nils-herrmann/clean_scirepeval huggingface dataset:
Urban air pollution and emergency admissions for asthma in four European cities: the APHEA Project.

A study was undertaken to assess the combined association between urban air pollution and emergency admissions for asthma during the years 1986-92 in Barcelona, Helsinki, Paris and London.



Daily counts were made of asthma admissions and visits to the emergency room in adults (age range 15-64 years) and children (< 15 years). Covariates were short term fluctuations in temperature and humidity, viral epidemics, day of the week effects, and seasonal and secular trends. Estimates from all the cities were obtained for the entire period and separately by warm or cold seasons using Poisson time-series regression models. Combined associations were estimated using meta-analysis techniques.



Daily admissions for asthma in adults increased significantly with increasing ambient levels of nitrogen dioxide (NO2) (relative risk (RR) per 50 micrograms/m3 increase 1.029, 95% CI 1.003 to 1.055) and non-significantly with particles measured as black smoke (RR 1.021, 95% CI 0.985 to 1.059). The association between asthma admissions and ozone (O3) was heterogeneous among cities. In children, daily admissions increased significantly with sulphur dioxide (SO2) (RR 1.075, 95% CI 1.026 to 1.126) and non-significantly with black smoke (RR 1.030, 95% CI 0.979 to 1.084) and NO2, though the latter only in cold seasons (RR 1.080, 95% CI 1.025 to 1.140). No association was observed for O3. The associations between asthma admissions and NO2 in adults and SO2 in children were independent of black smoke.



The evidence of an association between air pollution at current urban levels and emergency room visits for asthma has been extended to Europe. In addition to particles, NO2 and SO2--by themselves or as a constituent of a pollution mixture--may be important in asthma exacerbations in European cities.
Molecular characterisation of formalin-fixed paraffin-embedded (FFPE) breast tumour specimens using a custom 512-gene breast cancer bead array-based platform

Formalin-fixed, paraffin-embedded (FFPE) tumour tissue represents an immense but mainly untapped resource with respect to molecular profiling. The DASL (cDNA-mediated Annealing, Selection, extension, and Ligation) assay is a recently described, RT–PCR-based, highly multiplexed high-throughput gene expression platform developed by Illumina specifically for fragmented RNA typically obtained from FFPE specimens, which enables expression profiling. In order to extend the utility of the DASL assay for breast cancer, we have custom designed and validated a 512-gene human breast cancer panel.The RNA from FFPE breast tumour specimens were analysed using the DASL assay. Breast cancer subtype was defined from pathology immunohistochemical (IHC) staining. Differentially expressed genes between the IHC-defined subtypes were assessed by prediction analysis of microarrays (PAM) and then used in the analysis of two published data sets with clinical outcome data.Gene expression signatures on our custom breast cancer panel were very reproducible between replicates (average Pearson's R2=0.962) and the 152 genes common to both the standard cancer DASL panel (Illumina) and our breast cancer DASL panel were similarly expressed for samples run on both panels (average R2=0.877). Moreover, expression of ESR1, PGR and ERBB2 corresponded well with their respective pathology-defined IHC status. A 30-gene set indicative of IHC-defined breast cancer subtypes was found to segregate samples based on their subtype in our data sets and published data sets. Furthermore, several of these genes were significantly associated with overall survival (OS) and relapse-free survival (RFS) in these previously published data sets, indicating that they are biomarkers of the different breast cancer subtypes and the prognostic outcomes associated with these subtypes.We have demonstrated the ability to expression profile degraded RNA transcripts derived from FFPE tissues on the DASL platform. Importantly, we have identified a 30-biomarker gene set that can classify breast cancer into subtypes and have shown that a subset of these markers is prognostic of OS and RFS.
On authentication factors: "what you can" and "how you do it"

In this paper, we discuss "alternatives" or derivations to the three well known authentication factors: "what you know" (passwords, ...), "what you own" (id-cards, ...), "what you are" (biometrics, ...). We discuss and propose the factors "what you can do" and "how you do it" (mind biometric with behavioral approach). Inspired by statistical learning models, we propose a formal model for these two alternatives and describe a challenge response protocol based on these two factors. We illustrate the potential of the protocol with games unused for such purpose until now and discuss the advantages and drawbacks of our proposal compared to usual implementations of the three well known factors and also how they could complement each other.
Comparative effect of disopyramide and ethmozine in suppressing complex ventricular arrhythmias by use of a double-blind, placebo-controlled, longitudinal crossover design.

This placebo-controlled, double-blind, longitudinal crossover study compares the efficacy of disopyramide and ethmozine, a new investigational drug, in suppressing frequent (40 or more per hour) ventricular premature depolarizations (VPDs) in 27 patients completing a 37 day protocol. Although both drugs significantly reduced VPDs relative to placebo, ethmozine was a superior antiarrhythmic drug in ach9eving near-total abolition of VPDs (30% of patients), which was never observed during disopyramide dosing (p less than .05). At the 80% VPD reduction level, ethmozine was effective in 56% of all patients compared with an effectiveness in only 22% of patients during disopyramide therapy (p less than .05). The mean peak plasma level of ethmozine was 0.66 +/- 0.8 micrograms/ml, which significantly fell to a trough level of 0.1 +/- 0.08 micrograms/ml (p less than .001). Mean peak and trough plasma levels of disopyramide exhibited less fluctuation (2.6 +/- 0.9 micrograms/ml vs 2.2 +/- 0.9 micrograms/ml). Ethmozine had no effect on the QT interval, whereas disopyramide prolonged it significantly. Importantly, while disopyramide produced serious side effects in 30% of patients, ethmozine was well tolerated with no statistically significant side effects compared with placebo.
The treatment of advanced chronic lower limb ischaemia with marrow stem cell autotransplantation.

Conventional methods of critical leg ischaemia treatment are of limited efficacy. Amputation, as an ultimate solution, is not so rare. The results of marrow stem cell therapy as a potential novel approach to peripheral artery disease management were presented in 2002 by Tateishi-Yuyamy.



To assess efficacy and safety of critical lower limb ischaemia treatment with marrow stem cell autotransplantation.



Ten patients suffering from chronic leg ischaemia in Fontaine IV stadium were involved in the study. They did not require emergency amputation and had previously been unsuccessfully treated with conventional therapy. Autologic marrow stem cells were condensated by a separator from bone marrow samples taken from the iliac crest. The cells were delivered intramuscularly by repeated injections into the pedal and tibial regions. The number of CD34 and AC133 positive mononuclear cells in each sample was evaluated by flow cytometry. After two weeks and one, two, three and twelve months the following parameters were measured: Laser Doppler Flux (LDF), percutaneous oxygen partial pressure, ankle-brachial index (ABI), visual analgesic scale (VAS), analgesic therapy requirement and ulceration area. Also, lower leg angiography and scintigraphy were performed.



An improvement of the peripheral blood flow assessed by Laser Doppler Flux and percutaneous oxygen partial pressure was found. Pain severity decreased in the majority of patients. Amputation was required in three patients in whom the therapy failed. No side effects of the therapy were observed. The clinical effect of the treatment did not correlate with the amount of cells injected.



Marrow stem cell autotransplantation into the ischaemic lower limb seems to be a potentially effective method of peripheral perfusion enhancement. Further studies are needed to clarify the underlying mechanisms of such improvement.
Collagen plug vascular closure devices and reduced risk of bleeding with bivalirudin versus heparin plus abciximab in patients undergoing percutaneous coronary intervention for non st-segment elevation myocardial infarction.

In ISAR-REACT-4 (abciximab and heparin vs. bivalirudin for non-ST-elevation myocardial infarction [NSTEMI]), bivalirudin reduced the risk of bleeding after percutaneous coronary intervention (PCI) compared with unfractionated heparin plus abciximab (UFH + abciximab). Vascular closure devices (VCDs) may also prevent bleeding complications, and thus attenuate the benefit of bivalirudin. This analysis examined whether there exists an interaction on bleeding between VCDs and bivalirudin versus UFH + abciximab after PCI.



Patients with NSTEMI were randomly assigned to either receive UFH + abciximab or bivalirudin for PCI. The use of a VCD after femoral access was left to the operator's discretion. The effect of randomized treatment in patients who received a VCD was compared to that in patients with manual compression of the femoral access site. The primary end-point of this analysis was the 30-day incidence of ISAR-REACT-4 major bleeding.



A total of 1,711 patients were enrolled in this analysis. Among the 365 (21.3%) patients receiving a VCD, 188 (51.5%) were treated with UFH + abciximab and 177 (48.5%) with bivalirudin. ISAR- REACT-4 major bleeding was higher with UFH + abciximab than with bivalirudin, independent of whether a VCD was used (4.8% vs. 2.3% with VCD and 4.6% vs. 2.7% without VCD, Pint = 0.76). There were also no interactions between randomized treatment and VCDs with respect to any of the ischemic end-points or net clinical outcome (Pint > 0.56).



In patients undergoing PCI for NSTEMI, the reduction of major bleeding by bivalirudin compared with UFH + abciximab was not affected whether a VCD was used.
Efficacy of ⁹⁰Yttrium-ibritumomab tiuxetan in relapsed/refractory extranodal marginal-zone lymphoma.

We evaluated clinical activity of ⁹⁰Yttrium-ibritumomab (⁹⁰Y-ibritumomab) tiuxetan in extranodal marginal-zone lymphoma. From May 2004 to April 2011, 30 patients affected by relapsed/refractory marginal-zone lymphoma--arisen at any extranodal site--received ⁹⁰Y-ibritumomab tiuxetan at the activity of 0.4 mCi/kg. Median age was 57 years. At time of treatment, 13 out of 30 patients had disseminated disease (stage III/IV). All patients had received a previous treatment with a maximum of 7. Overall response rate was 90%: 23 patients achieved a complete response (77%); partial response occurred in 4 patients (13%), stable disease in 2 patients (7%) and 1 progression (3%). With a median follow-up of 5.3 years, median time to relapse was not reached; 2 patients relapsed after complete response; 18 out of 23 complete responses are still responders after >3 years, 12 of them after >5 years. ⁹⁰Y-ibritumomab tiuxetan seems to be active in patients with extranodal marginal-zone lymphoma relapsed/refractory to conventional treatment including radiotherapy. These results suggest that radioimmunotherapy could represent a possible option for the treatment in this subset of patients.
Influence of rhTSH on [18F]fluorodeoxyglucose uptake by differentiated thyroid carcinoma

The influence of serum TSH levels on fluorine-18 fluorodeoxyglucose (FDG) uptake by recurrences or metastases of differentiated thyroid carcinomas has not yet been clarified. The aim of this study was to ascertain whether the administration of recombinant human thyrotropin (rhTSH) stimulates FDG uptake by such lesions. In this prospective study, 30 patients with positive or equivocal thyroglobulin (Tg) levels and negative or equivocal iodine-131 and/or morphological imaging results (ultrasound, MRI, CT) underwent FDG positron emission tomography (PET) under exogenous TSH suppression and under exogenous TSH stimulation of serum levels by injection of rhTSH. The mean interval between the FDG-PET studies under these two conditions was 9.3±8.8 weeks. Serum TSH levels and free thyroid hormones were determined on each occasion. FDG uptake was quantitated using tumour to background ratios (TBRs) and standardised uptake values (SUVs). Under TSH suppression there was focal FDG accumulation in nine subjects (22 tumour-like lesions). The total number of foci was 45. After exogenous TSH stimulation, the number of patients in whom FDG foci were detected was 19, and the number of foci identified was 82 (78 tumour-like lesions). TBR of regions showing positive FDG contrast with either of the modalities averaged 2.54±1.89, and under stimulated TSH levels, 5.51±2.99 (P<0.0001). Corresponding SUVs were 2.05±1.45 versus 2.77±1.58 (P<0.001). In a small number (n=4) of foci related to inflammatory lymph nodes, TBR and SUV were only marginally increased under TSH stimulation (2.01±0.38 and 1.07±0.38, respectively), and the values did not differ significantly from those obtained under suppression. These results provide the first direct evidence that TSH stimulates FDG uptake by differentiated thyroid carcinoma and that, therefore, FDG-PET is more accurate under rhTSH than under suppression.
A randomized controlled trial of the effect of standardized patient scenarios on dental hygiene students' confidence in providing tobacco dependence counseling.

Dental hygienists report a lack of confidence in initiating Tobacco Dependence Counseling (TDC) with their patients who smoke. The purpose of this study was to determine if the confidence of dental hygiene students in providing TDC can be increased by Standardized Patient (SP) training, and if that confidence can be sustained over time.



This 2-parallel group randomized design was used to compare the confidence of students receiving SP training to stu dents with no SP training. After a classroom lecture, all subjects (n=27) received a baseline test of knowledge and confidence. Subjects were randomly assigned to test and control groups with equivalent mean knowledge scores. The test group subjects participated in a SP TDC session. Both groups gained parallel experience to treating patients who were smokers and giving TDC in clinical scenarios during the 6 month time period. One week end-training and 6 month post-training assessments were administered to both groups. ANCOVA compared mean confidence scores.



End-training scores at 1 week showed a statistically significant increase (p=0.002) in overall mean confidence following SP training for individuals in the test group. The 6 month follow-up test results showed a slight decline in confidence scores among subjects in the test group and an overall gain in confidence for control group participants. However, overall confidence scores were comparable for the groups.



SP training improved dental hygiene students' initial confidence in providing TDC and was sustained, but not to a significant degree. Clinical experience alone increased confidence. Further studies may help determine how the initial confidence gained by SP training can be sustained and what the role of clinical experience plays in overall confidence in providing TDC.
Aromatase inhibitors and calcium absorption in early stage breast cancer

To investigate the effect of aromatase inhibitors (AI) on intestinal calcium absorption, measured using the gold-standard dual stable calcium isotope method. In this pilot study, we recruited 10 postmenopausal women with hormone receptor-positive breast cancer who planned to initiate AI therapy; women receiving chemotherapy were excluded. Women completed two 24 h inpatient calcium absorption study visits, the first prior to AI therapy and the second at least 6 weeks following onset of AI therapy. We calculated total fractional calcium absorption (TFCA) using the dose-corrected fractional recovery of two stable isotopes from 24 h urine collections. Ten postmenopausal women (mean ± SD age, 66 ± 7 years; 25(OH)D 40 ± 7 ng/mL, and total calcium intake of 1,714 ± 640 mg/day) exhibited no change in TFCA related to AI therapy (0.155 ± 0.042 prior to and 0.160 ± 0.064 following AI therapy, p = 1.0). Subjects exhibited a surprisingly small decline in serum estradiol levels with AI therapy that was not statistically significant. However, there was a significant correlation between duration of AI therapy and the decline in serum estradiol levels (r = −0.65, p = 0.040). In this pilot study, AI therapy did not decrease TFCA. Women with early stage breast cancer exhibited an unexpectedly low TFCA, most likely due to their high calcium intake. The null effect of AI therapy on TFCA might relate to the brief duration of AI therapy, the minimal effect of AI therapy on estradiol levels, subjects’ high calcium intake or excellent vitamin D status.
A phase II trial of imatinib mesylate in merkel cell carcinoma (neuroendocrine carcinoma of the skin): A Southwest Oncology Group study (S0331).

Imatinib mesylate (Gleevec) was evaluated as a treatment for Merkel cell carcinoma (MCC, neuroendocrine carcinoma of the skin) based on the identification of strong c-KIT staining of these neoplasms.



Eligibility included patients with measurable metastatic or unresectable MCC, c-KIT (CD117) expression and a Zubrod performance status of 0 to 2. Imatinib 400 mg daily was administered orally in 28-day cycles to 23 patients.



Overall, imatinib was well tolerated with grade 1 or 2 nausea, diarrhea, and hematologic toxicity as the most frequent side effects. A partial response was seen in 1 patient (4%; 95% CI: 0%-22%). Median progression-free survival was 1 month (95% CI: 1-2 months). Median overall survival was 5 months (95% CI: 2-8 months). One patient achieved a partial response and another had prolonged disease stabilization while receiving treatment.



The majority of patients progressed rapidly within 1 to 2 cycles of treatment. The observed progression-free survival and overall survival were not adequate to conclude that this agent was active in advanced MCC, and thus the planned second stage of patient accrual was not opened.
Virtual Simulation of a Boost Field in Adjuvant Radiotherapy of the Breast

In CT-based adjuvant radiotherapy of the breast, virtual simulation techniques have been developed. This paper demonstrates a simple virtual simulation of a boost field. 41 fields were planned virtually, 26 as electron beams, 15 as tangential photon beams. Depending on the user’s expertise the geometric accuracy was high; possible sources of error are illustrated. Resulting field sizes tended to be slightly larger compared to conventional simulation when applying the same rules of field definition. Differences in focus-skin distances with consecutive divergence effects as well as partial volume effects were discussed to be causal. Virtual simulation of a boost field has the potential to elegantly link the simplicity of a conventional simulation with the accurate tumor bed identification provided by a CT data set. It was shown to be feasible and favorable with regard to the patient, the medical staff, and the simulator time. Moreover, it offers a visualization of dose distributions, which was found helpful in some cases. Für die CT-geplante adjuvante Strahlentherapie der Brust sind Techniken der virtuellen Simulation entwickelt worden. In dieser Arbeit wird eine einfache virtuelle Simulation eines Boostfeldes demonstriert. 41 Felder wurden virtuell geplant, 26 als Elektronenfelder, 15 als tangentiale Photonenfelder (Abbildung 1). Für erfahrene Anwender war die geometrische Genauigkeit hoch; mögliche Fehlerquellen werden illustriert. Tendenziell waren die resultierenden Felder etwas größer als bei konventioneller Simulation, wenn die gleichen Felddefinitionsregeln angewandt wurden (Tabelle 1).  Fokus-Haut-Abstände mit konsekutiven Divergenzeffekten und Teilvolumeneffekte waren als ursächlich zu diskutieren. Die virtuelle Simulation eines Boostfeldes hat das Potential, die einfache Technik einer konventionellen Simulation mit der Genauigkeit der Tumorbettidentifizierung im CT-Datensatz elegant zu verbinden. Sie erwies sich als einfach zu handhaben und zeitsparend für die Patientin, das beteiligte medizinische Personal sowie die Simulatornutzung (Tabelle 2). Darüber hinaus ermöglichte sie eine Visualisierung der Dosisverteilung, die in einigen Fällen als hilfreich empfunden wurde (Abbildung 2).
Conventional monotherapy compared to a "sawtooth" treatment strategy in the radiographic progression of rheumatoid arthritis over the first eight years.

To describe the treatment with disease-modifying antirheumatic drugs (DMARDs) in two inception cohorts of rheumatoid arthritis (RA) patients and to compare their radiographic outcomes.



A recent onset RA cohort was collected in Heinola in 1973-1975, and another in Jyväskylä in 1983-1989. The cohorts were followed up prospectively and treated with available DMARDs. The radiographic outcomes of 103 and 85 seropositive cohort patients from Heinola and Jyväskylä respectively were assigned Larsen scores (0-100) for their wrist, hand and foot radiographs in years 0, 1, 3, and 8, and compared with each other.



In this study it was seen that DMARD treatment for RA became more extensive over time. The earlier cohort patients were treated with gold sodium thiomalate, chloroquine and D-penicillamine, while 8 additional DMARDs and various DMARD combinations were used for the later cohort patients. At the 8 year visit, 23%, 33%, and 2% of the Heinola patients, and 6%, 45%, and 21% of the Jyväskylä patients respectively were being treated with chloroquine, other single DMARDs, or DMARD combinations. Destruction in the peripheral joints remained lower in the more extensively treated cohort; from 0 to 8 years the median Larsen score increased from 1 to 25.5 and from 0 to 12 (p = 0.001) for the Heinola and the Jyväskylä patients, respectively.



Our result supports a role of DMARDs in preventing joint destruction in RA in the long-term.