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https://www.readbyqxmd.com/read/29224151/a-guide-to-illumina-beadchip-data-analysis
#1
Michael C Wu, Pei-Fen Kuan
The Illumina Infinium BeadChips are a powerful array-based platform for genome-wide DNA methylation profiling at approximately 485,000 (450K) and 850,000 (EPIC) CpG sites across the genome. The platform is used in many large-scale population-based epigenetic studies of complex diseases, environmental exposures, or other experimental conditions. This chapter provides an overview of the key steps in analyzing Illumina BeadChip data. We describe key preprocessing steps including data extraction and quality control as well as normalization strategies...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29161890/impact-of-physical-activity-on-the-risk-of-cardiovascular-disease-in-middle-aged-and-older-adults-epic-norfolk-prospective-population-study
#2
Sangeeta Lachman, S Matthijs Boekholdt, Robert N Luben, Stephen J Sharp, Soren Brage, Kay-Tee Khaw, Ron Jg Peters, Nicholas J Wareham
Background There is broad consensus that regular physical activity yields major health benefits. However, current guidelines on physical activity are mainly aimed at middle-aged adults. It is unclear whether physical activity also translates into cardiovascular health benefits in older adults. Therefore, we aimed to compare the association between different levels of physical activity and the risk of cardiovascular disease (CVD) in elderly to middle-aged individuals. Methods We analysed data from the EPIC Norfolk prospective population study...
January 1, 2017: European Journal of Preventive Cardiology
https://www.readbyqxmd.com/read/29077003/antibiotic-prescribing-for-uncomplicated-acute-bronchitis-is-highest-in-younger-adults
#3
Larissa Grigoryan, Roger Zoorob, Jesal Shah, Haijun Wang, Monisha Arya, Barbara W Trautner
Reducing inappropriate antibiotic prescribing is currently a global health priority. Current guidelines recommend against antibiotic treatment for acute uncomplicated bronchitis. We studied antibiotic prescribing patterns for uncomplicated acute bronchitis and identified predictors of inappropriate antibiotic prescribing. We used the Epic Clarity database (electronic medical record system) to identify all adult patients with acute bronchitis in family medicine clinics from 2011 to 2016. We excluded factors that could justify antibiotic use, such as suspected pneumonia, COPD or immunocompromising conditions...
October 27, 2017: Antibiotics
https://www.readbyqxmd.com/read/29020414/separate-and-combined-associations-of-obesity-and-metabolic-health-with-coronary-heart-disease-a-pan-european-case-cohort-analysis
#4
Camille Lassale, Ioanna Tzoulaki, Karel G M Moons, Michael Sweeting, Jolanda Boer, Laura Johnson, José María Huerta, Claudia Agnoli, Heinz Freisling, Elisabete Weiderpass, Patrik Wennberg, Daphne L van der A, Larraitz Arriola, Vassiliki Benetou, Heiner Boeing, Fabrice Bonnet, Sandra M Colorado-Yohar, Gunnar Engström, Anne K Eriksen, Pietro Ferrari, Sara Grioni, Matthias Johansson, Rudolf Kaaks, Michail Katsoulis, Verena Katzke, Timothy J Key, Giuseppe Matullo, Olle Melander, Elena Molina-Portillo, Concepción Moreno-Iribas, Margareta Norberg, Kim Overvad, Salvatore Panico, J Ramón Quirós, Calogero Saieva, Guri Skeie, Annika Steffen, Magdalena Stepien, Anne Tjønneland, Antonia Trichopoulou, Rosario Tumino, Yvonne T van der Schouw, W M Monique Verschuren, Claudia Langenberg, Emanuele Di Angelantonio, Elio Riboli, Nicholas J Wareham, John Danesh, Adam S Butterworth
Aims: The hypothesis of 'metabolically healthy obesity' implies that, in the absence of metabolic dysfunction, individuals with excess adiposity are not at greater cardiovascular risk. We tested this hypothesis in a large pan-European prospective study. Methods and results: We conducted a case-cohort analysis in the 520 000-person European Prospective Investigation into Cancer and Nutrition study ('EPIC-CVD'). During a median follow-up of 12.2 years, we recorded 7637 incident coronary heart disease (CHD) cases...
August 14, 2017: European Heart Journal
https://www.readbyqxmd.com/read/28834167/feasibility-and-safety-of-focal-irreversible-electroporation-as-salvage-treatment-for-localized-radio-recurrent-prostate-cancer
#5
Matthijs J Scheltema, Willemien van den Bos, Amila R Siriwardana, Anton M F Kalsbeek, James E Thompson, Francis Ting, Maret Böhm, Anne-Maree Haynes, Ron Shnier, Warick Delprado, Phillip D Stricker
OBJECTIVES: To evaluate the feasibility, safety, early quality-of-life (QoL) and oncological outcomes of salvage focal irreversible electroporation (IRE) for radio-recurrent prostate cancer (PCa). PATIENTS AND METHODS: Patients with localized, radio-recurrent PCa without evidence of metastatic or nodal disease were offered focal IRE according to the consensus guidelines. Patients with a minimum follow-up of 6 months were eligible for analysis. Adverse events were monitored using the National Cancer Institute Common Terminology Criteria for Adverse Events (CTCAE version 4...
November 2017: BJU International
https://www.readbyqxmd.com/read/28531783/prototypical-versus-contemporary-mediterranean-diet
#6
W Rizza, L De Gara, R Antonelli Incalzi, C Pedone
BACKGROUND AND AIMS: To investigate the evolution of the Mediterranean Diet (MD) in a delimited area of Southern Italy, by comparing the diet adopted 60-70 years ago (Prototypical Mediterranean Diet, PMD) with the contemporary one (Contemporary Mediterranean Diet, CMD), and to verify to what extent they fitted the recommendations of the Italian and the USDA dietary guidelines. METHODS: We recruited a total of 106 participants, divided in two groups. PMD group included 52 women aged >80 years, with a good cognitive function and full independence in basic and instrumental activities of daily living...
October 2016: Clinical Nutrition ESPEN
https://www.readbyqxmd.com/read/28360503/the-role-of-copy-and-paste-function-in-orthopedic-trauma-progress-notes
#7
Wesley Winn, Irshad A Shakir, Heidi Israel, Lisa K Cannada
INTRODUCTION: The electronic medical record (EMR) is standard in institutions. While there is not concern for legibility of notes and access to charts, there is an ease of copy and paste for daily notes. This may not lead to accurate portrayal of patient's status. Our purpose was to evaluate the use of copy and paste functions in daily notes of patients with injuries at high risk for complications. METHODS: IRB approval was obtained for a retrospective review. Inclusion criteria included patients aged 18 and older treated at our Level 1 Trauma Center after implementation of Epic Systems Corporation, Verona, WI, USA...
January 2017: Journal of Clinical Orthopaedics and Trauma
https://www.readbyqxmd.com/read/28152859/faster-ways-of-pursuing-quality-control-using-ehr-electronic-health-record
#8
Samip R Master, Glenn Morris Mills, Richard P Mansour
169 Background: In this era of electronic health records (EHR), quality monitoring can be a fast repetitive process. Having access to the relational database of the EHR permits rapid case identification and quality indicator determination. We hereby describe evaluation of hepatitis B testing prior to rituximab administration, a quality measure as per ASCO guidelines. METHODS: We connected SQL Query Manager with EPIC Clarity database. Using the object model for medication orders, location and department, we used SQL language to build a temporary dataset of all patients who have a completed order for a Rituximab infusion at a specific department location within the past 6 months...
March 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/27943174/the-dutch-score-based-risk-charts-seriously-underestimate-the%C3%A2-risk-of-cardiovascular-disease
#9
H T Jørstad, S M Boekholdt, N J Wareham, K T Khaw, R J G Peters
INTRODUCTION: Dutch cardiovascular disease (CVD) prevention guidelines recommend the use of modified SCORE risk charts to estimate 10-year risk of fatal and nonfatal CVD (myocardial infarction, cerebrovascular disease and congestive heart failure). This combined risk is derived from the SCORE mortality risk using multipliers. These multipliers have been shown to underestimate overall CVD risk. We aimed to compare the current Dutch risk charts with charts that estimate a broader range of clinically relevant CVD using updated multipliers...
March 2017: Netherlands Heart Journal
https://www.readbyqxmd.com/read/27919373/improving-the-effectiveness-of-drug-safety-alerts-to-increase-adherence-to-the-guideline-for-gastrointestinal-prophylaxis
#10
Soufiane Lilih, Marieke Pereboom, Ruud T M van der Hoeven, Aukje K Mantel-Teeuwisse, Matthijs L Becker
OBJECTIVE: Gastrointestinal bleedings are the most frequently occurring reason for medication-related hospital admissions, which are potentially preventable. We implemented a clinical decision support system that recommends to prescribe gastrointestinal prophylaxis in patients with an increased risk according to the Dutch guideline. Our primary objective was to determine whether the implementation resulted in improved compliance with this guideline for gastrointestinal prophylaxis. A secondary objective was to determine whether implementation resulted in a reduction of the number of drug safety alerts...
January 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/27540190/prolonged-infusions-of-ketamine-and-impact-on-infections-and-waste
#11
Joanne Wong, Adam Sutherland
AIM: Ketamine is used for post-operative analgesia. There has been recent disruption in it's supply. It is usually prescribed by patient's weight (3 mg/kg in 50 ml 0.9% saline) at a rate of 1-5 ml/hr (1-5 microgram/kg/minute). To conserve ketamine supplies our policy was changed to a concentrated "standardised" concentration of ketamine (250 mg in 50 ml 0.9% sodium chloride) that could be run for a maximum of 72 hrs. There is evidence demonstrating no relationship between duration of infusion and microbiological contamination for 72 hrs...
September 2016: Archives of Disease in Childhood
https://www.readbyqxmd.com/read/27193442/pre-diagnostic-meat-and-fibre-intakes-in-relation-to-colorectal-cancer-survival-in-the-european-prospective-investigation-into-cancer-and-nutrition
#12
Heather A Ward, Teresa Norat, Kim Overvad, Christina C Dahm, H Bas Bueno-de-Mesquita, Mazda Jenab, Veronika Fedirko, Fränzel J B van Duijnhoven, Guri Skeie, Dora Romaguera-Bosch, Anne Tjønneland, Anja Olsen, Franck Carbonnel, Aurélie Affret, Marie-Christine Boutron-Ruault, Verena Katzke, Tilman Kühn, Krassimira Aleksandrova, Heiner Boeing, Antonia Trichopoulou, Pagona Lagiou, Christina Bamia, Domenico Palli, Sabina Sieri, Rosario Tumino, Alessio Naccarati, Amalia Mattiello, Petra H Peeters, Elisabete Weiderpass, Lene Angell Åsli, Paula Jakszyn, J Ramón Quirós, María-José Sánchez, Miren Dorronsoro, José-María Huerta, Aurelio Barricarte, Karin Jirström, Ulrika Ericson, Ingegerd Johansson, Björn Gylling, Kathryn E Bradbury, Kay-Tee Khaw, Nicholas J Wareham, Magdalena Stepien, Heinz Freisling, Neil Murphy, Amanda J Cross, Elio Riboli
Improvements in colorectal cancer (CRC) detection and treatment have led to greater numbers of CRC survivors, for whom there is limited evidence on which to provide dietary guidelines to improve survival outcomes. Higher intake of red and processed meat and lower intake of fibre are associated with greater risk of developing CRC, but there is limited evidence regarding associations with survival after CRC diagnosis. Among 3789 CRC cases in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, pre-diagnostic consumption of red meat, processed meat, poultry and dietary fibre was examined in relation to CRC-specific mortality (n 1008) and all-cause mortality (n 1262) using multivariable Cox regression models, adjusted for CRC risk factors...
July 2016: British Journal of Nutrition
https://www.readbyqxmd.com/read/27130217/quality-of-ehr-data-extractions-for-studies-of-preterm-birth-in-a-tertiary-care-center-guidelines-for-obtaining-reliable-data
#13
COMPARATIVE STUDY
Lindsey A Knake, Monika Ahuja, Erin L McDonald, Kelli K Ryckman, Nancy Weathers, Todd Burstain, John M Dagle, Jeffrey C Murray, Prakash Nadkarni
BACKGROUND: The use of Electronic Health Records (EHR) has increased significantly in the past 15 years. This study compares electronic vs. manual data abstractions from an EHR for accuracy. While the dataset is limited to preterm birth data, our work is generally applicable. We enumerate challenges to reliable extraction, and state guidelines to maximize reliability. METHODS: An Epic™ EHR data extraction of structured data values from 1,772 neonatal records born between the years 2001-2011 was performed...
April 29, 2016: BMC Pediatrics
https://www.readbyqxmd.com/read/27049891/psychometric-testing-of-the-norwegian-version-of-the-expanded-prostate-cancer-index-composite-26-item-version-epic-26
#14
Sophie D Fosså, Anne Holck Storås, Eivind A Steinsvik, Tor Aa Myklebust, Lars M Eri, Jon H Loge, Alv A Dahl
OBJECTIVES: In patients with prostate cancer, evaluation of quality of care requires the inclusion of patient-reported outcomes measures assessed by validated and reliable instruments. Basic psychometric tests of the Norwegian version of the Expanded Prostate Cancer Index Composite with 26 items (EPIC-26) were performed in this study. MATERIAL AND METHODS: Translation of the original questionnaire (University of California, Los Angeles Prostate Cancer Index Composite), field testing and retranslation were done according to published guidelines...
August 2016: Scandinavian Journal of Urology
https://www.readbyqxmd.com/read/26808155/the-influence-of-hormonal-factors-on-the-risk-of-developing-cervical-cancer-and-pre-cancer-results-from-the-epic-cohort
#15
Esther Roura, Noémie Travier, Tim Waterboer, Silvia de Sanjosé, F Xavier Bosch, Michael Pawlita, Valeria Pala, Elisabete Weiderpass, Núria Margall, Joakim Dillner, Inger T Gram, Anne Tjønneland, Christian Munk, Domenico Palli, Kay-Tee Khaw, Kim Overvad, Françoise Clavel-Chapelon, Sylvie Mesrine, Agnès Fournier, Renée T Fortner, Jennifer Ose, Annika Steffen, Antonia Trichopoulou, Pagona Lagiou, Philippos Orfanos, Giovanna Masala, Rosario Tumino, Carlotta Sacerdote, Silvia Polidoro, Amalia Mattiello, Eiliv Lund, Petra H Peeters, H B as Bueno-de-Mesquita, J Ramón Quirós, María-José Sánchez, Carmen Navarro, Aurelio Barricarte, Nerea Larrañaga, Johanna Ekström, David Lindquist, Annika Idahl, Ruth C Travis, Melissa A Merritt, Marc J Gunter, Sabina Rinaldi, Massimo Tommasino, Silvia Franceschi, Elio Riboli, Xavier Castellsagué
BACKGROUND: In addition to HPV, high parity and hormonal contraceptives have been associated with cervical cancer (CC). However, most of the evidence comes from retrospective case-control studies. The aim of this study is to prospectively evaluate associations between hormonal factors and risk of developing cervical intraepithelial neoplasia grade 3 (CIN3)/carcinoma in situ (CIS) and invasive cervical cancer (ICC). METHODS AND FINDINGS: We followed a cohort of 308,036 women recruited in the European Prospective Investigation into Cancer and Nutrition (EPIC) Study...
2016: PloS One
https://www.readbyqxmd.com/read/26709388/developing-a-cookbook-with-lifestyle-tips-a-community-engaged-approach-to-promoting-diet-related-cancer-prevention-guidelines
#16
Selina A Smith, Joyce Q Sheats, Mary S Whitehead, Ernestine Delmoor, Thomas Britt, Cassandra L Harris, Janette Robinson-Flint, L Monique Porche-Smith, Kayellen Edmonds Umeakunne, Steven S Coughlin
Supplementing nutrition education with skills-building activities may enhance community awareness of diet-related cancer prevention guidelines. To develop a cookbook with lifestyle tips, recipes were solicited from the National Black Leadership Initiative on Cancer (NBLIC) community coalitions and dietary intake advice from participants in the Educational Program to Increase Colorectal Cancer Screening (EPICS). With guidance from a chef and registered dietitian, recipes were tested, assessed, and transformed; lifestyle advice was obtained from focus groups...
2015: Jacobs Journal of Food and Nutrition
https://www.readbyqxmd.com/read/26662849/thyroid-dysfunction-and-anaemia-in-a-large-population-based-study
#17
Khadija M'Rabet-Bensalah, Carole E Aubert, Michael Coslovsky, Tinh-Hai Collet, Christine Baumgartner, Wendy P J den Elzen, Robert Luben, Anne Angelillo-Scherrer, Drahomir Aujesky, Kay-Tee Khaw, Nicolas Rodondi
OBJECTIVE AND BACKGROUND: Anaemia and thyroid dysfunction are common and often co-occur. Current guidelines recommend the assessment of thyroid function in the work-up of anaemia, although evidence on this association is scarce. PATIENTS AND METHODS: In the 'European Prospective Investigation of Cancer' (EPIC)-Norfolk population-based cohort, we aimed to examine the prevalence and type of anaemia (defined as haemoglobin <13 g/dl for men and <12 g/dl for women) according to different thyroid function groups...
April 2016: Clinical Endocrinology
https://www.readbyqxmd.com/read/26555907/-early-postoperative-outcomes-and-evaluation-of-hemodynamics-after-mitral-valve-replacement-with-epic-mitral-bioprosthesis
#18
Keisuke Kanda, Teruki Kotegawa, Satoshi Kawatsu, Goro Takahashi, Ichiro Yoshioka, Hidenori Fujiwara, Osamu Adachi, Masatoshi Akiyama, Kiichiro Kumagai, Shunsuke Kawamoto, Yoshikatsu Saiki
BACKGROUND: In Guideline for Surgical and Interventional Treatment of Valvular Heart Disease, revised by Japanese Circulation Society in 2012, mitral valve replacement (MVR) with bioprosthesis is class II b recommendation for patients aged 70 years or older who have no risk factors for thromboembolism. The aim of this study was to evaluate the early postoperative surgical outcomes and the hemodynamic performance with the Epic mitral bioprosthesis. METHODS: Twenty-six consecutive patients underwent MVR with Epic mitral bioprostesis at Tohoku University Hospital between April 2011 and July 2014...
November 2015: Kyobu Geka. the Japanese Journal of Thoracic Surgery
https://www.readbyqxmd.com/read/26424938/improving-compliance-with-cervical-cancer-screening-guidelines
#19
Jessica Langsjoen, Cara Goodell, Eduardo Castro, Jen Thomas, Thomas J Kuehl, Hania Wehbe-Janek, Meghan Hinskey
Current cervical cancer screening guidelines for the care of healthy women include HPV cotesting with all Papanicolaou (Pap) smears after the age of 30. To improve compliance with current guidelines, we instituted two processes: first, simplifying the ordering process to a single order for Pap smear plus HPV cotesting using an electronic medical record system (EMR); and second, providing education for clinic staff. Baseline and postintervention data were collected by retrospective chart review. Patients were selected during three intervals: prior to the transition to Epic EMR, after the transition to Epic, and after an educational intervention...
October 2015: Proceedings of the Baylor University Medical Center
https://www.readbyqxmd.com/read/26342536/the-association-of-substituting-carbohydrates-with-total-fat-and-different-types-of-fatty-acids-with-mortality-and-weight-change-among-diabetes-patients
#20
Marjo J Campmans-Kuijpers, Ivonne Sluijs, Ute Nöthlings, Heinz Freisling, Kim Overvad, Heiner Boeing, Giovanna Masala, Salvatore Panico, Rosario Tumino, Sabina Sieri, Ingegerd Johansson, Anna Winkvist, Verena A Katzke, Tilman Kuehn, Peter M Nilsson, Jytte Halkjær, Anne Tjønneland, Annemieke M Spijkerman, Larraitz Arriola, Carlotta Sacerdote, Aurelio Barricarte, Anne M May, Joline W Beulens
BACKGROUND: Substitution of carbohydrates with fat in a diet for type 2 diabetes patients is still debated. OBJECTIVE: This study aimed to investigate the association between dietary carbohydrate intake and isocaloric substitution with (i) total fat, (ii) saturated fatty acids (SFA), (iii) mono-unsaturated fatty acids (MUFA) and (iv) poly-unsaturated fatty acids (PUFA) with all-cause and cardiovascular (CVD) mortality risk and 5-year weight change in patients with type 2 diabetes...
October 2016: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
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