nils-herrmann/clean_scirepeval huggingface dataset:
Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue

Next generation sequencing (NGS) technologies have revolutionized cancer research allowing the comprehensive study of cancer using high throughput deep sequencing methodologies. These methods detect genomic alterations, nucleotide substitutions, insertions, deletions and copy number alterations. SOLiD (Sequencing by Oligonucleotide Ligation and Detection, Life Technologies) is a promising technology generating billions of 50 bp sequencing reads. This robust technique, successfully applied in gene identification, might be helpful in detecting novel genes associated with cancer initiation and progression using formalin fixed paraffin embedded (FFPE) tissue. This study's aim was to compare the validity of whole exome sequencing of fresh-frozen vs. FFPE tumor tissue by normalization to normal prostatic FFPE tissue, obtained from the same patient. One primary fresh-frozen sample, corresponding FFPE prostate cancer sample and matched adjacent normal prostatic tissue was subjected to exome sequencing. The sequenced reads were mapped and compared. Our study was the first to show comparable exome sequencing results between FFPE and corresponding fresh-frozen cancer tissues using SOLiD sequencing. A prior study has been conducted comparing the validity of sequencing of FFPE vs. fresh frozen samples using other NGS platforms. Our validation further proves that FFPE material is a reliable source of material for whole exome sequencing.
Assessment of use of specific features of subcutaneous insulin infusion systems and their relationship to metabolic control in patients with type 1 diabetes.

Patients with type 1 diabetes (T1DM) treated with continuous subcutaneous insulin infusion (CSII) have available several specific features of these devices. The aim of this study was to evaluate the relationship between real use of them and the degree of glycemic control in patients using this therapy.



Forty-four T1DM patients on CSII therapy with or without real-time continuous glucose monitoring (CGM) were included. Data from 14 consecutive days were retrospectively collected using the therapy management software CareLink Personal/Pro(®) and HbA1c measurement performed at that period. The relationship between the frequency of usie of specific features of insulin pumps (non-sensor augmented or sensor-augmented) and glycemic control was analyzed.



Mean HbA1c in the group was 7.5 ± .8%. Mean daily number of boluses administered was 5.1 ± 1.8, with 75.4% of them being bolus wizards (BW). Daily number of boluses was significantly greater in patients with HbA1c <7.5% than in those with HbA1c>7.5% (5.3 ± 1.6 vs. 4.3 ± 1.6, P=.056). There was a trend to greater use of BW in patients with better control (82.8 ± 21.4% vs. 69.9 ± 29.1%, P=.106). HbA1c was lower in patients using CGM (n=8) as compared to those not using sensor-augmented pumps (7.6 ± .8 vs 7.1 ± .7, P=.067), but the difference was not statistically significant.



More frequent use of BW appears to be associated to better metabolic control in patients with T1DM using pump therapy. In standard clinical practice, augmentation of insulin pump with CGM may be associated to improved glycemic control.
Randomized controlled trial of an early discharge rehabilitation service: the Belfast Community Stroke Trial.

To compare a community-based multidisciplinary stroke team (CST) approach with hospital-based rehabilitation in terms of hospital stay, functioning, quality of life, and service use and costs.



Stroke patients who met pre-agreed criteria were allocated randomly to the CST service (n=59) or to usual inpatient rehabilitation and follow-up care (n=54). Assessments were completed at randomization and 12 months later. Caregiver strain and satisfaction (n=55) were also assessed. Cost data were collected for a subsample of 38 patients.



Almost 80% of surviving patients (n=691) were discharged home and a small number (n=55) were readmitted. Approximately 17% (113/649) were randomized. There were no statistically significant differences in hospital duration, costs, or outcome measures at baseline and 12 months except for higher satisfaction reported by CST patients. Overall, both groups recorded improvement in most domains over time. Carers reported a high level of satisfaction although the level of strain among carers is cause for concern. The community group (n=18) cost less than the hospital group (n=20).



A mixed model of hospital-based and community-based rehabilitation services is likely to lead to increased patient choice and satisfaction and a potential reduction in bed pressures for less severe stroke patients.
Translating the Hemoglobin A1C with More Easily Understood Feedback: A Randomized Controlled Trial

Previous work has indicated that for patients with diabetes, there is value in understanding glycemic control. Despite these findings, patient understanding of the hemoglobin A1C value (A1C) is notably poor. In this study, we test the effect of two alternative communication formats of the A1C on improving glycemic control among patients with poorly controlled diabetes. 177 patients with poorly controlled diabetes were randomized to one of three study arms that varied in the information they received: (1) a “diabetes report card” containing individualized information about glycemic control for each participant with letter grades ranging from A to F; (2) a “report card” containing a face whose emotion reflected current glycemic control; or (3) a “report card” with glycemic control expressed with the A1C value (standard arm). The primary study outcome was change in A1C at 6 months. Secondary outcomes included changes in participant perceptions of their glycemic control. The average A1C for enrolled participants was 9.9 % (S.D. 1.7) and did not differ significantly among study arms. We noted no significant differences in change in A1C at 6 months between the standard and experimental arms. Using multiple imputation to account for missing A1C values, the changes in A1C for the letter grade, face, and standard arms were -0.55 % (-1.15, 0.05), -0.89 % (-1.49, -0.29), and -0.74 % (-1.51, 0.029), respectively (p = 0.67 for control vs. grade, p = 0.76 for control vs. face). Feedback to patients with poorly controlled diabetes in the form of letter grades and faces did not differentially impact glycemic control at 6 months or participant perceptions of current control. These efforts to improve communication and patient understanding of disease management targets need further refinement to significantly impact diabetes outcomes.
Cytokeratin 19-fragments (CYFRA 21-1) as a novel serum biomarker for response and survival in patients with advanced pancreatic cancer

CYFRA 21-1 serves as biomarker in several epithelial malignancies. However, its role in pancreatic cancer (PC) has not yet been investigated.Within a prospective single-centre study serial blood samples were collected from patients with confirmed advanced PC. Pre-treatment values and weekly measurements of CYFRA 21-1, carbohydrate antigen 19-9 (CA 19-9) and carcinoembryonic antigen (assessed by Elecsys 2010, Roche Diagnostics) during palliative first-line chemotherapy were obtained. Biomarker data were correlated with objective response (determined by RECIST) as well as time to progression (TTP) and overall survival (OS) using uni- and multivariate analyses.Seventy-eight patients were included, 45% of these received treatment in prospective clinical trials. Median TTP was 3.9 months, median OS 7.7 months. Pre-treatment CYFRA 21-1 levels were significantly associated with performance status (P=0.0399) and stage of disease (P=0.0001). Marker values before chemotherapy and at the 2-month staging of all three markers were considered significant predictors for objective treatment response. Pre-treatment CYFRA 21-1 levels, as well as CA 19-9 values, could be applied to define subgroups (categorised by tertiles) with a different OS outcome (CYFRA: 14.8 vs 7.1 vs 4.8 months, CA 19-9: 14.2 vs 7.1 vs 5.2 months; P<0.0001). CYFRA 21-1 and CA 19-9 (both as categorised and as continuous variables) showed a highly significant correlation with TTP and OS at nearly all-time points assessed in univariate analysis. In multivariate analysis, only CYFRA 21-1 and performance status were independent predictors for OS.Conclusions:CYFRA 21-1 may serve as a valuable tool for monitoring treatment response and assessing prognosis in advanced PC.
Late vascular response to repeat stenting for in-stent restenosis with and without radiation: an intravascular ultrasound volumetric analysis.

Re-stenting of in-stent restenosis (ISR) improves acute angiographic results.  Results- Volumetric intravascular ultrasound analysis was performed in 70 ISR lesions that received either placebo (n=36) or (192)Ir radiation (n=34). ISR lesions treated by re-stenting were divided into 3 groups: old stent not re-stented (A), old/new stent overlap (B), and new stent only (C). ISR lesions treated without re-stenting were categorized as D. In placebo patients, postintervention lumen volume index (LVI) was significantly greater in re-stented segments B and C than in non-re-stented segment A (P<0.05).At follow-up, however, LVI was similar in all 4 segments secondary to the increased intimal hyperplasia (IH) reaccumulation within the re-stented segments. In patients treated with (192)Ir radiation, LVI was maintained from baseline to follow-up only in non-re-stented segments A and D. Conversely, there was a significant decrease in LVI in re-stented segments B and C (P<0.05). Qualitatively, 79% of patients in the irradiated group had stent struts with undetectable neointimal versus only 27% in the placebo group (P<0.001). Coefficient of variation of IH reaccumulation was greater in re-stented segments of (192)Ir patients (B=57.3% and C=58.9%) than in re-stented segments in placebo patients (B=27.3% and C 26.8%) and non-re-stented segments in irradiated patients.



Additional lumen gain from re-stenting ISR lesions is counteracted by exaggerated neointimal proliferation in placebo patients. Maximum effectiveness and safety of radiation can be achieved for ISR lesions when treated without re-stenting. Thus, regardless of supplementary intravascular brachytherapy, repeat stenting strategies provided little long-term advantage.
Dendritic cell-based vaccination in metastatic melanoma patients: Phase II clinical trial

Metastatic and chemoresistant melanoma can be a good target of immunotherapy             because it is an intractable cancer with a very poor prognosis. Previously, we             tested a dendritic cell (DC)-based phase I vaccine, and confirmed that it was             safe. In the present study, we performed a phase II trial of a DC vaccine for             metastatic melanoma patients with mainly the HLA-A24 genotype, and investigated             the efficacy of the vaccine. Twenty-four patients with metastatic melanoma were             enrolled into a phase II study of DC-based immunotherapy. The group included 19             HLA-A24-positive (A*2402) patients and 3 HLA-A2-positive (A*0201) patients. The             protocol for DC production was similar to that in the phase I trial. Briefly,             a cocktail of 5 melanoma-associated synthetic peptides (gp100, tyrosinase, MAGE-A2,             MAGE-A3 and MART-1 or MAGE‑A1) restricted to HLA-A2 or A24 and KLH were used for             DC pulsing. Finally, DCs were injected subcutaneously (s.c.) into the inguinal             region in the dose range of 1-5x107 per shot. The DC ratio (lin-HLA-DR+) of the             vaccine was 38.1±13.3% and the frequency of CD83+ DCs was 25.7±20.8%. Other parameters             regarding DC processing were not different from phase I. Immune response-related             parameters including the ELISPOT assay, DTH reaction to peptide or KLH, DC injection             numbers were shown to be related to a good prognosis. The ELISPOT reaction was             positive in 75% of the patients vaccinated. The increase of anti-melanoma antigen             antibody titer before vaccination was also shown to be a prognosis factor, but             that post-vaccination was not. Based on immunohistochemical analysis, CD8 and             IL-17 were not involved in the prognosis. Adverse effects of more than grade III             were not seen. Overall survival analysis revealed a significant survival prolongation             effect in DC-given melanoma patients. These results suggest that peptide cocktail-treated             DC vaccines may be a safe and effective therapy against metastatic melanoma in             terms of prolongation of overall survival time.
Reinforced Feedback in Virtual Environment for Rehabilitation of Upper Extremity Dysfunction after Stroke: Preliminary Data from a Randomized Controlled Trial

To study whether the reinforced feedback in virtual environment (RFVE) is more effective than traditional rehabilitation (TR) for the treatment of upper limb motor function after stroke, regardless of stroke etiology (i.e., ischemic, hemorrhagic).



Randomized controlled trial. Participants. Forty-four patients affected by stroke.  The patients were randomized into two groups: RFVE (N = 23) and TR (N = 21), and stratified according to stroke etiology. The RFVE treatment consisted of multidirectional exercises providing augmented feedback provided by virtual reality, while in the TR treatment the same exercises were provided without augmented feedbacks. Outcome Measures. Fugl-Meyer upper extremity scale (F-M UE), Functional Independence Measure scale (FIM), and kinematics parameters (speed, time, and peak).



The F-M UE (P = 0.030), FIM (P = 0.021), time (P = 0.008), and peak (P = 0.018), were significantly higher in the RFVE group after treatment, but not speed (P = 0.140). The patients affected by hemorrhagic stroke significantly improved FIM (P = 0.031), time (P = 0.011), and peak (P = 0.020) after treatment, whereas the patients affected by ischemic stroke improved significantly only speed (P = 0.005) when treated by RFVE.



These results indicated that some poststroke patients may benefit from RFVE program for the recovery of upper limb motor function.
Effet de gènes liés au sexe sur la taille corporelle et la reproduction

Quoique la production d’oeufs ait plafonné à partir du taux protéique de 15 p. 100, la taille des oeufs a continué à augmenter jusqu’à 21 p. 100. L’addition de 0,05 p. 100 de méthionine a augmenté la ponte et le poids des oeufs significativement et à des niveaux comparables à ceux observés avec une ration à 21 p. 100 de protéines. Actuellement, un faible taux de protamone est donné aux pondeuses élevées avec ou sans supplément de protamone, mais ce taux a dû être réduit de moitié, jusqu’à 0,0167 p. 100, car il abaissait la ponte. Les études physiologiques ont inclus l’observation des hypophyses, thyroïdes, surrénales et ovaires, à la fois pour des femelles en croissance et adultes, ainsi qu’un test biologique d’homogénats hypophysaires sur des rates immatures hypophysectomisées. Quoique les thyroïdes des femelles naines soient apparues plus petites que celles des normales à 7-13 mois d’âge, le test biologique n’a pu prouver que les modifications thyroïdiennes chez les naines soient dues à des altérations de l’activité thyréotrope de leur hypophyse. Le résultat du test biologique des hypophyses ne confirme pas l’hypothèse de l’accumulation d’hormone somatotrope dans les hypophyses d’oiseaux nains. L’observation de l’ACTH et de l’activité gonatrodope a été faite aussi sur les hypophyses naines.
A patient decision aid for antidepressant use in pregnancy: study protocol for a randomized controlled trial

Many women with depression experience significant difficulty making a decision about whether or not to use antidepressant medication in pregnancy. Patient decision aids (PDAs) are tools that assist patients in making complex health decisions. PDAs can reduce decision-making difficulty and lead to better treatment outcomes. We describe the methods for a pilot randomized controlled trial of an interactive web-based PDA for women who are having difficulty deciding about antidepressant drug use in pregnancy.



This is a pilot randomized controlled trial that aims to assess the feasibility of a larger, multi-center efficacy study. The PDA aims to help a woman: (1) understand why an antidepressant is being recommended, (2) be knowledgeable about potential benefits and risks of treatment and non-treatment with antidepressants, and (3) be clear about which benefits and risks are most important to her, with the goal of improving confidence in her decision-making. We include women aged 18 years or older who are: (1) planning a pregnancy or are pregnant (gestational age less than 30 weeks), (2) diagnosed with major depressive disorder, (3) deciding whether or not to use a selective serotonin reuptake inhibitor (SSRI) or serotonin norepinephrine reuptake inhibitor (SNRI) antidepressant in pregnancy, and (4) having at least moderate decision-making difficulty as per a Decisional Conflict Scale (DCS) Score ≥25. Participants are randomized to receive the PDA or an informational resource sheet via a secure website, and have access to the stated allocation until their final study follow-up. The primary outcomes of the pilot study are feasibility of recruitment and retention, acceptability of the intervention, and adherence to the trial protocol. The primary efficacy outcome is DCS score at 4 weeks post randomization, with secondary outcomes including depressive and anxiety symptoms.



Our PDA represents a key opportunity to optimize the decision-making process for women around antidepressants in pregnancy, leading to effective decision-making and optimizing improved maternal and child outcomes related to depression in pregnancy. The electronic nature of the PDA will facilitate keeping it up-to-date, and allow for widespread dissemination after efficacy is demonstrated.
Fish oil for the reduction of atrial fibrillation recurrence, inflammation, and oxidative stress.

Recent trials of fish oil for the prevention of atrial fibrillation (AF) recurrence have provided mixed results. Notable uncertainties in the existing evidence base include the roles of high-dose fish oil, inflammation, and oxidative stress in patients with paroxysmal or persistent AF not receiving conventional antiarrhythmic (AA) therapy.



The aim of this study was to evaluate the influence of high-dose fish oil on AF recurrence, inflammation, and oxidative stress parameters.



We performed a double-blind, randomized, placebo-controlled, parallel-arm study in 337 patients with symptomatic paroxysmal or persistent AF within 6 months of enrollment. Patients were randomized to fish oil (4 g/day) or placebo and followed, on average, for 271 ± 129 days.



The primary endpoint was time to first symptomatic or asymptomatic AF recurrence lasting >30 s. Secondary endpoints were high-sensitivity C-reactive protein (hs-CRP) and myeloperoxidase (MPO). The primary endpoint occurred in 64.1% of patients in the fish oil arm and 63.2% of patients in the placebo arm (hazard ratio: 1.10; 95% confidence interval: 0.84 to 1.45; p = 0.48). hs-CRP and MPO were within normal limits at baseline and decreased to a similar degree at 6 months (Δhs-CRP, 11% vs. -11%; ΔMPO, -5% vs. -9% for fish oil vs. placebo, respectively; p value for interaction = NS).



High-dose fish oil does not reduce AF recurrence in patients with a history of AF not receiving conventional AA therapy. Furthermore, fish oil does not reduce inflammation or oxidative stress markers in this population, which may explain its lack of efficacy.
ISSQoL: A New Questionnaire for Evaluating the Quality of Life of People Living with HIV in the HAART Era*

To design a Health-related Quality of Life (HRQoL) instrument for HIV-infected people in the era of highly active antiretroviral therapy (HAART).  The self-administered questionnaire was developed by an Italian network including researchers, physicians, people living with HIV, national institutions and community-based organizations (CBO) through several steps: (1) review of existing HRQoL literature and questionnaires for HIV-infected people; (2) selection of relevant domains measuring HRQoL in HIV-infected people, and identification of new domains related to new aspects of HRQoL concerning HAART-treated individuals; (3) conduction of two pre-test analyses in independent groups of Italian HIV-positive people (n≌100) distributed throughout the country. The objectives of the first pre-test were to verify the usefulness of the questionnaire, to construct a form easily understandable by everyone, to define the domains and their significance; the second pre-test aimed at evaluating and reshaping the questionnaire based on a statistical analysis of the outcomes of first pre-test; (4) validation analysis. A large cohort of people with HIV infection was recruited for the last step. The internal consistence reliability (Cronbach’s α) was ≥0.70 for all domains. Most domains had Cronbach’s coefficient >0.80. All domains demonstrated convergent and discriminant validity. The final version of ISSQoL includes two sections: HRQoL Core Evaluation Form (9 domains) and Additional Important Areas for HRQoL (6 domains). The ISSQoL was administered together with two additional forms: a Daily Impact of Symptoms Form and a Demographic Information Form. The Additional Important Areas for HRQoL include social support, interaction with medical staff, treatment impact, body changes, life planning, and motherhood/fatherhood. The data reported in the present paper provide preliminary evidence of the reliability and validity of the ISSQoL questionnaire for the measurement of HRQoL in HIV-infected people. The direct involvement of HIV-positive people in all the phases of the project was a key aspect of our work.
Rotational acetabular osteotomy for advanced osteoarthrosis secondary to dysplasia of the hip

Clinical and radiological studies were done on the results of rotational acetabular osteotomy for advanced osteoarthrosis secondary to dysplasia of 29 adult hips followed up for 6 to 11 years postoperatively (mean 8 years). Clinical evaluation by Merle d’Aubigne and Postel’s system showed improvement from a preoperative mean of 12.8 to a follow-up mean of 14.8, with aggravation being observed in 8 joints. Radiologically, this procedure produced adequated improvement regarding femoral head coverage, but improvement in joint congruency could not necessarily be obtained due to joint deformity and progression of arthrosis, with aggravation of joint congruency being observed in 6 joints. The most important factor influencing the postoperative results of this procedure was postoperative joint congruency. If the postoperative joint congruency is satisfactory, with the joint congruent index being more than 6.0, progression of arthrosis can be prevented in the long term by this procedure, even in advanced cases.
The <ce:italic>Dominant-STN phenomenon</ce:italic> in bilateral STN DBS for Parkinson's disease

In some patients with Parkinson's disease (PD) and bilateral STN-DBS the motor benefit from one STN alone appears similar to the improvement obtained with bilateral STN-DBS. Thus, we hypothesized that some patients have a "dominant-STN," whose stimulation achieves similar results than bilateral stimulation. Twenty-two consecutive PD patients with bilateral STN-DBS were assessed in 4 randomized conditions: bilateral off-stimulation, bilateral on-stimulation, unilateral right- and unilateral left-stimulation. A hierarchical agglomerative cluster analysis of the motor UPDRS scores in these 4 conditions showed that 11 patients (50%) presented with a "dominant-STN." Interestingly, in 3 of these patients the dominant-STN was ipsilateral to the most affected side of the body. Our results support the presence of different phenotypes of response to bilateral STN stimulation. In our sample 50% of the patients presented with a dominant-STN, suggesting that a non-negligible part of PD patients might not need bilateral STN-DBS surgery.