keyword
MENU ▼
Read by QxMD icon Read
search

Dataset

keyword
https://www.readbyqxmd.com/read/28340142/multigene-signature-for-predicting-prognosis-of-patients-with-1p19q-co-deletion-diffuse-glioma
#1
Xin Hu, Emmanuel Martinez-Ledesma, Siyuan Zheng, Hoon Kim, Floris Barthel, Tao Jiang, Kenneth R Hess, Roel G W Verhaak
Background.: Co-deletion of 1p and 19q marks a diffuse glioma subtype associated with relatively favorable overall survival; however, heterogeneous clinical outcomes are observed within this category. Methods.: We assembled gene expression profiles and sample annotation of 374 glioma patients carrying the 1p/19q co-deletion. We predicted 1p/19q status using gene expression when annotation was missing. A first cohort was randomly split into training (n = 170) and a validation dataset (n = 163)...
March 8, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28340104/personalizing-lung-cancer-risk-prediction-and-imaging-follow-up-recommendations-using-the-national-lung-screening-trial-dataset
#2
Jason M Hostetter, James J Morrison, Michael Morris, Jean Jeudy, Kenneth C Wang, Eliot Siegel
Objective: To demonstrate a data-driven method for personalizing lung cancer risk prediction using a large clinical dataset. Materials and Methods: An algorithm was used to categorize nodules found in the first screening year of the National Lung Screening Trial as malignant or nonmalignant. Risk of malignancy for nodules was calculated based on size criteria according to the Fleischner Society recommendations from 2005, along with the additional discriminators of pack-years smoking history, sex, and nodule location...
March 10, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339748/genotype-based-gene-signature-of-glioma-risk
#3
Yen-Tsung Huang, Yi Zhang, Zhijin Wu, Dominique S Michaud
Background.: Glioma accounts for 80% of malignant brain tumors, but its etiologic determinants remain elusive. Despite genetic susceptibility loci identified by genome-wide association study (GWAS), the agnostic approach leaves open the possibility that other susceptibility genes remain to be discovered. Here we conduct a gene-centric integrative GWAS (iGWAS) of glioma risk that combines transcriptomics and genetics. Methods.: We synthesized a brain transcriptomics dataset (n = 354), a GWAS dataset (n = 4203), and an advanced glioma tumor transcriptomic dataset (n = 483) to conduct an iGWAS...
February 22, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28339747/deep-learning-for-pharmacovigilance-recurrent-neural-network-architectures-for-labeling-adverse-drug-reactions-in-twitter-posts
#4
Anne Cocos, Alexander G Fiks, Aaron J Masino
Objective: Social media is an important pharmacovigilance data source for adverse drug reaction (ADR) identification. Human review of social media data is infeasible due to data quantity, thus natural language processing techniques are necessary. Social media includes informal vocabulary and irregular grammar, which challenge natural language processing methods. Our objective is to develop a scalable, deep-learning approach that exceeds state-of-the-art ADR detection performance in social media...
February 22, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339723/leveraging-molecular-datasets-for-biomarker-based-clinical-trial-design-in-glioblastoma
#5
Shyam K Tanguturi, Lorenzo Trippa, Shakti H Ramkissoon, Kristine Pelton, David Knoff, David Sandak, Neal I Lindeman, Azra H Ligon, Rameen Beroukhim, Giovanni Parmigiani, Patrick Y Wen, Keith L Ligon, Brian M Alexander
Background.: Biomarkers can improve clinical trial efficiency, but designing and interpreting biomarker-driven trials require knowledge of relationships among biomarkers, clinical covariates, and endpoints. We investigated these relationships across genomic subgroups of glioblastoma (GBM) within our institution (DF/BWCC), validated results in The Cancer Genome Atlas (TCGA), and demonstrated potential impacts on clinical trial design and interpretation. Methods.: We identified genotyped patients at DF/BWCC, and clinical associations across 4 common GBM genomic biomarker groups were compared along with overall survival (OS), progression-free survival (PFS), and survival post-progression (SPP)...
February 20, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28339690/automated-classification-of-eligibility-criteria-in-clinical-trials-to-facilitate-patient-trial-matching-for-specific-patient-populations
#6
Kevin Zhang, Dina Demner-Fushman
Objective: To develop automated classification methods for eligibility criteria in ClinicalTrials.gov to facilitate patient-trial matching for specific populations such as persons living with HIV or pregnant women. Materials and Methods: We annotated 891 interventional cancer trials from ClinicalTrials.gov based on their eligibility for human immunodeficiency virus (HIV)-positive patients using their eligibility criteria. These annotations were used to develop classifiers based on regular expressions and machine learning (ML)...
February 19, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339684/embedding-nursing-interventions-into-the-world-health-organization-s-international-classification-of-health-interventions-ichi
#7
Nicola Fortune, Nicholas R Hardiker, Gillian Strudwick
Objective: : The International Classification of Health Interventions, currently being developed, seeks to span all sectors of the health system. Our objective was to test the draft classification's coverage of interventions commonly delivered by nurses, and propose changes to improve the utility and reliability of the classification for aggregating and analyzing data on nursing interventions. Materials and methods: : A 2-phase content mapping method was used: (1) three coders independently applied the classification to a dataset comprising 100 high-frequency nursing interventions; (2) the coders reached consensus for each intervention and identified reasons for initial discrepancies...
February 11, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339683/addressing-beacon-re-identification-attacks-quantification-and-mitigation-of-privacy-risks
#8
Jean Louis Raisaro, Florian Tramèr, Zhanglong Ji, Diyue Bu, Yongan Zhao, Knox Carey, David Lloyd, Heidi Sofia, Dixie Baker, Paul Flicek, Suyash Shringarpure, Carlos Bustamante, Shuang Wang, Xiaoqian Jiang, Lucila Ohno-Machado, Haixu Tang, XiaoFeng Wang, Jean-Pierre Hubaux
The Global Alliance for Genomics and Health (GA4GH) created the Beacon Project as a means of testing the willingness of data holders to share genetic data in the simplest technical context-a query for the presence of a specified nucleotide at a given position within a chromosome. Each participating site (or "beacon") is responsible for assuring that genomic data are exposed through the Beacon service only with the permission of the individual to whom the data pertains and in accordance with the GA4GH policy and standards...
February 20, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339644/development-and-validation-of-a-structured-query-language-implementation-of-the-elixhauser-comorbidity-index
#9
Richard H Epstein, Franklin Dexter
Objective: Comorbidity adjustment is often performed during outcomes and health care resource utilization research. Our goal was to develop an efficient algorithm in structured query language (SQL) to determine the Elixhauser comorbidity index. Materials and Methods: We wrote an SQL algorithm to calculate the Elixhauser comorbidities from Diagnosis Related Group and International Classification of Diseases (ICD) codes. Validation was by comparison to expected comorbidities from combinations of these codes and to the 2013 Nationwide Readmissions Database (NRD)...
February 16, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339559/using-a-stakeholder-engaged-approach-to-develop-and-validate-electronic-clinical-quality-measures
#10
Jill Boylston Herndon, Krishna Aravamudhan, Ronald L Stephenson, Ryan Brandon, Jesley Ruff, Frank Catalanotto, Huong Le
Objective: To describe the stakeholder-engaged processes used to develop, specify, and validate 2 oral health care electronic clinical quality measures. Materials and Methods: A broad range of stakeholders were engaged from conception through testing to develop measures and test feasibility, reliability, and validity following National Quality Forum guidance. We assessed data element feasibility through semistructured interviews with key stakeholders using a National Quality Forum-recommended scorecard...
October 7, 2016: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339547/effectiveness-of-the-strengthening-families-programme-10-14-in-poland-cluster-randomized-controlled-trial
#11
David R Foxcroft, Howard Callen, Emma L Davies, Katarzyna Okulicz-Kozaryn
: The Strengthening Families Programme for youth aged 10-14 and parents/carers (SFP10-14) is a family-based prevention intervention with positive results in trials in the United States. We assessed the effectiveness of SFP10-14 for preventing substance misuse in Poland. : Cluster randomized controlled trial with 20 communities (511 families; 614 young people) were allocated to SFP10-14 or a control arms. Primary outcomes were alcohol, smoking and other drug use. Secondary outcomes included parenting practices, parent-child relations, and child problem behaviour...
October 24, 2016: European Journal of Public Health
https://www.readbyqxmd.com/read/28339121/connecting-today-s-climates-to-future-analogs-to-facilitate-species-movement-under-climate-change
#12
Caitlin E Littlefield, Brad H McRae, Julia Michalak, Joshua J Lawler, Carlos Carroll
Increasing connectivity is an important strategy for facilitating species range shifts and maintaining biodiversity in the face of climate change. To date, however, few studies have included future climate projections in efforts to prioritize areas for increasing connectivity. Here, we identify key areas likely to facilitate climate-induced species movement across western North America. Using historical climate datasets and future climate projections, we mapped potential routes between current climates and their future analogs with a novel moving-window analysis based on electrical circuit theory...
March 24, 2017: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/28339103/iterative-dataset-optimization-in-automated-planning-implementation-for-breast-and-rectal-cancer-radiotherapy
#13
Jiawei Fan, Jiazhou Wang, Zhen Zhang, Weigang Hu
PURPOSE: To develop a new automated treatment planning solution for breast and rectal cancer radiotherapy. METHODS: The automated treatment planning solution developed in this study includes selection of the iterative optimized training dataset, dose volume histogram (DVH) prediction for the organs at risk (OARs), and automatic generation of clinically acceptable treatment plans. The iterative optimized training dataset is selected by an iterative optimization from 40 treatment plans for left-breast and rectal cancer patients who received radiation therapy...
March 24, 2017: Medical Physics
https://www.readbyqxmd.com/read/28339085/integrated-analysis-of-mrna-and-mirna-expression-profiles-in-pancreatic-ductal-adenocarcinoma
#14
Hongwei Sun, Liang Zhao, Kehua Pan, Zhao Zhang, Mengtao Zhou, Guoquan Cao
In the present study, to investigate the potential molecular mechanism of pancreatic ductal adenocarcinoma (PDAC), mRNA and miRNA expression profiles were integrated for systematic analysis. Results showed that a total of 76 common differentially expressed genes (DEGs) were identified from 2 mRNA expression profiles that contained 39 tumor and 15 normal samples. Notably, the tumor and normal samples were able to be clearly classified into 4 groups based on the DEGs. mRNA‑miRNA regulation network analysis indicated that 22 out of the 76 DEGs including MUC4, RRM2 and CCL2 are regulated by 5 reported miRNAs...
March 24, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28338966/a-comparison-of-sensitivity-specificity-imputation-direct-imputation-and-fully-bayesian-analysis-to-adjust-for-exposure-misclassification-when-validation-data-are-unavailable
#15
Marine Corbin, Stephen Haslett, Neil Pearce, Milena Maule, Sander Greenland
Purpose: Measurement error is an important source of bias in epidemiological studies. We illustrate three approaches to sensitivity analysis for the effect of measurement error: imputation of the 'true' exposure based on specifying the sensitivity and specificity of the measured exposure (SS); direct imputation (DI) using a regression model for the predictive values; and adjustment based on a fully Bayesian analysis. Methods: We deliberately misclassify smoking status in data from a case-control study of lung cancer...
March 14, 2017: International Journal of Epidemiology
https://www.readbyqxmd.com/read/28338943/dysfunction-of-large-scale-brain-networks-in-schizophrenia-a-meta-analysis-of-resting-state-functional-connectivity
#16
Debo Dong, Yulin Wang, Xuebin Chang, Cheng Luo, Dezhong Yao
Schizophrenia is a complex mental disorder with disorganized communication among large-scale brain networks, as demonstrated by impaired resting-state functional connectivity (rsFC). Individual rsFC studies, however, vary greatly in their methods and findings. We searched for consistent patterns of network dysfunction in schizophrenia by using a coordinate-based meta-analysis. Fifty-six seed-based voxel-wise rsFC datasets from 52 publications (2115 patients and 2297 healthy controls) were included in this meta-analysis...
March 11, 2017: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/28338845/computational-psychiatry-and-the-challenge-of-schizophrenia
#17
John H Krystal, John D Murray, Adam M Chekroud, Philip R Corlett, Genevieve Yang, Xiao-Jing Wang, Alan Anticevic
Schizophrenia research is plagued by enormous challenges in integrating and analyzing large datasets and difficulties developing formal theories related to the etiology, pathophysiology, and treatment of this disorder. Computational psychiatry provides a path to enhance analyses of these large and complex datasets and to promote the development and refinement of formal models for features of this disorder. This presentation introduces the reader to the notion of computational psychiatry and describes discovery-oriented and theory-driven applications to schizophrenia involving machine learning, reinforcement learning theory, and biophysically-informed neural circuit models...
March 8, 2017: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/28338722/dissecting-the-transcriptional-patterns-of-social-dominance-across-teleosts
#18
Suzy C P Renn, Cynthia F O'Rourke, Nadia Aubin-Horth, Eleanor J Fraser, Hans A Hofmann
In many species, under varying ecological conditions, social interactions among individuals result in the formation of dominance hierarchies. Despite general similarities, there are robust differences among dominance hierarchies across species, populations, environments, life stages, sexes, and individuals. Understanding the proximate mechanisms underlying the variation is an important step toward understanding the evolution of social behavior. However, physiological changes associated with dominance, such as gonadal maturation and somatic growth, often complicate efforts to identify the specific underlying mechanisms...
December 16, 2016: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/28338472/robust-cardiac-motion-estimation-using-ultrafast-ultrasound-data-a-low-rank-topology-preserving-approach
#19
Angelica I Aviles, Thomas Widlak, Alicia Casals, Maartje Nillesen, Habib Ammari
Cardiac motion estimation is an important diagnostic tool to detect heart diseases and it has been explored with modalities such as MRI and conventional ultrasound (US) sequences. US cardiac motion estimation still presents challenges because of the complex motion patterns and the presence of noise. In this work, we propose a novel approach to estimate the cardiac motion using ultrafast ultrasound data. -- Our solution is based on a variational formulation characterized by the L2-regularized class. The displacement is represented by a lattice of b-splines and we ensure robustness by applying a maximum likelihood type estimator...
March 24, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28338471/generalized-psf-modelling-for-optimized-quantitation-in-pet-imaging
#20
Saeed Ashrafinia, Hassan Mohy-Ud-Din, Nicolas Karakatsanis, Abhinav Jha, Michael Casey, Dan Kadrmas, Arman Rahmim
Point-Spread Function (PSF) modelling offers the capability to account for resolution degrading phenomena within the PET reconstruction framework. PSF modelling improves resolution and enhances contrast, but at the same time significantly alters image noise properties and induces edge overshoot effect. Thus, studying the effect of PSF modelling on quantitation task performance can be very important. Frameworks explored in the past involve a dichotomy of PSF vs. no-PSF modelling. By contrast, the present work focuses on quantitative performance evaluation of standard uptake value (SUV) PET images, while incorporating a wide spectrum of PSF models, including those that under- and over-estimate the true PSF, for the potential of enhanced quantitation of standardized uptake values (SUVs)...
March 24, 2017: Physics in Medicine and Biology
keyword
keyword
34174
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"