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https://www.readbyqxmd.com/read/29582645/quality-of-breast-cancer-surgical-pathology-reports
#1
Anita Vallacha, Ghulam Haider, Wiky Raja, Dinesh Kumar
Background: Surgical pathology reporting of breast cancer is needed for appropriate staging and treatment decisions. We here checked the quality of surgical pathology reports of breast cancer from different laboratories of Karachi, Pakistan. Methods: One hundred surgical pathology reports from ten different laboratories of Karachi were assessed for documentation of elements against a checklist adopted from the CAP guideline over a period of six months from January, 2017 to June, 2017 in the Oncology Department, Jinnah Postgraduate Medical Centre, Karachi...
March 27, 2018: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/29575351/measuring-the-impact-of-pharmacoepidemiologic-research-using-altmetrics-a-case-study-of-a-cnodes-drug-safety-article
#2
J M Gamble, Robyn L Traynor, Anatoliy Gruzd, Philip Mai, Colin R Dormuth, Ingrid S Sketris
PURPOSE: To provide an overview of altmetrics, including their potential benefits and limitations, how they may be obtained, and their role in assessing pharmacoepidemiologic research impact. METHODS: Our review was informed by compiling relevant literature identified through searching multiple health research databases (PubMed, Embase, and CIHNAHL) and grey literature sources (websites, blogs, and reports). We demonstrate how pharmacoepidemiologists, in particular, may use altmetrics to understand scholarly impact and knowledge translation by providing a case study of a drug-safety study conducted by the Canadian Network of Observational Drug Effect Studies...
March 24, 2018: Pharmacoepidemiology and Drug Safety
https://www.readbyqxmd.com/read/29566132/quimp-analyzing-transmembrane-signalling-in-highly-deformable-cells
#3
Piotr Baniukiewicz, Sharon Collier, Till Bretschneider
Summary: Transmembrane signalling plays important physiological roles, with G protein-coupled cell surface receptors being particularly important therapeutic targets. Fluorescent proteins are widely used to study signalling, but analyses of image time series can be challenging, in particular when cells change shape. QuimP software semi-automatically tracks spatio-temporal patterns of fluorescence at the cell membrane at high spatial resolution. This makes it a unique tool for studying transmembrane signalling, particularly during cell migration in immune or cancer cells for example...
March 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29548336/rop-dumpster-diving-in-rna-sequencing-to-find-the-source-of-1-trillion-reads-across-diverse-adult-human-tissues
#4
Serghei Mangul, Harry Taegyun Yang, Nicolas Strauli, Franziska Gruhl, Hagit T Porath, Kevin Hsieh, Linus Chen, Timothy Daley, Stephanie Christenson, Agata Wesolowska-Andersen, Roberto Spreafico, Cydney Rios, Celeste Eng, Andrew D Smith, Ryan D Hernandez, Roel A Ophoff, Jose Rodriguez Santana, Erez Y Levanon, Prescott G Woodruff, Esteban Burchard, Max A Seibold, Sagiv Shifman, Eleazar Eskin, Noah Zaitlen
High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease...
February 15, 2018: Genome Biology
https://www.readbyqxmd.com/read/29538614/exploiting-and-assessing-multi-source-data-for-supervised-biomedical-named-entity-recognition
#5
Dieter Galea, Ivan Laponogov, Kirill Veselkov
Motivation: Recognition of biomedical entities from scientific text is a critical component of natural language processing and automated information extraction platforms. Modern named entity recognition approaches rely heavily on supervised machine learning techniques, which are critically dependent on annotated training corpora. These approaches have been shown to perform well when trained and tested on the same source. However, in such scenario, the performance and evaluation of these models may be optimistic, as such models may not necessarily generalize to independent corpora, resulting in potential non-optimal entity recognition for large-scale tagging of widely diverse articles in databases such as PubMed...
March 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29533182/replication-study-fusobacterium-nucleatum-infection-is-prevalent-in-human-colorectal-carcinoma
#6
John Repass, Elizabeth Iorns, Alexandria Denis, Stephen R Williams, Nicole Perfito, Timothy M Errington
As part of the <ext-link ext-link-type="uri" xlink:href="https://osf.io/e81xl/wiki/home/">Reproducibility Project: Cancer Biology</ext-link>, we published a Registered Report (Repass et al., 2016), that described how we intended to replicate an experiment from the paper ' Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma' (Castellarin et al., 2012). Here we report the results. When measuring Fusobacterium nucleatum DNA by qPCR in colorectal carcinoma (CRC), adjacent normal tissue, and separate matched control tissue, we did not detect a signal for F...
March 13, 2018: ELife
https://www.readbyqxmd.com/read/29509185/beyond-social-media-a-cross-sectional-survey-of-other-internet-and-mobile-phone-applications-in-a-community-psychiatry-population
#7
Michelle Colder Carras, Ramin Mojtabai, Bernadette Cullen
OBJECTIVE: Popular media applications have been shown to benefit people with severe mental illness by facilitating communication and social support, helping patients cope with or manage symptoms, and providing a way to monitor or predict mental health states. Although many studies of technology use by individuals with severe mental illness have focused primarily on use of social media, this study provides additional information about use of Internet applications such as blogs, wikis (websites that allow collaborative editing of content and structure by users), video games, and Skype by a community psychiatry population...
March 2018: Journal of Psychiatric Practice
https://www.readbyqxmd.com/read/29474523/progressive-approach-for-snp-calling-and-haplotype-assembly-using-single-molecular-sequencing-data
#8
Fei Guo, Dan Wang, Lusheng Wang
Motivation: Haplotype information is essential to the complete description and interpretation of genomes, genetic diversity and genetic ancestry. The new technologies can provide Single Molecular Sequencing (SMS) data that cover about 90% of positions over chromosomes. However, the SMS data has a higher error rate comparing to 1% error rate for short reads. Thus, it becomes very difficult for SNP calling and haplotype assembly using SMS reads. Most existing technologies do not work properly for the SMS data...
February 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29469598/supporting-ethics-educators-in-canadian-occupational-therapy-and-physical-therapy-programs-a-national-interprofessional-knowledge-exchange-project
#9
Anne Hudon, Émilie Blackburn, Maude Laliberté, Kadija Perreault, Barbara Mazer, Debbie Ehrmann Feldman, Bryn Williams-Jones, Matthew Hunt
Ethics education is the cornerstone of professional practice, fostering knowledge and respect for core ethical values among healthcare professionals. Ethics is also a subject well-suited for interprofessional education and collaboration. However, there are few initiatives to gather experiences and share resources among ethics educators in rehabilitation. We thus undertook a knowledge exchange project to: 1) share knowledge about ethics training across Canadian occupational and physical therapy programs, and 2) build a community of educators dedicated to improving ethics education...
February 22, 2018: Journal of Interprofessional Care
https://www.readbyqxmd.com/read/29454060/aop-db-a-database-resource-for-the-exploration-of-adverse-outcome-pathways-through-integrated-association-networks
#10
Maureen E Pittman, Stephen W Edwards, Cataia Ives, Holly M Mortensen
The Adverse Outcome Pathway (AOP) framework describes the progression of a toxicity pathway from molecular perturbation to population-level outcome in a series of measurable, mechanistic responses. The controlled, computer-readable vocabulary that defines an AOP has the ability to, automatically and on a large scale, integrate AOP knowledge with publically available sources of biological high-throughput data and its derived associations. To support the discovery and development of putative (existing) and potential AOPs, we introduce the AOP-DB, an exploratory database resource that aggregates association relationships between genes and their related chemicals, diseases, pathways, species orthology information, ontologies, and gene interactions...
February 14, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29447297/development-of-a-decision-aid-for-cardiopulmonary-resuscitation-and-invasive-mechanical-ventilation-in-the-intensive-care-unit-employing-user-centered-design-and-a-wiki-platform-for-rapid-prototyping
#11
Ariane Plaisance, Holly O Witteman, Annie LeBlanc, Jennifer Kryworuchko, Daren Keith Heyland, Mark H Ebell, Louisa Blair, Diane Tapp, Audrey Dupuis, Carole-Anne Lavoie-Bérard, Carrie Anna McGinn, France Légaré, Patrick Michel Archambault
BACKGROUND: Upon admission to an intensive care unit (ICU), all patients should discuss their goals of care and express their wishes concerning life-sustaining interventions (e.g., cardiopulmonary resuscitation (CPR)). Without such discussions, interventions that prolong life at the cost of decreasing its quality may be used without appropriate guidance from patients. OBJECTIVES: To adapt an existing decision aid about CPR to create a wiki-based decision aid individually adapted to each patient's risk factors; and to document the use of a wiki platform for this purpose...
2018: PloS One
https://www.readbyqxmd.com/read/29394970/remission-rate-of-acute-lymphoblastic-leukemia-all-in-adolescents-and-young-adults-aya
#12
Anita Vallacha, Ghulam Haider, Wiky Raja, Dinesh Kumar
OBJECTIVE: To determine the remission rate in adolescent and young adult (AYA) patients with acute lymphoblastic leukemia (ALL). STUDY DESIGN: Descriptive study. PLACE AND DURATION OF STUDY: Department of Oncology, Jinnah Postgraduate Medical Centre (JPMC), Karachi from January, 2016 to March, 2017. METHODOLOGY: Adolescent and young adult (AYA) patients aged 15-39 years, newly diagnosed with acute lymphoblastic leukemia from January, 2016 to March, 2017...
February 2018: Journal of the College of Physicians and Surgeons—Pakistan: JCPSP
https://www.readbyqxmd.com/read/29280050/niftypet-a-high-throughput-software-platform-for-high-quantitative-accuracy-and-precision-pet-imaging-and-analysis
#13
Pawel J Markiewicz, Matthias J Ehrhardt, Kjell Erlandsson, Philip J Noonan, Anna Barnes, Jonathan M Schott, David Atkinson, Simon R Arridge, Brian F Hutton, Sebastien Ourselin
We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis...
January 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29233408/structured-academic-discussions-through-an-online-education-specific-platform-to-improve-pharm-d-students-learning-outcomes
#14
Srikanth Kolluru, James T Varughese
OBJECTIVE: To facilitate active academic discussions using an online, education-centered platform and reinforce concepts, in order to improve overall course outcomes. MATERIALS AND METHODS: A third year integrated pharmacotherapy course was enrolled on an online searchable platform, Piazza®, to facilitate academic discussions. Students could ask, answer, and explore content, and build on submitted answers in wiki style in collaboration. Instructor posted learning objectives, endorsed student responses with correct answers and led follow-up discussions...
March 2017: Currents in Pharmacy Teaching & Learning
https://www.readbyqxmd.com/read/29196478/efficacy-of-hypnotherapy-compared-to-cognitive-behavioural-therapy-for-mild-to-moderate-depression-study-protocol-of-a-randomised-controlled-rater-blind-trial-wiki-d
#15
Kristina Fuhr, Cornelie Schweizer, Christoph Meisner, Anil Batra
INTRODUCTION: Despite a substantial number of studies providing evidence for the efficacy of psychological treatment for mild-to-moderate depression, maximally only 50% of participants respond to treatment, even when using gold-standard treatments such as cognitive-behavioural therapy (CBT) and interpersonal therapy. New approaches such as the 'third wave' psychotherapies have provided promising results; however, studies concerning the comparison with evidence-based treatments are lacking...
December 1, 2017: BMJ Open
https://www.readbyqxmd.com/read/29186298/simulate-simulating-complex-landscapes-of-transposable-elements-of-populations
#16
Robert Kofler
Motivation: Estimating the abundance of transposable elements (TEs) in populations (or tissues) promises to answer many open research questions. However, progress is hampered by the lack of concordance between different approaches for TE identification and thus potentially unreliable results. Results: To address this problem, we developed SimulaTE a tool that generates TE landscapes for populations using a newly developed domain specific language (DSL). The simple syntax of our DSL allows for easily building even complex TE landscapes that have, for example, nested, truncated and highly diverged TE insertions...
November 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29178606/empowering-students-with-the-hidden-curriculum
#17
Hilary Neve, Tracey Collett
BACKGROUND: The hidden curriculum (HC) refers to unscripted, ad hoc learning that occurs outside the formal, taught curriculum and can have a powerful influence on the professional development of students. While this learning may be positive, it may conflict with that taught in the formal curriculum. Medical schools take a range of steps to address these negative effects; however, the existence and nature of the concept tends to be hidden from students. METHODS: Since 2007, our medical school has incorporated into its small group programme an educational activity exploring the concept of the hidden curriculum...
November 27, 2017: Clinical Teacher
https://www.readbyqxmd.com/read/29149304/tobacco-content-in-video-games-categorization-of-tobacco-typologies-and-gamer-recall
#18
Susan R Forsyth, Ruth E Malone
Introduction: Tobacco content has been identified in popular video games played by adolescents. To date, there are no established instruments for categorizing tobacco content. We describe development and demonstrate the use of an instrument to categorize types of tobacco content. Methods: Interviews were conducted with 61 participants: 20 adolescents (mean age 17.7), and 41 adults (mean age 23.9), who discussed favorite games and recalled tobacco content. All games mentioned were examined for tobacco content by watching movies of game play on YouTube, examining individual game Wiki sites, and reviewing content descriptors provided by the Entertainment Software Rating Board (ESRB), Common Sense Media and the Internet Movie Database (IMDb)...
November 15, 2017: Nicotine & Tobacco Research: Official Journal of the Society for Research on Nicotine and Tobacco
https://www.readbyqxmd.com/read/29126402/using-social-media-to-support-small-group-learning
#19
Duncan Cole, Emma Rengasamy, Shafqat Batchelor, Charles Pope, Stephen Riley, Anne Marie Cunningham
BACKGROUND: Medical curricula are increasingly using small group learning and less didactic lecture-based teaching. This creates new challenges and opportunities in how students are best supported with information technology. We explored how university-supported and external social media could support collaborative small group working on our new undergraduate medical curriculum. METHODS: We made available a curation platform (Scoop.it) and a wiki within our virtual learning environment as part of year 1 Case-Based Learning, and did not discourage the use of other tools such as Facebook...
November 10, 2017: BMC Medical Education
https://www.readbyqxmd.com/read/29118973/the-2017-bioinformatics-open-source-conference-bosc
#20
EDITORIAL
Nomi L Harris, Peter J A Cock, Brad Chapman, Christopher J Fields, Karsten Hokamp, Hilmar Lapp, Monica Munoz-Torres, Bastian Greshake Tzovaras, Heather Wiencko
The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year's theme, open data...
2017: F1000Research
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