bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract PR2: Pathway-based gene-environment interactions in ovarian cancer.
Authors: Braem Marieke GM , Charlotte Onland-Moret N. , H. Moore Jason , HM Peeters Petra 
Published: August 2013

Abstract
Genome-wide association studies (GWAS) have identified 19 loci associated with the risk of ovarian cancer. In this post-GWAS era interest shifts towards elucidating the interplay of these susceptibility loci and known risk factors for ovarian cancer, i.e. reproductive and hormonal factors, height and smoking.
In this study, we investigate gene-environment interactions between the GWAS loci and single nucleotide polymorphisms (SNPs) in the accompanying genetic pathways and risk factors for ovarian cancer. Currently, a golden standard for the analysis of gene-environment interactions is lacking. Therefore, we use a multifaceted analytical approach by using a series of machine learning methods, including regression analysis, multifactor dimensionality reduction (MDR), entropy-based interaction networks, computational evolution systems and learning classifier systems.
A case-control study nested within the European Prospective Investigation into Cancer and Nutrition (EPIC) is being conducted including 590 ovarian cancer cases and 1190 healthy controls. In addition to all known GWAS hits for ovarian cancer, genetic pathways were selected in which the genes of these GWAS hits are potentially involved. A total of 754 SNPs are investigated. The environmental factors of interest are parity, miscarriages, breastfeeding, oral contraceptive (OC) use, age at menarche, age at menopause, height and smoking.
Preliminary results from regression analyses show statistically significant interactions between SNPs identified through GWAS and smoking (in interaction with rs12379687, p=0.0435), height (in interaction with rs2072590, p=0.01563) and OC use (in interaction with rs10098821, p=0.03621). These interactions were confirmed by multifactor dimensionality reduction, based on 10-fold cross-validation and 1000-fold permutation testing. Subsequent analyses are still ongoing and will be presented at the conference. Moreover, the analyses will be supplemented by an additional 289 cases and 578 controls from the Nijmegen Polygene and the Nijmegen Biomedical Study.
The results of this study will provide important insight into the etiology of ovarian cancer and reveal better understanding of the complexity of this disease.
This proffered talk is also presented as Poster 41.
Citation Format: Marieke GM Braem, N. Charlotte Onland-Moret, Jason H. Moore, Petra HM Peeters. Pathway-based gene-environment interactions in ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Post-GWAS Horizons in Molecular Epidemiology: Digging Deeper into the Environment; 2012 Nov 11-14; Hollywood, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(11 Suppl):Abstract nr PR2.
The Invisible Arm of Immunity in Common Cancer Chemoprevention Agents
Authors: Marzbani Edmond , Inatsuka Carol , Lu Hailing , Disis Mary L. 
Published: August 2013

Abstract
Immunoprevention refers to a strategy of preventing pathogen-associated and spontaneous cancers through the use of vaccines, antibodies, and immune modulators. Immune modulators function by enhancing the endogenous ability of the immune system to monitor for malignancy, so-called “immunosurveillance.” There is growing evidence that many of the most promising cancer chemoprevention agents including aspirin, COX-2 inhibitors, aromatase inhibitors, and bisphosphonates mediate their effects, in part, by enhancing immunosurveillance and reversing the immune evasive mechanisms that premalignant lesions use. In the following review, we introduce critical components of the human immune surveillance system—dendritic cells, T cells, and immune suppressive cells—and discuss the emerging data suggesting that common chemoprevention agents may modulate the function of these immunologic cells. Cancer Prev Res; 6(8); 764–73. ©2013 AACR.
Stages of Processing in Associative Recognition: Evidence from Behavior, EEG, and Classification
Authors: Borst Jelmer P. , Schneider Darryl W. , Walsh Matthew M. , Anderson John R. 
Published: August 2013

Abstract
In this study, we investigated the stages of information processing in associative recognition. We recorded EEG data while participants performed an associative recognition task that involved manipulations of word length, associative fan, and probe type, which were hypothesized to affect the perceptual encoding, retrieval, and decision stages of the recognition task, respectively. Analyses of the behavioral and EEG data, supplemented with classification of the EEG data using machine-learning techniques, provided evidence that generally supported the sequence of stages assumed by a computational model developed in the Adaptive Control of Thought-Rational cognitive architecture. However, the results suggested a more complex relationship between memory retrieval and decision-making than assumed by the model. Implications of the results for modeling associative recognition are discussed. The study illustrates how a classifier approach, in combination with focused manipulations, can be used to investigate the timing of processing stages.
Correlated mRNAs and miRNAs from co-expression and regulatory networks affect porcine muscle and finally meat properties
Authors: Ponsuksili Siriluck , Du Yang , Hadlich Frieder , Siengdee Puntita , Murani Eduard , Schwerin Manfred , Wimmers Klaus 
Published: August 2013

AbstractBackgroundPhysiological processes aiding the conversion of muscle to meat involve many genes associated with muscle structure and metabolic processes. MicroRNAs regulate networks of genes to orchestrate cellular functions, in turn regulating phenotypes.ResultsWe applied weighted gene co-expression network analysis to identify co-expression modules that correlated to meat quality phenotypes and were highly enriched for genes involved in glucose metabolism, response to wounding, mitochondrial ribosome, mitochondrion, and extracellular matrix. Negative correlation of miRNA with mRNA and target prediction were used to select transcripts out of the modules of trait-associated mRNAs to further identify those genes that are correlated with post mortem traits.ConclusionsPorcine muscle co-expression transcript networks that correlated topost mortemtraits were identified. The integration of miRNA and mRNA expression analyses, as well as network analysis, enabled us to interpret the differentially-regulated genes from a systems perspective. Linking co-expression networks of transcripts and hierarchically organized pairs of miRNAs and mRNAs to meat properties yields new insight into several biological pathways underlying phenotype differences. These pathways may also be diagnostic for many myopathies, which are accompanied by deficient nutrient and oxygen supply of muscle fibers.
Practice assistants in primary care in Germany – associations with organizational attributes on job satisfaction
Authors: Gavartina Amina , Zaroti Stavria , Szecsenyi Joachim , Miksch Antje , Ose Dominik , Campbell Stephen M , Goetz Katja 
Published: August 2013

Abstract

Background
Job satisfaction and organizational attributes in primary care teams are important issues as they affect clinical outcomes and the quality of health care provided. As practice assistants are an integral part of these teams it is important to gain insight into their views on job satisfaction and organizational attributes. The aim of this study was to evaluate the job satisfaction of practice assistants and the organizational attributes within their general practices in Germany and to explore the existence of possible associations.

Methods
This observational study was based on a job satisfaction survey and measurement of organizational attributes in general practices in the German federal state of Baden-Wuerttemberg. Job satisfaction was measured with the 10-item ‘Warr-Cook-Wall job satisfaction scale’. Organizational attributes were evaluated with the 21-items ‘survey of organizational attributes for primary care’ (SOAPC). Linear regression analyses were performed in which each of SOAPC scales and the overall score of SOAPC was treated as outcome variables.

Results
586 practice assistants out of 794 respondents (73.8%) from 234 general practices completed the questionnaire. Practice assistants were mostly satisfied with their colleagues and least of all satisfied with their income and recognition for their work. The regression analysis showed that ‘freedom of working method’ and ‘recognition of work’, the employment status of practice assistants and the mode of practice were almost always significantly associated with each subscale and overall score of SOAPC.

Conclusions
Job satisfaction is highly associated with different aspects of organizational attributes for primary care (‘communication’, ‘decision-making’ and ‘stress’). Consequently, improved job satisfaction could lead to a better-organized primary care team. This implication should be investigated directly in further intervention studies with a special focus on improving the recognition for work and income.
Eat, drink and gamble: marketing messages about ‘risky’ products in an Australian major sporting series
Authors: Lindsay Sophie , Thomas Samantha , Lewis Sophie , Westberg Kate , Moodie Rob , Jones Sandra 
Published: August 2013

AbstractBackgroundTo investigate the alcohol, gambling, and unhealthy food marketing strategies during a nationally televised, free to air, sporting series in Australia.Methods/approachUsing the Australian National Rugby League 2012 State of Origin three-game series, we conducted a mixed methods content analysis of the frequency, duration, placement and content of advertising strategies, comparing these strategies both within and across the three games.ResultsThere were a total of 4445 episodes (mean = 1481.67, SD = 336.58), and 233.23 minutes (mean = 77.74, SD = 7.31) of marketing for alcoholic beverages, gambling products and unhealthy foods and non-alcoholic beverages during the 360 minutes of televised coverage of the three State of Origin 2012 games. This included an average per game of 1354 episodes (SD = 368.79) and 66.29 minutes (SD = 7.62) of alcohol marketing; 110.67 episodes (SD = 43.89), and 8.72 minutes (SD = 1.29) of gambling marketing; and 17 episodes (SD = 7.55), and 2.74 minutes (SD = 0.78) of unhealthy food and beverage marketing. Content analysis revealed that there was a considerable embedding of product marketing within the match play, including within match commentary, sporting equipment, and special replays.ConclusionsSport is increasingly used as a vehicle for the promotion of range of ‘risky consumption’ products. This study raises important ethical and health policy questions about the extent and impact of saturation and incidental marketing strategies on health and wellbeing, the transparency of embedded marketing strategies, and how these strategies may influence product consumption.
Facilitating education in pulmonary rehabilitation using the Living Well with COPD programme for pulmonary rehabilitation: a process evaluation
Authors: Cosgrove Denise , MacMahon Joseph , Bourbeau Jean , Bradley Judy M , O’Neill Brenda 
Published: August 2013

Abstract

Background
Standardised evidenced-based materials and mechanisms to facilitate the delivery of the education component of pulmonary rehabilitation are not widely available. The aims of this study were: 1) to adapt the self-management programme Living Well with COPD (LWWCOPD) programme, for embedding in pulmonary rehabilitation; and, 2) to conduct a process evaluation of the adapted programme.

Methods
The adaptations to the LWWCOPD programme were informed by focus groups, current practice, relevant research and guideline documents. Pulmonary rehabilitation sites used the adapted programme, the LWWCOPD programme for pulmonary rehabilitation, to deliver the education component of pulmonary rehabilitation. A process evaluation was conducted: elements included reach (patients’ attendance rates), dose delivered (amount of programme delivered), dose received (health professional and patient satisfaction) and fidelity (impact on patients’ knowledge, understanding and self-efficacy on the Understanding COPD questionnaire). Descriptive statistics (mean, SD) were used to summarise demographics and key data from the feedback questionnaires. Qualitative feedback on the programme was collated and categorised. Changes in the Understanding COPD questionnaire were examined using paired t-tests.

Results
The LWWCOPD programme for pulmonary rehabilitation was delivered in eleven hospital- and community-based programmes (n=25 health professionals, n=57 patients with COPD). It consisted of six weekly 30–45 minute sessions. The process evaluation showed positive results: 62.3% of patients attended ≥ 4 education sessions (reach); mean (SD) 90 (10)% of the session content were delivered (dose delivered); the majority of sessions were rated as excellent or good by health professionals and patients. Patients’ satisfaction was high: mean (SD) Section B of the Understanding COPD questionnaire: 91.67 (9.55)% (dose received). Knowledge, understanding and self-efficacy improved significantly: mean change (95% CI): Section A of the Understanding COPD questionnaire: 26.75 (21.74 to 31.76)%, BCKQ 10.64 (6.92 to 14.37)% (fidelity).

Conclusion
This rigorous process evaluation has demonstrated that the LWWCOPD programme for pulmonary rehabilitation can be used to deliver high quality, consistent and equitable education sessions during hospital and community-based pulmonary rehabilitation. This programme is now available worldwide (http://www.livingwellwithcopd.com/living-well-and-pulmonary-rehabilitation.html).

Trial registration
This study was registered with clinicaltrials.gov (reference number: NCT01226836)
Thyroid surgery in geriatric patients: a literature review
Authors: Gervasi Rita , Orlando Giulio , Lerose Maria Antonietta , Amato Bruno , Docimo Giovanni , Zeppa Pio , Puzziello Alessandro 
Published: August 2013

Abstract

Background
Thyroid disease is common in the elderly population. The incidence of hypothyroidism and multinodular goitre gradually increases with age. In view of a growth of aging population, we performed a literature review about the feasibility of thyroid surgery in the elderly.

Methods
We conducted a literature search in the PubMed database in September 2012 and all English-language publications on thyroidectomy in geriatric patients since 2002 were retrieved. The potential original articles mainly focusing on thyroidectomy in elderly patients were all identified and full texts were obtained and reviewed for further hand data retrieving.

Results
We retrieved five papers based on different primary end-point. Four were retrospective non randomized studies and one was prospective non randomized study. At last 65, 70, 75 and 80 years were used as an age cut-off. All studies evaluate the indications of thyroidectomy in geriatric patients, postoperative morbility and mortality. Only one study specifically assesses the rate of the rehospitalization after thyroidectomy among the elderly.

Conclusions
Thyroid nodules are particularly important in elderly patients, as the incidence of malignancy increases and they are usually more aggressive tumors. An age of at least 70 years is an independent risk factor for complications after general surgery procedures. Thyroid surgery in patients aged 70 years or older is safe and the relatively high rate of thyroid carcinoma and toxic goiter may justify an aggressive approach. A programmed operation with a careful pre-operative evaluation and a risk stratification should make the surgical procedures less hazardous, specially in 80 years old patients with an high ASA score.
Ankle/brachial index to everyone
Authors: Giugliano Giuseppe , Sannino Anna , Brevetti Linda , Perrino Cinzia , Schiattarella Gabriele Giacomo , Franzone Anna , Serino Federica , Ferrone Marco , Scudiero Fernando , Carbone Andreina , De Paulis Michele , Izzo Raffaele , Amato Bruno , Trimarco Bruno , Esposito Giovanni 
Published: August 2013

Abstract

Background
In the last years significant attention has been paid in identifying markers of subclinical atherosclerosis or of increased cardiovascular risk.

Method
An abnormal ankle/brachial index (ABI) identifies patients affected by lower extremity peripheral arterial disease, and even more important, represents a powerful predictor of the development of future ischemic cardiovascular events.

Conclusions
In our opinion, ABI is a cardiovascular risk prediction tool with very desirable properties that might become a routine measurement in clinical practice.
Tunical plication in the management of penile curvature due La Peyronie’s disease. Our experience on 47 cases
Authors: Iacono Fabrizio , Prezioso Domenico , Ruffo Antonio , Illiano Ester , Romeo Giuseppe , Amato Bruno 
Published: August 2013

Abstract

Background
Peyronie’s disease is an acquired connective tissue disorder of the penile tunica albuginea with fibrosis and inflammation. The disease produces palpable plaques, penile curvature and pain during erections. Patients report negative effects in four major domains: physical appearance and self-image, sexual function and performance. These changes damage sexual life and compromise the quality of life. Our objective is to review the patient's sexual life after penile tunical plicature using the International Index of Erectile Function (IIEF) and the Sexual Encounter Profile (SEP) questionnaires.

Methods
A total of 47 patients with Peyronie's disease (PD) were enrolled at our urology department and they underwent correction of penile deviation between February 2009 and March 2010. Mean patient age was 56 years and mean follow-up was 24 months. Patients with painless PD plaque with no progression in angulation for at least 12 months were chosen for surgery. They underwent a penile tunical plication.
IIEF and SEP questionnaire were administered to all patients.

Results
Of all treated patients, 94% were able to insert their penis in the partner's vagina (p<0.01; SEP question 2), compared with 62% preoperatively and 90% of them was satisfied overall with the sexual intercourse (p<0.01; SEP question 5) .Patients had a significantly higher endpoint and a greater change from baseline for the remaining SEP questions related to achievement of an erection, satisfaction of erection hardness (SEP questions 1 and 4; p < 0:001).
We reported a significant improvement in the IIEF scores (from a baseline total score of 25.2 +/- 3.2 to a final score of 38.3 +/- 5.2; P<0.01). It resulted in significantly higher endpoint IIEF scores across all five IIEF domains: Erectile Function, Intercourse Satisfaction, Orgasmic Function, Sexual Desire and Overall Satisfaction. The main complaint was penile shortening (28 patients, 60%), feeling of the suture during flaccidity and tumescence (37 patients, 80%).

Conclusion
Patient quality of life improved after surgery thanks to the improvement of their sexual life. The complications are unimportant and few bother symptoms are reported. The significant improvement in erectile function was also supported by IIEF and SEP questionnaire data. Nowadays tunical plication is a safe, advantageous and useful technique to treat patients suffering of Peyronie’s disease.
Epigenetic silencing of RASSF1A deregulates cytoskeleton and promotes malignant behavior of adrenocortical carcinoma
Authors: Korah Reju , Healy James M , Kunstman John W , Fonseca Annabelle L , Ameri Amir H , Prasad Manju L , Carling Tobias 
Published: August 2013

AbstractBackgroundAdrenocortical carcinoma (ACC) is a rare endocrine malignancy with high mutational heterogeneity and a generally poor clinical outcome. Despite implicated roles of deregulated TP53, IGF-2 and Wnt signaling pathways, a clear genetic association or unique mutational link to the disease is still missing. Recent studies suggest a crucial role for epigenetic modifications in the genesis and/or progression of ACC. This study specifically evaluates the potential role of epigenetic silencing ofRASSF1A, the most commonly silenced tumor suppressor gene, in adrenocortical malignancy.ResultsUsing adrenocortical tumor and normal tissue specimens, we show a significant reduction in expression ofRASSF1AmRNA and protein in ACC. Methylation-sensitive and -dependent restriction enzyme based PCR assays revealed significant DNA hypermethylation of theRASSF1Apromoter, suggesting an epigenetic mechanism forRASSF1Asilencing in ACC. Conversely, theRASSF1Apromoter methylation profile in benign adrenocortical adenomas (ACAs) was found to be very similar to that found in normal adrenal cortex. Enforced expression of ectopicRASSF1Ain the SW-13 ACC cell line reduced the overall malignant behavior of the cells, which included impairment of invasion through the basement membrane, cell motility, and solitary cell survival and growth. On the other hand, expression ofRASSF1A/A133S, a loss-of-function mutant form ofRASSF1A, failed to elicit similar malignancy-suppressing responses in ACC cells. Moreover, association of RASSF1A with the cytoskeleton inRASSF1A-expressing ACC cells and normal adrenal cortex suggests a role for RASSF1A in modulating microtubule dynamics in the adrenal cortex, and thereby potentially blocking malignant progression.ConclusionsDownregulation of RASSF1A via promoter hypermethylation may play a role in the malignant progression of adrenocortical carcinoma possibly by abrogating differentiation-promotingRASSF1A- microtubule interactions.
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling
Authors: Hug Laura A , Castelle Cindy J , Wrighton Kelly C , Thomas Brian C , Sharon Itai , Frischkorn Kyle R , Williams Kenneth H , Tringe Susannah G , Banfield Jillian F 
Published: August 2013

Abstract

Background
Sediments are massive reservoirs of carbon compounds and host a large fraction of microbial life. Microorganisms within terrestrial aquifer sediments control buried organic carbon turnover, degrade organic contaminants, and impact drinking water quality. Recent 16S rRNA gene profiling indicates that members of the bacterial phylum Chloroflexi are common in sediment. Only the role of the class Dehalococcoidia, which degrade halogenated solvents, is well understood. Genomic sampling is available for only six of the approximate 30 Chloroflexi classes, so little is known about the phylogenetic distribution of reductive dehalogenation or about the broader metabolic characteristics of Chloroflexi in sediment.

Results
We used metagenomics to directly evaluate the metabolic potential and diversity of Chloroflexi in aquifer sediments. We sampled genomic sequence from 86 Chloroflexi representing 15 distinct lineages, including members of eight classes previously characterized only by 16S rRNA sequences. Unlike in the Dehalococcoidia, genes for organohalide respiration are rare within the Chloroflexi genomes sampled here. Near-complete genomes were reconstructed for three Chloroflexi. One, a member of an unsequenced lineage in the Anaerolinea, is an aerobe with the potential for respiring diverse carbon compounds. The others represent two genomically unsampled classes sibling to the Dehalococcoidia, and are anaerobes likely involved in sugar and plant-derived-compound degradation to acetate. Both fix CO2 via the Wood-Ljungdahl pathway, a pathway not previously documented in Chloroflexi. The genomes each encode unique traits apparently acquired from Archaea, including mechanisms of motility and ATP synthesis.

Conclusions
Chloroflexi in the aquifer sediments are abundant and highly diverse. Genomic analyses provide new evolutionary boundaries for obligate organohalide respiration. We expand the potential roles of Chloroflexi in sediment carbon cycling beyond organohalide respiration to include respiration of sugars, fermentation, CO2 fixation, and acetogenesis with ATP formation by substrate-level phosphorylation.