keyword
MENU ▼
Read by QxMD icon Read
search

Wiki

keyword
https://www.readbyqxmd.com/read/29921469/transgenic-artifacts-caused-by-passenger-human-growth-hormone
#1
Geoffroy de Faudeur, Bas Brouwers, Frans Schuit, John W M Creemers, Bruno Ramos-Molina
The minigene encoding human growth hormone (hGH) has been incorporated into over 300 transgenic mouse lines to improve transgene expression. However, unexpected and functional hGH expression can drastically alter physiology. We list here the mouse lines in which ectopic hGH has been confirmed, and we provide a wiki for lines awaiting analysis.
June 16, 2018: Trends in Endocrinology and Metabolism: TEM
https://www.readbyqxmd.com/read/29912344/prioritizing-predictive-biomarkers-for-gene-essentiality-in-cancer-cells-with-mrna-expression-data-and-dna-copy-number-profile
#2
Yuanfang Guan, Tingyang Li, Hongjiu Zhang, Fan Zhu, Gilbert S Omenn
Motivation: Finding driver genes that are responsible for the aberrant proliferation rate of cancer cells is informative for both cancer research and the development of targeted drugs. The established experimental and computational methods are labor-intensive. To make algorithms feasible in real clinical settings, methods that can predict driver genes using less experimental data are urgently needed. Results: We designed an effective feature selection method and used Support Vector Machines (SVM) to predict the essentiality of the potential driver genes in cancer cell lines with only 10 genes as features...
June 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29903697/taking-constructivism-one-step-further-post-hoc-analysis-of-a-student-created-wiki
#3
Michael Pascoe, Forrest Monroe, Helen Macfarlane
BACKGROUND: Wiki platform use has potential to improve student learning by improving engagement with course material. A student-created wiki was established to serve as a repository of study tools for students in a medical school curriculum. There is a scarcity of information describing student-led creation of wikis in medical education. OBJECTIVE: The aim is to characterize website traffic of a student-created wiki and evaluate student perceptions of usage via a short anonymous online survey...
June 14, 2018: JMIR Medical Education
https://www.readbyqxmd.com/read/29791443/traceability-reproducibility-and-wiki-exploration-for-%C3%A3-la-carte-reconstructions-of-genome-scale-metabolic-models
#4
Méziane Aite, Marie Chevallier, Clémence Frioux, Camille Trottier, Jeanne Got, María Paz Cortés, Sebastián N Mendoza, Grégory Carrier, Olivier Dameron, Nicolas Guillaudeux, Mauricio Latorre, Nicolás Loira, Gabriel V Markov, Alejandro Maass, Anne Siegel
Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics methods. Consequently, many recent models result from "à la carte" pipelines, combining the use of platforms, individual tools and biological expertise to enhance the quality of the reconstruction...
May 23, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29761463/using-zfin-data-types-organization-and-retrieval
#5
Ceri E Van Slyke, Yvonne M Bradford, Douglas G Howe, David S Fashena, Sridhar Ramachandran, Leyla Ruzicka
The Zebrafish Model Organism Database (ZFIN; zfin.org) was established in 1994 as the primary genetic and genomic resource for the zebrafish research community. Some of the earliest records in ZFIN were for people and laboratories. Since that time, services and data types provided by ZFIN have grown considerably. Today, ZFIN provides the official nomenclature for zebrafish genes, mutants, and transgenics and curates many data types including gene expression, phenotypes, Gene Ontology, models of human disease, orthology, knockdown reagents, transgenic constructs, and antibodies...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29722876/necklace-combining-reference-and-assembled-transcriptomes-for-more-comprehensive-rna-seq-analysis
#6
Nadia M Davidson, Alicia Oshlack
Background: RNA sequencing (RNA-seq) analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating an assembled transcriptome with reference annotation are lacking. Findings: Necklace is a software pipeline that runs genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data...
May 1, 2018: GigaScience
https://www.readbyqxmd.com/read/29582645/quality-of-breast-cancer-surgical-pathology-reports
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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...
March 15, 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
#17
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
#18
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
#19
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
#20
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
keyword
keyword
11271
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"