nils-herrmann/clean_scirepeval huggingface dataset:
Multicenter evaluation of an investigational prostate cancer methylation assay.

Prostate specific antigen tests have low specificity, which frequently results in unnecessary biopsy and typically limits screening to patients with prostate specific antigen greater than 4.0 ng/ml. We evaluated an investigational prostate cancer methylation specific polymerase chain reaction assay that detects aberrant methylation in 3 markers (GSTP1, RARbeta2 and APC) that indicate the presence of prostate cancer.



The assay was evaluated in 337 post-digital rectal examination urine samples (178 cancer and 159 noncancer) collected prospectively at a total of 9 clinical sites. Samples were processed wholly or after division into equal portions. Subject prostate specific antigen was 2.0 to 10.0 ng/ml. All subjects underwent transrectal ultrasound guided needle biopsy with 6 or greater cores sampled. Detection of 1 or greater markers indicated positivity.



Methylation specific polymerase chain reaction assay performance was better in whole than in divided urine cohorts (p = 0.035). Assay AUC was 0.72 in the whole urine cohort and 0.67 in the combined population. These values were higher than those of prostate specific antigen alone using 4.0 ng/ml as the cutoff (p = 0.00 and 0.01, respectively). Moreover, the assay together with the Prostate Cancer Prevention Trial risk calculator or a standard nomogram significantly improved AUC in the whole urine cohort and the combined population vs predictive algorithms alone (p <0.05). Assay positive predictive value was 54% in whole urine cohort with prostate specific antigen 2.0 to 4.0 ng/ml and negative predictive value was 87% with prostate specific antigen 4.1 to 10.0 ng/ml. Assay positive predictive value was higher in subjects with all 3 methylation markers positive.



These data demonstrate that this investigational assay used in conjunction with current screening algorithms may potentially add value to the biopsy decision making process.
Diffusion-weighted imaging and cognition in the leukoariosis and disability in the elderly study.

The mechanisms by which leukoariosis impacts on clinical and cognitive functions are not yet fully understood. We hypothesized that ultrastructural abnormalities of the normal-appearing brain tissue (NABT) assessed by diffusion-weighted imaging played a major and independent role.



In addition to a comprehensive clinical, neuropsychologic, and imaging work-up, diffusion-weighted imaging was performed in 340 participants of the multicenter leukoariosis and disability study examining the impact of white matter hyperintensities (WMH) on 65- to 85-year old individuals without previous disability. WMH severity was rated according to the Fazekas score. Multivariate regression analysis served to assess correlations of histogram metrics of the apparent diffusion coefficient (ADC) of whole-brain tissue, NABT, and of the mean ADC of WMH with cognitive functions.



Increasing WMH scores were associated with a higher frequency of hypertension, a greater WMH volume, more brain atrophy, worse overall cognitive performance, and changes in ADC. We found strong associations between the peak height of the ADC histogram of whole-brain tissue and NABT with memory performance, executive dysfunction, and speed, which remained after adjustment for WMH lesion volume and brain atrophy and were consistent among centers. No such association was seen with the mean ADC of WMH.



Ultrastructural abnormalities of NABT increase with WMH severity and have a strong and independent effect on cognitive functions, whereas diffusion-weighted imaging metrics within WMH have no direct impact. This should be considered when defining outcome measures for trials that attempt to ameliorate the consequences of WMH progression.
[Procalcitonin and early-onset seizures: When do we offer a higher diagnostic yield?].

1. Certificación de Centros y Unidades Sanitarias. DG-06.02.01 Documento General de Certificación de Servicios (Rev. 5) 4 de febrero de 2014. Agencia de Calidad Sanitaria de Andalucía. Consejería de Igualdad, Salud y Políticas Sociales. Junta de Andalucía [accessed 1 September 2014]. Available: http://www.acsa.juntaandalucia.es:8080/opencms851/opencms/.content/galerias/ documentos/documentos-certificacion/Centros/Documento General de Certificacion de Servicios R6.pdf 2. Manual de estándares de Centros del Sistema Sanitario de Andalucía. ME 2 1 04. Agencia de Calidad Sanitaria de Andalucía. Consejería de Igualdad, Salud y Políticas Sociales. Junta de Andalucía [accessed 1 September 2014].  http:// www.acsa.junta-andalucia.es/.content/galerias/documentos/ documentos-certificacion/Centros/Manual estandares centros sistema ME2 1 04.pdf 3. Proceso Asistencial Integrado Asma en la edad pediátrica. Consejería de Salud. 2003. Junta de Andalucía [accessed 1 September 2014]. Available en: http://www.csalud.junta-andalucia.es/ salud/export/sites/csalud/galerias/documentos/p 3 p 3 procesos asistenciales integrados/asma pediatrica/asma pediatrica sustituido.pdf 4. Antonio Pons Tubío et al. Proceso Asistencial Integrado Atención temprana. Seguimiento recién nacido de riesgo. Consejería de Salud. 2009. Junta de Andalucía [accessed 1 September 2014]. Available: http://www.csalud.junta-andalucia.es/salud/ export/sites/csalud/galerias/documentos/p 3 p 3 procesos asistenciales integrados/seguimiento/0 riesgo.pdf 5. Proceso Asistencial Integrado Otitis Media Consejería de Salud. 2002. Junta de Andalucía [accessed 1 September 2014]. Available: http://www.csalud.junta-andalucia.es/salud/ export/sites/csalud/galerias/documentos/p 3 p 3 procesos asistenciales integrados/otitis media/otitis media.pdf 6. Proceso Asistencial Integrado Amigdalectomíaadenoidectomía. Consejería de Salud. 2003. Junta de Andalucía [accessed 1 September 2014].  3 procesos asistenciales integrados/amigdalectomia/ amigdalectomia nuevo.pdf
Second international workshop on emerging trends in Free/Libre/Open Source Software research and development - FLOSS09

The Workshop on “Emerging Trends in FLOSS Research and Development” is based on the ever growing interest of researchers and practitioners on Free/Libre/Open Source Software (FLOSS), and will be specifically based on discussing the phenomenon of global FLOSS development and how to identify and define, if any, how FLOSS communities could benefit from traditional Software Engineering practices, and viceversa. For this purpose, the overarching theme of this workshop is “Closing the Gap between Software Engineering and FLOSS Development”. Its main goal will be to bring together academic researchers, industry members and FLOSS developers and to discuss what aspects and practices are common in both the Software Engineering and the FLOSS development modes, and where and how these practices differ substantially.
[Evolution of the interventional reperfusion strategy and reperfusion times in acute ST-segment elevation myocardial infarction].

In patients with acute ST-segment elevation myocardial infarction (STEMI) treated with primary percutaneous coronary intervention (pPCI), the recommended times (first medical contact-to-balloon (M2B) <120 or <90min, and door-to-balloon (D2B) <45min) are reached in less than 50% of patients.



To compare the interventional reperfusion strategy and reperfusion times between two series of consecutive STEMI patients referred for pPCI within 12hours of symptom onset, in 2007 and 2012.



Retrospective study of 182 patients, 87 admitted from January 2007 to March 2008 (period 1), and 95 admitted from January to December 2012 (period 2). The procedural characteristics and the different times between onset of pain and mechanical reperfusion were gathered and compared by non-parametric tests.



Radial access, thromboaspiration, and drug eluting stents were more frequent, and cardiogenic shock was less common during period 2, compared with the period 1. The median time from first medical contact to balloon (M2B) decreased by 26% (135min,  in 2007 versus 100 [76-137] in 2012, P<0.001), in relation to the reduction in both prehospital times and time in the catheterization laboratory (D2B: 51 [44-65] and 44min [37-55], respectively, P<0.01).



The D2B and M2B times significantly decreased in our centre between 2007 and 2012, and reached the recommended values in >60% of the cases. This may be explained by better coordination between emergency medical units and interventional cardiologists, and by the presence of two paramedics in the catheterization laboratory for 24/24 7/7 pPCI since 2010 in France, in accordance with recent national regulation.
Computerized lifestyle intervention in routine primary health care : Evaluation of usage on provider and responder levels

The aim of this study was to evaluate the use of a computerized concept for lifestyle intervention in routine primary health care (PHC).  Nine PHC units were equipped with computers providing a lifestyle test and tailored printed advice. Patients were referred by staff, and performed the test anonymously. Data were collected over a period of one year.  An average of 5.7% of the individuals visiting PHC during the study period performed the test. There were great differences between the units in the number of tests performed and in the proportion of patients referred. One-fifth of the respondents scored for hazardous alcohol consumption, and one-fourth reported low levels of physical activity. A majority of respondents found the test easy to perform, and a majority of those referred to the test found referral positive.  The computerized test can be used for screening and intervention regarding lifestyle behaviour in primary care. Responders are positive to the test and to referral. Practice implications A more widespread implementation of computerized lifestyle tests could be a beneficial complement to face-to-face interventions in primary care.
11C-Acetate as a new biomarker for PET/CT in patients with multiple myeloma: initial staging and postinduction response assessment

We investigated the potential value of 11C-acetate (ACT) PET/CT in characterizing multiple myeloma (MM) compared with 18F-FDG PET/CT. Bone marrow histological and whole-body (WB) MRI findings served as the reference standards. In this prospective study, 15 untreated MM patients (10 men and 5 women, age range 48−69 years) underwent dual-tracer 11C-ACT and 18F-FDG PET/CT and WB MRI for pretreatment staging, and 13 of them had repeated examinations after induction therapy. Diffuse and focal bone marrow uptake was assessed by visual and quantitative analyses, including measurement of the maximum standardized uptake value (SUVmax). Between-group differences and correlations were assessed with the Mann-Whitney U test and the Pearson test. At staging, all 15 patients had diffuse myeloma involvement upon bone marrow examination with 30–90 % of plasma cell infiltrates. Diffuse infiltration was detected in all of them (100 %) using 11C-ACT with a positive correlation between bone marrow uptake values and percentages of plasma cell infiltrates (r = +0.63, p = 0.01). In contrast, a diagnosis of diffuse infiltration could be established using 18F-FDG in only six patients (40 %). Focal lesions were shown in 13 patients on both 11C-ACT PET/CT and WB MRI, and in 10 patients on 18F-FDG PET/CT. Focal lesions demonstrated 11C-ACT uptake with a mean SUVmax of 11.4 ± 3.3 (range 4.6−19.6, n = 59), which was significantly higher than the 18F-FDG uptake (mean SUVmax 6.6 ± 3.1, range 2.3−13.7, n = 29; p < 0.0001). After treatment, the diffuse bone marrow 11C-ACT uptake showed a mean SUVmax reduction of 66 % in patients with at least a very good partial response versus 34 % in those with at most a partial response only (p = 0.01). PET/CT using 11C-ACT as a biomarker showed a higher detection rate for both diffuse and focal myeloma lesions at diagnosis than using 18F-FDG, and may be valuable for response assessment.
Non-parametric 3D surface completion

We consider the completion of the hidden or missing portions of 3D objects after the visible portions have been acquired with 2 1/2 D (or 3D) range capture. Our approach uses a combination of global surface fitting, to derive the underlying geometric surface completion, together with an extension, from 2D to 3D, of nonparametric texture synthesis in order to complete localised surface texture relief and structure. Through this combination and adaptation of existing completion techniques we are able to achieve realistic, plausible completion of 2 1/2 D range captures.
Remark on algorithm 282 [S22] derivatives of ex/x, cos(x)/x, and sin (x)/x

We now prove separately the inequality for every term of the summation. Let us assume the thesis is wrong > ([(XLk+:-Xi,k) 2 + (yLk+:-yl.~)~] t "Jr [(X2.k+x-X2,k) 2 + (y2,k+l-Y2,k)2]t). which is contradictory. We can have equality to zero iff i.e. if all the corresponding sides of the two polygons are parallel.  We must prove that the minimal polygon has at least one vertex on the boundary of the corresponding domain. In fact, consider a minimal polygon: there will be at least a couple of adjaeent noncollinear sides. The corresponding vertex must lie on the boundary, otherwise a shorter perimeter polygon could be found . Furthermore, from simple geometrical considerations it can be deduced that the normal to the boundary must bisect the angle between the two adjacent sides (Figure 7 (b)). Conversely, if a constraint is not active, i.e. a vertex is not on the boundary, the adjacent sides in the minimal polygon must be collinear.  From the convexity properties of the domain D and of the function f it can be deduced that: (i) all local minima are global; (ii) any convex linear combination of minima is a minimum as well; (iii) Jensen's relation (3) applied to two minima obviously holds with equality. We have proved in (b) that in our ease Jensen's relation holds with equality if and only if the corresponding sides of the two polygons are parallel. Now assume to have found a (global) minimum: any vertex between two noncollineax sides will satisfy the bisection property proved in (d). If no straight line segments axe present on the boundary of domain C (e.g. if domain C is a circle), it is not possible to translate two adjacent noncollinear sides still satisfying the bisection property. Therefore, all minimal polygons have the vertices between two noncollinear sides in the same position. Thus they differ only in the position of vertices corresponding to nonactive constraints: the minimal reduced polygon is unique.  The work forms part of a research program supported by the Bundesministerium fiir wissenschaftliche Forsehung and the Fritz ter Meer-Stiftung. c o m m e n t If a Laplace transform P(s) is given in the form of a real procedure, L/nv produces an approximate value Fa of the inverse F(t) at T. Fa is evaluated according to Fa =-~-~=: N must be even. Since the V~ depend on …
Impact of fatty liver on hepatitis B virus replication and virologic response to tenofovir and entecavir.

We aimed to evaluate the impact of non-alcoholic fatty liver disease (NAFLD) on viral kinetics and virologic response to tenofovir and entecavir treatment in patients with chronic hepatitis B virus (HBV) infection.



This study was designed as a retrospective multicenter cohort study. The impact of hepatosteatosis on pre-treatment serum HBV DNA levels and also on the virologic response to either tenofovir or entecavir at 6 and 12 months of therapy was investigated.



A total of 145 cases were involved in the study [median age 40 (18-73) years, 90 (62%) males]. In multivariate analysis, it was detected that patients with NAFLD were older and had a higher body mass index (BMI) [Odds ratio (95% confidence interval) and p-value for age were 1.040 (1.003-1.079) and 0.033 and for BMI were 1.348 (1.190-1.528) and 0.0001, respectively]. When only the 43 patients who were younger than 35.5 years old and who had a BMI less than 27.59 were investigated, serum high-density lipoprotein (HDL) levels and serum HBV DNA levels were lower in patients with NAFLD in multivariate analysis [Odds ratio (95% confidence interval) and p-values for serum HDL level and HBV DNA level were 0.864 (0.061-0.980) and 0.023 and 0.995 (0.990-0.999) and 0.025, respectively]. Totally, 57 and 75 of the patients had received entecavir and tenofovir, respectively.



Viral replication decreases in patients with chronic HBV infection in the presence of NAFLD, and NAFLD had no impact on the virologic response to entecavir and tenofovir treatment.
Melatonin analgesia is associated with improvement of the descending endogenous pain-modulating system in fibromyalgia: a phase II, randomized, double-dummy, controlled trial

Central disinhibition is a mechanism involved in the physiopathology of fibromyalgia. Melatonin can improve sleep quality, pain and pain threshold. We hypothesized that treatment with melatonin alone or in combination with amitriptyline would be superior to amitriptyline alone in modifying the endogenous pain-modulating system (PMS) as quantified by conditional pain modulation (CPM), and this change in CPM could be associated with serum brain-derived neurotrophic factor (BDNF). We also tested whether melatonin improves the clinical symptoms of pain, pain threshold and sleep quality. Sixty-three females, aged 18 to 65, were randomized to receive bedtime amitriptyline (25 mg) (n = 21), melatonin (10 mg) (n = 21) or melatonin (10 mg) + amitriptyline (25 mg) (n = 21) for a period of six weeks. The descending PMS was assessed with the CPM-TASK. It was assessed the pain score on the Visual Analog Scale (VAS 0-100 mm), the score on Fibromyalgia Impact Questionnaire (FIQ), heat pain threshold (HPT), sleep quality and BDNF serum. Delta values (post- minus pre-treatment) were used to compare the treatment effect. The outcomes variables were collected before, one and six weeks after initiating treatment. Melatonin alone or in combination with amitriptyline reduced significantly pain on the VAS compared with amitriptyline alone (P < 0.01). The delta values on the VAS scores were-12.85 (19.93),-17.37 (18.69) and-20.93 (12.23) in the amitriptyline, melatonin and melatonin+amitriptyline groups, respectively. Melatonin alone and in combination increased the inhibitory PMS as assessed by the Numerical Pain Scale [NPS(0-10)] reduction during the CPM-TASK:-2.4 (2.04) melatonin + amitriptyline,-2.65 (1.68) melatonin, and-1.04 (2.06) amitriptyline, (P < 0.05). Melatonin + amitriptyline treated displayed better results than melatonin and amitriptyline alone in terms of FIQ and PPT improvement (P < 0.05, fort both). Melatonin increased the inhibitory endogenous pain-modulating system as assessed by the reduction on NPS(0-10) during the CPM-TASK. Melatonin alone or associated with amitriptyline was better than amitriptyline alone in improving pain on the VAS, whereas its association with amitriptyline produced only marginal additional clinical effects on FIQ and PPT. Current controlled trail is registered at clinical trials.gov upon under number NCT02041455 . Registered January 16, 2014.
Concordance of performance metrics among U.S. trauma centers caring for injured children.

Several indicators of quality pediatric trauma care have been proposed including low in-hospital mortality, nonoperative management of blunt splenic injury, use of intracranial pressure monitors after severe traumatic brain injury, and craniotomy for children with severe subdural or epidural hematomas. It is not known if center-level performance is consistent in each of these metrics. We evaluated whether center performance in one area of quality predicted similar performance in other areas of quality.



We reviewed patients 18 years or younger who were hospitalized with an injury Abbreviated Injury Scale (AIS) score of 2 or greater from 2010 to 2011 at trauma centers (n = 150) participating in the Trauma Quality Improvement Program. Random-intercept multilevel modeling was used to generate center-specific adjusted odds ratios for each quality indicator. We evaluated correlations between center-specific adjusted odds ratios of each quality indicator and mortality using Pearson correlation coefficients. Weighted κ statistics were used to test multiple pairwise agreements between indicators and the overall agreement across all four indicators.



Among 84,880 children identified for analysis, 3,603 had blunt splenic injury, 3,503 had severe traumatic brain injury, and 1,286 had an epidural or subdural hematoma. A negative correlation between center-specific odds of mortality and craniotomy was present (Pearson correlation coefficient, -0.18; p = 0.03). There were no significant correlations between other indicators. Although κ statistics showed slight agreement for the pairwise comparison of odds of mortality and craniotomy (0.17, 0.02-0.32), there was no agreement for all other pairwise comparisons or the overall comparison of all four indicators (-0.01, -0.07 to 0.06).



Our findings demonstrate a lack of concordance in center-level performance across the four pediatric trauma quality indicators we evaluated. These findings should be considered by pediatric trauma quality improvement initiatives to allow for comprehensive measurement of hospital quality as opposed to benchmarking using a single indicator.
Studies of two novel sulfasalazine analogs, ipsalazide and balsalazide

Sulfasalazine appears to exert its beneficial effect in colitis by releasing 5-aminosalicylic acid in the colon, but its use can be limited by side effects. Ipsalazide and balsalazide are novel sulfasalazine analogs designed to release 5-aminosalicylic acid and a nontoxic carrier molecule in the gastrointestinal tract. They have a low oral toxicity following single or repeat administration to mouse, rat, and ferret, and balsalazide is not mutagenic in the Ames test. Ipsalazide and balsalazide are split in rat and man, and the urinary and fecal excretion pattern of the 5-aminosalicylic acid released is similar to that of sulfasalazine; the carrier molecules are absorbed to a lesser extent than the sulfapyridine derived from sulfasalazine. These two analogs deserve therapeutic trial.
Variability in Treatment of Post-coarctectomy Hypertension: A Multicenter Study

Many pharmacologic therapies are available for treatment of post-coarctectomy hypertension in pediatric patients, which may lead to variability in care. Evaluation of trends in pharmacotherapy is necessary to evaluate quality of care. The Pediatric Health Information System database was queried from 2004 to 2013 for patients >30 days of age who had an ICD-9 code for coarctation of the aorta repair of coarctation by end-to-end anastomosis and had a RACHS-1 score of 2. Patients were excluded if they were admitted for >30 days, underwent mechanical circulatory support, or expired during the admission. Patient demographic and hospital data were collected along with antihypertensive pharmacotherapy. Trends in antihypertensive, analgesic, and sedative pharmacotherapy were evaluated, and multivariable statistical analysis was used to determine variables that significantly influenced cost. A total of 1636 patients [66.6 % male, median age 1.5 years (IQR 0.31–5.3)] met study criteria. Patients received a median of 3 (IQR 2–4) antihypertensive medications for a median of 8 days (IQR 5–11). Intravenous antihypertensive therapy was prescribed for a median 3 days (IQR 2–5) and oral therapy for a median of 1 day (IQR 1–2). Antihypertensive therapy was continued at discharge in 79.8 % of patients. Hospital cost increased by 36 % over the study period (p < 0.01), and nicardipine, dexmedetomidine, and intravenous acetaminophen were most strongly associated with increased cost (p < 0.001). Variability in the pharmacotherapy of post-coarctectomy hypertension in pediatric patients exists, and the use of newer agents may be influencing the cost of care.