nils-herrmann/clean_scirepeval huggingface dataset:
A prospective multiple case study of the impact of emerging scientific evidence on established colorectal cancer screening programs: a study protocol

Health-policy decision making is a complex and dynamic process, for which strong evidentiary support is required. This includes scientifically produced research, as well as information that relates to the context in which the decision takes place. Unlike scientific evidence, this "contextual evidence" is highly variable and often includes information that is not scientifically produced, drawn from sources such as political judgement, program management experience and knowledge, or public values. As the policy decision-making process is variable and difficult to evaluate, it is often unclear how this heterogeneous evidence is identified and incorporated into "evidence-based policy" decisions. Population-based colorectal cancer screening poses an ideal context in which to examine these issues. In Canada, colorectal cancer screening programs have been established in several provinces over the past five years, based on the fecal occult blood test (FOBT) or the fecal immunochemical test. However, as these programs develop, new scientific evidence for screening continues to emerge. Recently published randomized controlled trials suggest that the use of flexible sigmoidoscopy for population-based screening may pose a greater reduction in mortality than the FOBT. This raises the important question of how policy makers will address this evidence, given that screening programs are being established or are already in place. This study will examine these issues prospectively and will focus on how policy makers monitor emerging scientific evidence and how both scientific and contextual evidence are identified and applied for decisions about health system improvement.



This study will employ a prospective multiple case study design, involving participants from Ontario, Alberta, Manitoba, Nova Scotia, and Quebec. In each province, data will be collected via document analysis and key informant interviews. Documents will include policy briefs, reports, meeting minutes, media releases, and correspondence. Interviews will be conducted in person with senior administrative leaders, government officials, screening experts, and high-level cancer system stakeholders.



The proposed study comprises the third and final phase of an Emerging Team grant to address the challenges of health-policy decision making and colorectal cancer screening decisions in Canada. This study will contribute a unique prospective look at how policy makers address new, emerging scientific evidence in several different policy environments and at different stages of program planning and implementation. Findings will provide important insight into the various approaches that are or should be used to monitor emerging evidence, the relative importance of scientific versus contextual evidence for decision making, and the tools and processes that may be important to support challenging health-policy decisions.
How Varroa Parasitism Affects the Immunological and Nutritional Status of the Honey Bee, Apis mellifera

We investigated the effect of the parasitic mite Varroa destructor on the immunological and nutritional condition of honey bees, Apis mellifera, from the perspective of the individual bee and the colony. Pupae, newly-emerged adults and foraging adults were sampled from honey bee colonies at one site in S. Texas, USA. Varroa‑infested bees displayed elevated titer of Deformed Wing Virus (DWV), suggestive of depressed capacity to limit viral replication. Expression of genes coding three anti-microbial peptides (defensin1, abaecin, hymenoptaecin) was either not significantly different between Varroa-infested and uninfested bees or was significantly elevated in Varroa-infested bees, varying with sampling date and bee developmental age. The effect of Varroa on nutritional indices of the bees was complex, with protein, triglyceride, glycogen and sugar levels strongly influenced by life-stage of the bee and individual colony. Protein content was depressed and free amino acid content elevated in Varroa-infested pupae, suggesting that protein synthesis, and consequently growth, may be limited in these insects. No simple relationship between the values of nutritional and immune-related indices was observed, and colony-scale effects were indicated by the reduced weight of pupae in colonies with high Varroa abundance, irrespective of whether the individual pupa bore Varroa.
An expert-supported monitoring system for patients with chronic obstructive pulmonary disease in general practice: results of a cluster randomised controlled trial.

To investigate the long-term effectiveness of a general practice monitoring system with respiratory expert recommendations for general practitioners' management of patients with chronic obstructive pulmonary disease (COPD), compared with usual care.



A multicentre randomised controlled trial of patients with COPD, clustered by general practices; 200 participants were recruited to maintain at least 75 participants per group for analysis. The trial took place from July 2005 to February 2008 in the south-western region of the Netherlands.



Ongoing half-yearly monitoring of COPD patients with respiratory expert recommendations for the GP was compared with usual care.



Primary outcome - Chronic Respiratory Questionnaire (CRQ) score; secondary outcomes - CRQ domain scores, generic health-related quality of life (Short-Form 12 and EuroQol-5D), breathlessness (Modified Medical Research Council score), exacerbations, and decline in forced expiratory volume in 1 second. A detailed process evaluation was performed along with the trial.



Data from 170 participants were analysed. Based on repeated measurement analyses, the additional gain in CRQ score during follow-up was 0.004 points for monitoring compared with usual care (95% CI, - 0.172 to 0.180). Also, no important differences between monitoring and the usual care group were found for secondary outcomes. Half the monitoring visits resulted in disease management recommendations by a respiratory expert, and 46% of these recommendations were implemented by the GPs. Patient adherence to lifestyle recommendations was low.



An expert-supported monitoring system for patients with COPD was not clinically effective. As patients had a pre-existing entry in the monitoring system, the population may be well regulated, with reduced room for improvement.
Twice daily beclomethasone dipropionate administered with a concentrated aerosol inhaler: efficacy and patient compliance.

The efficacy of twice daily inhaled beclomethasone dipropionate administered by a concentrated aerosol inhaler (one puff twice daily-500 micrograms/day) has been compared with that of treatment four times daily with a standard dose inhaler (two puffs four times daily-400 micrograms/day) in 21 patients with stable asthma. Double placebo inhalers were used in a randomised crossover fashion during two four week treatment periods. Mean peak expiratory flow (PEF), mean symptom scores, and number of extra salbutamol inhalations required were not significantly different between the two treatment periods. Local side effects were more common during treatment with the four times daily active preparation; overt oropharyngeal candidiasis, however, was not found in either group during the study. On completion of the crossover study patients were transferred to the twice daily regimen. At the three month follow up all patients had remained stable and the outpatient PEF was significantly higher (mean 382 (SD 26)l min-1) than at entry into the trial (mean 345 (24)l min-1) (p less than 0.05). Twice daily beclomethasone administered by a concentrated aerosol inhaler appears to be as effective as the standard four times daily regimen in controlling stable asthma.
Cefadroxil Compared with Cefaclor in the Treatment of Streptococcal Pneumonia in Adults

103 young male Black African gold-miners with pneumococcal pneumonia confirmed by culture or serology were randomly assigned to receive the long acting oral cephalosporin cefadroxil 1g every 12 hours or cefaclor 500mg every 8 hours for 10 days. Clinical cures were obtained in 94% of the group who received cefadroxil and in 94% of the cefaclor group. Similarly, the causative organism S. pneumoniae was eradicated in 98% and 96% of patients who received cefadroxil and cefaclor, respectively. Minimal side effects occurred in both groups, although 1 patient withdrew from therapy with cefaclor because of severe diarrhoea. Thus, cefadroxil and cefaclor both displayed effective antimicrobial activity with low toxicity in the treatment of pneumococcal pneumonia.
How musical expertise shapes speech perception: evidence from auditory classification images

It is now well established that extensive musical training percolates to higher levels of cognition, such as speech processing. However, the lack of a precise technique to investigate the specific listening strategy involved in speech comprehension has made it difficult to determine how musicians' higher performance in non-speech tasks contributes to their enhanced speech comprehension. The recently developed Auditory Classification Image approach reveals the precise time-frequency regions used by participants when performing phonemic categorizations in noise. Here we used this technique on 19 non-musicians and 19 professional musicians. We found that both groups used very similar listening strategies, but the musicians relied more heavily on the two main acoustic cues, at the first formant onset and at the onsets of the second and third formants onsets. Additionally, they responded more consistently to stimuli. These observations provide a direct visualization of auditory plasticity resulting from extensive musical training and shed light on the level of functional transfer between auditory processing and speech perception.
Evaluation of inter-fraction and intra-fraction errors during volumetric modulated arc therapy in nasopharyngeal carcinoma patients

This prospective study was conducted to evaluate inter- and intra-fraction errors in nasopharyngeal carcinoma (NPC) patients undergoing volumetric modulated arc therapy (VMAT) using cone-beam computed tomography (CBCT) and to thus obtain planning target volume (PTV) margins to effectively guide treatment in the future.



Fifteen NPC patients scheduled to undergo VMAT were prospectively enrolled in the study. For each patient, three CBCT scans were obtained; one after daily conventional positioning, one after online correction with 2 mm tolerance and one after 1 week of VMAT delivery. The scans were registered to the planning CT to determine the inter- and intra-fraction errors. Patient positioning errors were analyzed for time trends over the course of radiotherapy. PTV margins were calculated from the systematic (Σ) and random (σ) errors.



The average absolute values of the pre-correction, post-correction and intra-fraction errors (in order) were 1.1, 0.6 and 0.4 mm in the medial-lateral (ML) direction, 1.2, 0.7 and 0.5 mm in the superior-inferior (SI) direction and 1.1, 0.7 and 0.5 mm in the anterior-posterior (AP) direction. The corresponding Σ were 1.0-1.4 mm, 0.4-0.5 mm and 0.2-0.4 mm, while the corresponding σ were 0.7-0.8 mm, 0.6-0.7 mm and 0.5-0.6 mm. With time, gradual increases in both the inter- and intra-fraction three-dimensional displacements were observed (P = 0.019 and P = 0.044, respectively). The total PTV margins accounting for pre-correction and intra-fraction errors were 3.4-4.1 mm and those accounting for post-correction and intra-fraction errors were 1.7-2.2 mm.



CBCT is an effective modality to evaluate and improve the accuracy of VMAT in NPC patients. Inter- and intra-fraction three-dimensional displacements increased as a function of time during the course of radiotherapy. In our institution, we recommend a PTV margin of 5 mm for NPC patients undergoing VMAT without CBCT and 3 mm for those treated with rigorous daily CBCT scans.
Prevention of restenosis by a novel drug-eluting stent system with a dose-adjustable, polymer-free, on-site stent coating.

Drug-eluting stents (DES) represent a major advance in interventional cardiology. Along with the success shown, current DES also present limitations related to the presence of polymer-coating, fixed drug, and dose used. With the ISAR (Individualized Drug-Eluting Stent System to Abrogate Restenosis) project, a DES system has been developed that permits individualized choice of the drug and dose to use for the given patient. The objective of this prospective dose finding study was to assess the feasibility, safety, and efficacy of a polymer-free on-site stent coating with increasing rapamycin doses.



In this dose finding study, 602 patients were sequentially enrolled in four groups: microporous bare metal stent (BMS), DES stents coated with a 0.5, 1.0, and 2.0% rapamycin solution. The angiographic in-segment restenosis rate at follow-up angiography was the primary study endpoint. In-segment restenosis was significantly reduced from 25.9% with BMS to 18.9, 17.2, and 14.7% with 0.5, 1.0, and 2.0% rapamycin-eluting stents, respectively (P=0.024). Similarly, the need for target lesion revascularization at 1 year follow-up was reduced from 21.5% with BMS to 16.4, 12.6, and 8.8% with 0.5, 1.0, and 2.0% rapamycin-eluting stents, respectively (P=0.006).



The placement of polymer-free stents coated on-site with rapamycin is feasible and safe. Furthermore, a dose-dependent efficacy in restenosis prevention is achievable with this new DES concept.
Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer.

Panitumumab, a fully human antibody against the epidermal growth factor receptor (EGFR), has activity in a subset of patients with metastatic colorectal cancer (mCRC). Although activating mutations in KRAS, a small G-protein downstream of EGFR, correlate with poor response to anti-EGFR antibodies in mCRC, their role as a selection marker has not been established in randomized trials.



KRAS mutations were detected using polymerase chain reaction on DNA from tumor sections collected in a phase III mCRC trial comparing panitumumab monotherapy to best supportive care (BSC). We tested whether the effect of panitumumab on progression-free survival (PFS) differed by KRAS status.



KRAS status was ascertained in 427 (92%) of 463 patients (208 panitumumab, 219 BSC). KRAS mutations were found in 43% of patients. The treatment effect on PFS in the wild-type (WT) KRAS group (hazard ratio [HR], 0.45; 95% CI: 0.34 to 0.59) was significantly greater (P < .0001) than in the mutant group (HR, 0.99; 95% CI, 0.73 to 1.36). Median PFS in the WT KRAS group was 12.3 weeks for panitumumab and 7.3 weeks for BSC. Response rates to panitumumab were 17% and 0%, for the WT and mutant groups, respectively. WT KRAS patients had longer overall survival (HR, 0.67; 95% CI, 0.55 to 0.82; treatment arms combined). Consistent with longer exposure, more grade III treatment-related toxicities occurred in the WT KRAS group. No significant differences in toxicity were observed between the WT KRAS group and the overall population.



Panitumumab monotherapy efficacy in mCRC is confined to patients with WT KRAS tumors. KRAS status should be considered in selecting patients with mCRC as candidates for panitumumab monotherapy.
[Exclusive enteral nutrition continues to be first line therapy for pediatric Crohn's disease in the era of biologics].

Exclusive enteral nutrition (EEN) has been to be more effective than corticosteroids in achieving mucosal healing without their side effects.



To determine the efficacy of EEN in terms of inducing clinical remission in newly diagnosed CD children and to study the efficacy of this therapeutic approach in improving the degree of intestinal mucosa inflammation.



The medical records of patients with newly diagnosed Crohn's disease treated with EEN were reviewed retrospectively. The degree of mucosal inflammation was assessed by fecal calprotectin (FC). Remission was defined as a PCDAI<10.



Forty patients (24 males) were included, the age at diagnosis was 11.6 ± 3.6 years. Of the 34 patients who completed the EEN period, 32 (94% per-protocol analysis) achieved clinical remission. This percentage fell to 80% in the intention-to-treat analysis. The compliance rate was 95%. Duration of EEN was 6.42 weeks (IQR 6.0-8.14). FC was significantly higher in patients with moderate and severe disease. Median baseline FC levels (680 μg/g) decreased significantly to 218 μg/g (P<0.0001) after EEN. We found a statistically significant correlation between FC and PCDAI (rho=0.727; P<0.0001). Early use of thiopurines (< 8 weeks) versus subsequent use was not associated with improved outcomes during the follow-up.



EEN administered for 6-8 weeks is effective for inducing clinical remission and decreasing the degree of mucosal inflammation. We did not find differences in terms of maintenance of remission in patients treated early with thiopurines.
Validation of the seventh edition of the American Joint Committee on Cancer TNM staging system for gastric cancer.

The seventh edition of the American Joint Committee on Cancer (AJCC) TNM classification for gastric cancer was published in 2010 and included major revisions. The aim of the current study was to evaluate the validity of the seventh edition TNM classification for gastric cancer based on an Asian population.



A total of 2916 gastric cancer patients who underwent R0 surgical resection from 1989 through 2008 in a single institute were included, and were analyzed according to the seventh edition of the TNM classification for validation.



When adjusted using the seventh edition of the TNM classification, upstaging was observed in 771 patients (26.4%) and downstaging was observed in 178 patients (6.1%) compared with the sixth edition of the TNM classification. The relative risk (RR) of seventh edition pT classification was found to be increased with regular intensity compared with the sixth edition pT classification. The RR of seventh edition pN classification was found to be increased with irregular intensity compared with the sixth edition pN classification. In survival analysis, there were significant differences noted for each stage of disease, but only a marginal difference was demonstrated between stage IA and stage IB (P = .049). In the hybrid TNM classification, which combines the seventh edition pT classification and the sixth edition pN classification, both pT and pN classifications demonstrated a more ideal distribution of the RR, and 5-year survival rates also showed a significant difference for each stage (P <.01).



The seventh edition of the TNM classification was considered valid based on the results of the current study. However, the hybrid TNM classification, comprised of a combination of the seventh edition pT classification and sixth edition pN classification, should be considered for the next edition.
Characterization of Circulating and Endothelial Progenitor Cells in Patients With Extreme-Duration Type 1 Diabetes

We characterized and correlated endothelial progenitor cells (EPCs) and circulating progenitor cells (CPCs) with lack of vascular complications in the Joslin Medalist Study in patients with type 1 diabetes for 50 years or longer.



EPC and CPC levels were ascertained by flow cytometry and compared among Medalists (n = 172) with or without diabetic retinopathy (DR; n = 84 of 162), neuropathy (n = 94 of 165), diabetic nephropathy (DN; n = 18 of 172), cardiovascular disease (CVD; n = 63 of 168), age-matched controls (n = 83), type 2 diabetic patients (n = 36), and younger type 1 diabetic patients (n = 31). Mitogens, inflammatory cytokines, and oxidative markers were measured in blood or urine. Migration of cultured peripheral blood mononuclear cells (PBMCs) from Medalists and age-matched controls were compared.



Medalists' EPC and CPC levels equaled those of their nondiabetic age-matched controls, were 10% higher than those in younger type 1 diabetic patients, and were 20% higher than those in age-matched type 2 diabetic patients. CPC levels were 15% higher in Medalists without CVD and nephropathy than in those affected, whereas EPC levels were significantly higher in those without peripheral vascular disease (PVD) than those with PVD. Stromal-derived factor 1 (SDF-1) levels were higher in Medalists with CVD, DN, and DR than in those not affected and their controls. IGF-I levels were lower in Medalists and correlated inversely with CPC levels. Additionally, cultured PBMCs from Medalists migrated more than those from nondiabetic controls.



Normal levels of EPC and CPC in the Medalists, unlike other groups with diabetes, especially those without CVD, support the idea that endogenous factors exist to neutralize the adverse effects of metabolic abnormalities of diabetes on vascular tissues.
Beneficial effect of high-dose chemotherapy in multiple myeloma patients with unfavorable prognostic features.

It has been established that high-dose chemotherapy (HDT) improves the therapeutic outcome of patients with multiple myeloma (MM) as compared with standard-dose therapy (SDT); however, little is known about the impact of HDT on different prognostic groups of MM patients. We therefore compared the survival times of 77 patients with previously untreated MM who were enrolled in HDT regimens with those of 64 similar patients <65 years old, who would be eligible for HDT but were treated by SDT. Overall, HDT was superior to SDT with respect to achievement of complete remissions (28% versus 2%; P <0.0001) and improvement of progression-free survival (PFS) (30.2 versus 21.2 months; P = 0.01) as well as overall survival (OS) (median 54.9 versus 49.4 months; P = 0.048). According to the chromosome 13q14 status as determined by fluorescence in situ hybridization and serum levels of beta(2)-microglobulin (beta(2)M), MM patients were separated into a standard-risk group (normal chromosome 13q14 and beta(2)M </=4 mg/l) and a high-risk group (deletion of chromosome 13q14 and/or beta(2)M >4 mg/l). Among patients of the high-risk group, both PFS (26.4 versus 10.7 months; P = 0.004) and OS times (40 versus 23 months; P = 0.05) were longer in patients receiving HDT compared with patients treated by SDT. In the standard-risk group, PFS and OS times were not significantly different between HDT patients and SDT patients. Results of this retrospective analysis suggest that the beneficial effects of HDT are greater in MM patients with high-risk features than in patients with absence of such poor prognostic indicators.