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https://www.readbyqxmd.com/read/28333934/visualizing-the-structure-of-rna-seq-expression-data-using-grade-of-membership-models
#1
Kushal K Dey, Chiaowen Joyce Hsiao, Matthew Stephens
Grade of membership models, also known as "admixture models", "topic models" or "Latent Dirichlet Allocation", are a generalization of cluster models that allow each sample to have membership in multiple clusters. These models are widely used in population genetics to model admixed individuals who have ancestry from multiple "populations", and in natural language processing to model documents having words from multiple "topics". Here we illustrate the potential for these models to cluster samples of RNA-seq gene expression data, measured on either bulk samples or single cells...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28330635/the-association-between-muscle-weakness-and-incident-diabetes-in%C3%A2-older-mexican-americans
#2
Ryan McGrath, Brenda M Vincent, Soham Al Snih, Kyriakos S Markides, Mark D Peterson
OBJECTIVES: A natural decline of muscle strength occurs during the aging process; however, preserving muscle strength may lower the rate of many preventable diseases such as diabetes, especially in higher risk populations. The purpose of this study was to examine the sex-specific association between muscle weakness and incident diabetes in older Mexican Americans. DESIGN: Observational, longitudinal study. SETTING: Urban and rural households in the Southwestern United States...
March 18, 2017: Journal of the American Medical Directors Association
https://www.readbyqxmd.com/read/28329799/a-theory-of-relational-ageism-a-discourse-analysis-of-the-2015-white-house-conference-on-aging
#3
Tracey L Gendron, Jennifer Inker, Elizabeth Ayn Welleford
Purpose: The widespread use of ageist language is generally accepted as commonplace and routine in most cultures and settings. In order to disrupt ageism, we must examine the use of ageist language and sentiments among those on the front line of providing advocacy, services, and policy for older adults; the professional culture of the aging services network. The recorded video segments from the sixth White House Conference on Aging (WHCOA) provided a unique opportunity to examine discourse used by professionals and appointed representatives in the field of aging within a professional sociocultural context...
January 24, 2017: Gerontologist
https://www.readbyqxmd.com/read/28328939/multimodal-mr-imaging-reveals-large-scale-structural-and-functional-connectivity-changes-in-profound-early-blindness
#4
Corinna M Bauer, Gabriella V Hirsch, Lauren Zajac, Bang-Bon Koo, Olivier Collignon, Lotfi B Merabet
In the setting of profound ocular blindness, numerous lines of evidence demonstrate the existence of dramatic anatomical and functional changes within the brain. However, previous studies based on a variety of distinct measures have often provided inconsistent findings. To help reconcile this issue, we used a multimodal magnetic resonance (MR)-based imaging approach to provide complementary structural and functional information regarding this neuroplastic reorganization. This included gray matter structural morphometry, high angular resolution diffusion imaging (HARDI) of white matter connectivity and integrity, and resting state functional connectivity MRI (rsfcMRI) analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28328520/a-natural-language-processing-framework-for-assessing-hospital-readmissions-for-patients-with-copd
#5
Ankur Agarwal, Christopher Baechle, Ravi Behara, Xingquan Zhu
With the passage of recent federal legislation many medical institutions are now responsible for reaching target hospital readmission rates. Chronic diseases account for many hospital readmissions and Chronic Obstructive Pulmonary Disease has been recently added to the list of diseases for which the United States government penalizes hospitals incurring excessive readmissions. Though there have been efforts to statistically predict those most in danger of readmission, few have focused primarily on unstructured clinical notes...
March 17, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28328252/liberal-entity-extraction-rapid-construction-of-fine-grained-entity-typing-systems
#6
Lifu Huang, Jonathan May, Xiaoman Pan, Heng Ji, Xiang Ren, Jiawei Han, Lin Zhao, James A Hendler
The ability of automatically recognizing and typing entities in natural language without prior knowledge (e.g., predefined entity types) is a major challenge in processing such data. Most existing entity typing systems are limited to certain domains, genres, and languages. In this article, we propose a novel unsupervised entity-typing framework by combining symbolic and distributional semantics. We start from learning three types of representations for each entity mention: general semantic representation, specific context representation, and knowledge representation based on knowledge bases...
March 2017: Big Data
https://www.readbyqxmd.com/read/28327593/characterisation-of-mental-health-conditions-in-social-media-using-informed-deep-learning
#7
George Gkotsis, Anika Oellrich, Sumithra Velupillai, Maria Liakata, Tim J P Hubbard, Richard J B Dobson, Rina Dutta
The number of people affected by mental illness is on the increase and with it the burden on health and social care use, as well as the loss of both productivity and quality-adjusted life-years. Natural language processing of electronic health records is increasingly used to study mental health conditions and risk behaviours on a large scale. However, narrative notes written by clinicians do not capture first-hand the patients' own experiences, and only record cross-sectional, professional impressions at the point of care...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28322404/device-and-programming-abstractions-for-spatiotemporal-control-of-active-micro-particle-swarms
#8
Amy T Lam, Karina G Samuel-Gama, Jonathan Griffin, Matthew Loeun, Lukas C Gerber, Zahid Hossain, Nate J Cira, Seung Ah Lee, Ingmar H Riedel-Kruse
We present a hardware setup and a set of executable commands for spatiotemporal programming and interactive control of a swarm of self-propelled microscopic agents inside a microfluidic chip. In particular, local and global spatiotemporal light stimuli are used to direct the motion of ensembles of Euglena gracilis, a unicellular phototactic organism. We develop three levels of programming abstractions (stimulus space, swarm space, and system space) to create a scripting language for directing swarms. We then implement a multi-level proof-of-concept biotic game using these commands to demonstrate their utility...
March 21, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28316892/from-big-data-to-diagnosis-and-prognosis-gene-expression-signatures-in-liver-hepatocellular-carcinoma
#9
Hong Yang, Xin Zhang, Xiao-Yong Cai, Dong-Yue Wen, Zhi-Hua Ye, Liang Liang, Lu Zhang, Han-Lin Wang, Gang Chen, Zhen-Bo Feng
BACKGROUND: Liver hepatocellular carcinoma accounts for the overwhelming majority of primary liver cancers and its belated diagnosis and poor prognosis call for novel biomarkers to be discovered, which, in the era of big data, innovative bioinformatics and computational techniques can prove to be highly helpful in. METHODS: Big data aggregated from The Cancer Genome Atlas and Natural Language Processing were integrated to generate differentially expressed genes...
2017: PeerJ
https://www.readbyqxmd.com/read/28300761/incorporating-hypnosis-into-pediatric-clinical-encounters
#10
Robert A Pendergrast
Increasing numbers of licensed health professionals who care for children have been trained in clinical hypnosis. The evidence base for the safety and efficacy of this therapeutic approach in a wide variety of conditions is also growing. Pediatricians and other health professionals who have received training may wish to apply these skills in appropriate clinical scenarios but still may be unsure of the practical matters of how to incorporate this skill-set into day to day practice. Moreover, the practical application of such skills will take very different forms depending on the practice setting, types of acute or chronic conditions, patient and family preferences, and the developmental stages of the child or teen...
March 16, 2017: Children
https://www.readbyqxmd.com/read/28299240/validation-of-the-total-visual-acuity-extraction-algorithm-tova-for-automated-extraction-of-visual-acuity-data-from-free-text-unstructured-clinical-records
#11
Douglas M Baughman, Grace L Su, Irena Tsui, Cecilia S Lee, Aaron Y Lee
PURPOSE: With increasing volumes of electronic health record data, algorithm-driven extraction may aid manual extraction. Visual acuity often is extracted manually in vision research. The total visual acuity extraction algorithm (TOVA) is presented and validated for automated extraction of visual acuity from free text, unstructured clinical notes. METHODS: Consecutive inpatient ophthalmology notes over an 8-year period from the University of Washington healthcare system in Seattle, WA were used for validation of TOVA...
March 2017: Translational Vision Science & Technology
https://www.readbyqxmd.com/read/28294714/where-is-the-beat-the-neural-correlates-of-lexical-stress-and-rhythmical-well-formedness-in-auditory-story-comprehension
#12
Katerina D Kandylaki, Karen Henrich, Arne Nagels, Tilo Kircher, Ulrike Domahs, Matthias Schlesewsky, Ina Bornkessel-Schlesewsky, Richard Wiese
While processing continuous speech, humans use beat perception to correctly identify word boundaries. The beats of language are stress patterns that are created by combining lexical (word-specific) stress patterns and the rhythm of a specific language. Sometimes, the lexical stress pattern needs to be altered to obey the rhythm of the language. This study investigated this interplay of lexical stress patterns and rhythmical well-formedness in natural speech with fMRI. Previous electrophysiological studies on cases in which a regular lexical stress pattern may be altered to obtain rhythmical well-formedness showed that even subtle rhythmic deviations are detected by the brain if attention is directed toward prosody...
March 15, 2017: Journal of Cognitive Neuroscience
https://www.readbyqxmd.com/read/28293864/using-probabilistic-record-linkage-of-structured-and-unstructured-data-to-identify-duplicate-cases-in-spontaneous-adverse-event-reporting-systems
#13
Kory Kreimeyer, David Menschik, Scott Winiecki, Wendy Paul, Faith Barash, Emily Jane Woo, Meghna Alimchandani, Deepa Arya, Craig Zinderman, Richard Forshee, Taxiarchis Botsis
INTRODUCTION: Duplicate case reports in spontaneous adverse event reporting systems pose a challenge for medical reviewers to efficiently perform individual and aggregate safety analyses. Duplicate cases can bias data mining by generating spurious signals of disproportional reporting of product-adverse event pairs. OBJECTIVE: We have developed a probabilistic record linkage algorithm for identifying duplicate cases in the US Vaccine Adverse Event Reporting System (VAERS) and the US Food and Drug Administration Adverse Event Reporting System (FAERS)...
March 14, 2017: Drug Safety: An International Journal of Medical Toxicology and Drug Experience
https://www.readbyqxmd.com/read/28281211/bayesian-molecular-design-with-a-chemical-language-model
#14
Hisaki Ikebata, Kenta Hongo, Tetsu Isomura, Ryo Maezono, Ryo Yoshida
The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. We address the issue of accelerating the material discovery with state-of-the-art machine learning techniques. The method involves two different types of prediction; the forward and backward predictions. The objective of the forward prediction is to create a set of machine learning models on various properties of a given molecule. Inverting the trained forward models through Bayes' law, we derive a posterior distribution for the backward prediction, which is conditioned by a desired property requirement...
March 9, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28275425/a-clinical-and-ethical-review-on-late-results-and-benefits-after-evar
#15
REVIEW
Carlo Setacci, Pasqualino Sirignano, Vittorio Fineschi, Paola Frati, Giovanna Ricci, Francesco Speziale
INTRODUCTION: The aim of this review is to assess if late mortality after endovascular repair (EVAR) of abdominal aortic aneurysms (AAA) is a real problem, and whether it could be an issue in the case of medical litigation. MATERIAL AND METHODS: A review of all English language literature was performed on PubMed web-site, looking for all papers reporting EVAR long-term mortality rate. EVAR performances were reviewed also from an ethical and medico-legal point of view, based on current Italian laws...
April 2017: Annals of Medicine and Surgery
https://www.readbyqxmd.com/read/28270190/social-media-for-arthritis-related-comparative-effectiveness-and-safety-research-and-the-impact-of-direct-to-consumer-advertising
#16
Jeffrey R Curtis, Lang Chen, Phillip Higginbotham, W Benjamin Nowell, Ronit Gal-Levy, James Willig, Monika Safford, Joseph Coe, Kaitlin O'Hara, Roee Sa'adon
BACKGROUND: Social media may complement traditional data sources to answer comparative effectiveness/safety questions after medication licensure. METHODS: The Treato platform was used to analyze all publicly available social media data including Facebook, blogs, and discussion boards for posts mentioning inflammatory arthritis (e.g. rheumatoid, psoriatic). Safety events were self-reported by patients and mapped to medical ontologies, resolving synonyms. Disease and symptom-related treatment indications were manually redacted...
March 7, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28268855/the-effects-of-deep-network-topology-on-mortality-prediction
#17
Hao Du, Mohammad M Ghassemi, Mengling Feng
Deep learning has achieved remarkable results in the areas of computer vision, speech recognition, natural language processing and most recently, even playing Go. The application of deep-learning to problems in healthcare, however, has gained attention only in recent years, and it's ultimate place at the bedside remains a topic of skeptical discussion. While there is a growing academic interest in the application of Machine Learning (ML) techniques to clinical problems, many in the clinical community see little incentive to upgrade from simpler methods, such as logistic regression, to deep learning...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28268838/visualizing-patient-journals-by-combining-vital-signs-monitoring-and-natural-language-processing
#18
Adnan Vilic, John Asger Petersen, Karsten Hoppe, Helge B D Sorensen
This paper presents a data-driven approach to graphically presenting text-based patient journals while still maintaining all textual information. The system first creates a timeline representation of a patients' physiological condition during an admission, which is assessed by electronically monitoring vital signs and then combining these into Early Warning Scores (EWS). Hereafter, techniques from Natural Language Processing (NLP) are applied on the existing patient journal to extract all entries. Finally, the two methods are combined into an interactive timeline featuring the ability to see drastic changes in the patients' health, and thereby enabling staff to see where in the journal critical events have taken place...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28268720/s2ni-a-mobile-platform-for-nutrition-monitoring-from-spoken-data
#19
Niloofar Hezarjaribi, Cody A Reynolds, Drew T Miller, Naomi Chaytor, Hassan Ghasemzadeh
Diet and physical activity are important lifestyle and behavioral factors in self-management and prevention of many chronic diseases. Mobile sensors such as accelerometers have been used in the past to objectively measure physical activity or detect eating time. Diet monitoring, however, still relies on self-recorded data by end users where individuals use mobile devices for recording nutrition intake by either entering text or taking images. Such approaches have shown low adherence in technology adoption and achieve only moderate accuracy...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28267590/unsupervised-ensemble-ranking-of-terms-in-electronic-health-record-notes-based-on-their-importance-to-patients
#20
Jinying Chen, Hong Yu
BACKGROUND: Allowing patients to access their own electronic health record (EHR) notes through online patient portals has the potential to improve patient-centered care. However, EHR notes contain abundant medical jargon that can be difficult for patients to comprehend. One way to help patients is to reduce information overload and help them focus on medical terms that matter most to them. Targeted education can then be developed to improve patient EHR comprehension and the quality of care...
March 3, 2017: Journal of Biomedical Informatics
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