor management of ART care for HIV-infected patients.



This randomised non-inferiority trial was undertaken at two South African primary-care clinics. HIV-positive individuals with a CD4 cell count of less than 350 cells per microL or WHO stage 3 or 4 disease were randomly assigned to nurse-monitored or doctor-monitored ART care. Patients were randomly assigned by stratified permuted block randomisation, and neither the patients nor those analysing the data were masked to assignment. The primary objective was a composite endpoint of treatment-limiting events, incorporating mortality, viral failure, treatment-limiting toxic effects, and adherence to visit schedule. Analysis was by intention to treat. Non-inferiority of the nurse versus doctor group for cumulative treatment failure was prespecified as an upper 95% CI for the hazard ratio that was less than 1.40. 
408 patients were assigned to doctor-monitored ART care and 404 to nurse-monitored ART care; all participants were analysed. 371 (46%) patients reached an endpoint of treatment failure: 192 (48%) in the nurse group and 179 (44%) in the doctor group. The hazard ratio for composite failure was 1.09 (95% CI 0.89-1.33), which was within the limits for non-inferiority. After a median follow-up of 120 weeks (IQR 60-144), deaths (ten vs 11), virological failures (44 vs 39), toxicity failures (68 vs 66), and programme losses (70 vs 63) were similar in nurse and doctor groups, respectively.



Nurse-monitored ART is non-inferior to doctor-monitored therapy. Findings from this study lend support to task shifting to appropriately trained nurses for monitoring of ART.
Effect of dietary protein intake on serum total CO2 concentration in chronic kidney disease: Modification of Diet in Renal Disease study findings.

Metabolic acidosis is a feature of chronic kidney disease (CKD), but whether serum bicarbonate concentration is influenced by variations in dietary protein intake is unknown. For assessing the effect of diet, data that were collected in the Modification of Diet in Renal Disease study were used. In this study, patients with CKD were enrolled into a baseline period, then randomly assigned to follow either a low- or a usual-protein diet (study A, entry GFR 25 to 55 ml/min) or a low- or very low-protein diet, the latter supplemented with ketoanalogs of amino acids (study B, entry GFR 13 to 24 ml/min). Serum [total CO2] and estimated protein intake (EPI) were assessed at entry (n = 1676) and again at 1 yr after randomization, controlling for changes in GFR and other key covariates (n = 723). At entry, serum [total CO2] was inversely related to EPI (1.0 mEq/L lower mean serum [total CO2]/g per kg body wt increase in protein intake/d; P = 0.009). In an intention-to-treat analysis, the reduction in mean EPI in the low-protein group as compared with the usual-protein group (0.41 g/kg body wt per d) was independently associated with a 0.9-mEq/L increase in serum [total CO2], after adjustment for covariates (P < 0.001). No such effect was evident in study B, in which the very low-protein diet group received dietary supplements. Serum [total CO2] is inversely correlated with dietary protein intake in patients with CKD. A reduction in protein intake results in an increase in serum [total CO2].
Benefits of combined aerobic/resistance/inspiratory training in patients with chronic heart failure. A complete exercise model? A prospective randomised study.

We hypothesised that combined aerobic training (AT) with resistance training (RT) and inspiratory muscle training (IMT) could result in additional benefits over AT alone in patients with chronic heart failure (CHF).



Twenty-seven patients, age 58 ± 9 years, NYHA II/III and LVEF 29 ± 7% were randomly assigned to a 12-week AT (n=14) or a combined AT/RT/IMT (ARIS) (n=13) exercise program. AT consisted of bike exercise at 70-80% of max heart rate. ARIS training consisted of AT with RT of the quadriceps at 50% of 1 repetition maximum (1RM) and upper limb exercises using dumbbells of 1-2 kg as well as IMT at 60% of sustained maximal inspiratory pressure (SPI(max)). At baseline and after intervention patients underwent cardiopulmonary exercise testing, echocardiography, evaluation of dyspnea, muscle function and quality of life (QoL) scores.



The ARIS program as compared to AT alone, resulted in additional improvement in quadriceps muscle strength (1RM, p=0.005) and endurance (50%1 RM × number of max repetitions, p=0.01), SPI(max) (p<0.001), exercise time (p=0.01), circulatory power (peak oxygen consumption × peak systolic blood pressure, p=0.05), dyspnea (p=0.03) and QoL (p=0.03).



ARIS training was safe and resulted in incremental benefits in both peripheral and respiratory muscle weakness, cardiopulmonary function and QoL compared to that of AT. The present findings may add a new prospective to cardiac rehabilitation programs of heart failure patients whilst the clinical significance of these outcomes need to be addressed in larger randomised studies.
Global and disease-specific health-related quality of life after complete endoscopic resection of anterior skull base neoplasms.

Minimally invasive surgery for neoplasms of the anterior skull base has revolutionized the treatment of these diseases. The relative effect of endoscopic procedures, however, has not been described in terms of disease-specific and global health-related quality of life (QoL).



A single-center longitudinal study was performed of patients undergoing complete endoscopic resection of anterior skull base neoplasms. Patients presenting between October 2009 and September 2010 were enrolled. QoL assessments were based on the 22-question Sinonasal Outcomes Test (SNOT-22), Health Utilities Index Mark II (HUI-2), and Short-Form 12 (SF-12) and were completed preoperatively and at 3, 6, and 12 months postoperatively. Comparisons over time were made within subjects.



Fourteen patients were enrolled; 11 completed preoperative and postoperative assessments (79%). Our cohort consisted of five men and six women; mean age was 55 years. Six patients had malignant tumors; four required adjuvant therapy. SNOT-22 scores were stable or improved in 10 cases (91%), with a significant difference for the cohort (mean, -33 points; p < 0.01). Ten (91%) patients had stable or improved HUI-2 scores (mean utility change, +0.13). SF-12 scores were stable for both mental (p = 0.17) and physical (p = 0.26) components. Mean quality-adjusted life year gain over the study period was 0.07.



Complete endoscopic resection of anterior skull base neoplasms is oncologically sound with anecdotal QoL improvements relative to open craniofacial resection. We show positive, quantifiable QoL results with validated global and disease-specific instruments. Additional work will help to improve outcomes in this population and will be used in formal cost-effectiveness analysis.
Reliability and validity of a modified PHQ-9 item inventory (PHQ-12) as a screening instrument for assessing depression in Asian Indians (CURES-65).

To evaluate the validity and reliability of the modified Patient Health Questionnaire(PHQ) 12 item instrument as a screening tool for assessing depression compared to the PHQ-9 in a representative south Indian urban population.



The Chennai Urban Rural Epidemiology Study [CURES] is a large cross-sectional study conducted in Chennai, South India. In Phase 1 of CURES(urban component), 26,001 individuals aged > or =20 years individuals were selected by a systematic sampling technique of whom one hundred subjects were randomly selected, using computer-generated numbers, for this validation study. Two self-reported questionnaires (modified PHQ-12 item and PHQ-9 item) were administered to the subjects to compare their effectiveness in detecting depression. Reliability and validity were assessed and Receiver Operating Characteristic (ROC) curves were plotted. Pearson's correlation was used to compare the two questionnaires.



The mean age of the study was 38.6 +/- 11.6 years and 48% were males. Pearson's correlation coefficient between the modified PHQ-12 and the PHQ-9 item was 0.913 [p < 0.0001]. Factor Analysis revealed that the modified PHQ-12 item scale can be used as a unidimensional scale and had excellent internal consistency (Cronbach's alpha: 0.88). A cut point of >4 calculated using the ROC curves for the modified PHQ-12 item had the highest sensitivity (92.0%) and specificity (90.7%) using PHQ-9 as the gold standard. The positive predictive value was 76.7%, and the negative predictive value, 97.1% and the area under the ROC curve, 0.979 (95% Confidence Interval: 0.929 - 0.997, p < 0.0001).



The modified PHQ-12 item is a valid and reliable instrument for large scale population based screening of depression in Asian Indians and a cut point score of greater than 4 gave the highest sensitivity and specificity.
Immunohistochemical determination of her2 expression in breast cancer from core biopsy specimens: a reliable predictor of her2 status of the whole tumor

HER2 overexpression in breast cancer is associated with a poor prognosis, resistance to endocrine therapy and chemosensitivity to anthracyclines and paclitaxel. Moreover, trastuzumab (HerceptinR) shows therapeutic benefit in patients with HER2 overexpressing tumors. Therefore, knowledge of the pretherapeutical HER2 status allows an optimal selection of patients for treatment. In addition to a definitive histological diagnosis, core biopsies of tumors offer the opportunity to evaluate the HER2 status preoperatively. In 64 patients with invasive breast cancer, sections of core biopsies and of the subsequently removed whole tumor were investigated immuno-histochemically with the DAKO HercepTestTM. Fifteen tumors (23%) revealed HER2 overexpression, and 44 tumors (69%) were negative in both, the core biopsy and the whole tumor sections. Two core biopsies were negative whereas the corresponding final specimen was 2+ positive. In 3 cases weak overexpression was observed in the core biopsy, but the whole tumor was negative. The overall concordance of the results achieved at core biopsy and whole tumor sections was 92% κ=0.8). A negative HER2 result on core biopsy was never associated with a score 3+ tumor specimen nor was there a case of negative whole tumor specimen with a preceding 3+ score in the biopsy. If one demands the highest degree of overexpression (3+), 100% of our study patients would have been selected correctly using the results on core biopsy alone. We thus conclude, that the immunohistochemical investigation of core biopsies offers the opportunity for a valid preoperative estimation of HER2 overexpression.
Prospective, double-blind, randomized, placebo-controlled comparison of acetazolamide versus ibuprofen for prophylaxis against high altitude headache: the Headache Evaluation at Altitude Trial (HEAT).

High altitude headache (HAH) is the most common neurological complaint at altitude and the defining component of acute mountain sickness (AMS). However, there is a paucity of literature concerning its prevention. Toward this end, we initiated a prospective, double-blind, randomized, placebo-controlled trial in the Nepal Himalaya designed to compare the effectiveness of ibuprofen and acetazolamide for the prevention of HAH.



Three hundred forty-three healthy western trekkers were recruited at altitudes of 4280 m and 4358 m and assigned to receive ibuprofen 600 mg, acetazolamide 85 mg, or placebo 3 times daily before continued ascent to 4928 m. Outcome measures included headache incidence and severity, AMS incidence and severity on the Lake Louise AMS Questionnaire (LLQ), and visual analog scale (VAS).



Two hundred sixty-five of 343 subjects completed the trial. HAH incidence was similar when treated with acetazolamide (27.1%) or ibuprofen (27.5%; P = .95), and both agents were significantly more effective than placebo (45.3%; P = .01). AMS incidence was similar when treated with acetazolamide (18.8%) or ibuprofen (13.7%; P = .34), and both agents were significantly more effective than placebo (28.6%; P = .03). In fully compliant participants, moderate or severe headache incidence was similar when treated with acetazolamide (3.8%) or ibuprofen (4.7%; P = .79), and both agents were significantly more effective than placebo (13.5%; P = .03).



Ibuprofen and acetazolamide were similarly effective in preventing HAH. Ibuprofen was similar to acetazolamide in preventing symptoms of AMS, an interesting finding that implies a potentially new approach to prevention of cerebral forms of acute altitude illness.
Early lapses in a cessation attempt: lapse contexts, cessation success, and predictors of early lapse.

The great majority of smokers relapse when they make quit attempts. Therefore, understanding the process of relapse may guide the development of more effective smoking cessation or relapse prevention treatments. The goal of this research is to extend our understanding of the context of initial lapses that occur within 8 weeks of quitting by using more comprehensive assessments of context, a contemporary sample, and sophisticated analytic techniques.



Participants from a randomized controlled smoking cessation trial completed baseline assessments of demographics and tobacco dependence, a daily smoking calendar to determine latency to lapse and relapse (7 consecutive days of smoking), and an assessment of initial lapse context (affect, location, activity, interpersonal, smoke exposure, and cigarette availability). Latent class analysis (LCA) was used to analyze the 6 early lapse (within the first 8 weeks; N = 551) context dimensions; logistic regression and Cox regression were used to relate context to cessation outcomes.



LCA revealed 5 distinct initial lapse context classes (talking, with friends, angry; social; alone; with spouse, angry; and with smoking spouse) that were differentially related to cessation outcome. The easy availability of cigarettes characterized almost 75% of lapses, but being with friends, drinking, and not being at home were associated with a lower likelihood of progression to relapse.



Early lapsing is highly related to ultimate relapse, and lapsing in frequently experienced contexts seemed most strongly linked with progression to full relapse.
A trial of radiofrequency ablation for anal intraepithelial neoplasia

Radiofrequency ablation (RFA) effectively treats esophageal high-grade dysplasia, but its efficacy in treating anal canal high-grade squamous intraepithelial lesions (HSILs) is unsubstantiated. This prospective study assessed the safety and efficacy of applying hemi-circumferential RFA to anal canal HSIL. Twenty-one HIV-negative participants with HSIL occupying ≤ half the anal canal circumference were treated with hemi-circumferential anal canal RFA. Participants were assessed every 3 months for 12 months with high-resolution anoscopy; recurrence in the treatment zone was re-treated with focal RFA. Twenty-one participants with a mean of 1.7 lesions (range 1–4) enrolled and completed the trial. Six (29 %) participants had recurrent HSIL within the treated hemi-circumference within 1 year. Four participants (19 %) had persistence of an index lesion at 3 months. One (2.9 %) index HSIL persisted again at 12 months. No participants had more than two RFA treatments. KM curve-predicted HSIL-free survival within the treatment zone at 1 year was 76 % (95 % CI 52–89 %). Comparing the first 7 and last 14 participants, the predicted 1-year HSIL-free survivals are 43 % (95 % CI 10–73 %) and 93 % (95 % CI 59–99 %), respectively (p = 0.008), suggesting a learning curve with the treating physician. Multivariable analysis showed decreased recurrence in the last 14 participants (HR 0.02; 95 % CI 0.001–0.63) while increasing BMI increased recurrence (HR 1.43, 95 % CI 1.01–2.01). No participants had device or procedure-related serious adverse events, anal stricture, or heavy bleeding. Hemi-circumferential RFA yielded a high rate of anal HSIL eradication in HIV-negative patients at 1 year with minimal adverse events. Lesion persistence was probably related to incomplete initial ablation.