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Biomedical informatics

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https://www.readbyqxmd.com/read/29769172/privacy-preserving-predictive-modeling-harmonization-of-contextual-embeddings-from-different-sources
#1
Yingxiang Huang, Junghye Lee, Shuang Wang, Jimeng Sun, Hongfang Liu, Xiaoqian Jiang
BACKGROUND: Data sharing has been a big challenge in biomedical informatics because of privacy concerns. Contextual embedding models have demonstrated a very strong representative capability to describe medical concepts (and their context), and they have shown promise as an alternative way to support deep-learning applications without the need to disclose original data. However, contextual embedding models acquired from individual hospitals cannot be directly combined because their embedding spaces are different, and naive pooling renders combined embeddings useless...
May 16, 2018: JMIR Medical Informatics
https://www.readbyqxmd.com/read/29737976/uniform-resolution-of-compact-identifiers-for-biomedical-data
#2
Sarala M Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A McMurry, Niall Beard, Rafael Jimenez, Jeffrey S Grethe, Henning Hermjakob, Maryann E Martone, Tim Clark
Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement data citation in accordance with widely accepted principles. Local accessions may however be prefixed with a namespace identifier, providing global uniqueness. Such "compact identifiers" have been widely used in biomedical informatics to support global resource identification with local identifier assignment...
May 8, 2018: Scientific Data
https://www.readbyqxmd.com/read/29700073/biomedical-informatics-on-the-cloud-a-treasure-hunt-for-advancing-cardiovascular-medicine
#3
REVIEW
Peipei Ping, Henning Hermjakob, Jennifer S Polson, Panagiotis V Benos, Wei Wang
In the digital age of cardiovascular medicine, the rate of biomedical discovery can be greatly accelerated by the guidance and resources required to unearth potential collections of knowledge. A unified computational platform leverages metadata to not only provide direction but also empower researchers to mine a wealth of biomedical information and forge novel mechanistic insights. This review takes the opportunity to present an overview of the cloud-based computational environment, including the functional roles of metadata, the architecture schema of indexing and search, and the practical scenarios of machine learning-supported molecular signature extraction...
April 27, 2018: Circulation Research
https://www.readbyqxmd.com/read/29681029/history-of-romanian-medical-informatics-learning-from-the-past-to-reshape-the-future
#4
George I Mihalas, Lacramioara Stoicu-Tivadar
OBJECTIVES:  The paper presents a review of the history of medical informatics in Romania, starting from the pioneering works, relating the present, and foreseeing the future. METHODS:  Major milestones of the development of this field have not been simply enumerated, but described within the specific socio-political frame, grasping the entire context over the last four decades in Romania. Two main perspectives have been traced: education and training in medical informatics and implementations in healthcare...
April 22, 2018: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/29677992/biomedical-informatics-how-to-choose-the-best-tool-for-each-task
#5
Fábio Maia, Luís Bastião Silva, José Luís Oliveira
The ever-increasing number of bioinformatics software tools that are publicly available, is leading to greater expectations about its regular use in clinical practice. However, from the end-users' perspective, they face many time the challenge of choosing the right tool for each task, from a panoply of solutions that have been developed over the years. In this paper, we propose a benchmarking methodology, based on a set of performance indicators, which can be used to identify the best methods and tools for each particular use case, both in research as in clinical practice...
2018: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/29669066/does-health-informatics-have-a-replication-crisis
#6
Enrico Coiera, Elske Ammenwerth, Andrew Georgiou, Farah Magrabi
Objective: Many research fields, including psychology and basic medical sciences, struggle with poor reproducibility of reported studies. Biomedical and health informatics is unlikely to be immune to these challenges. This paper explores replication in informatics and the unique challenges the discipline faces. Methods: Narrative review of recent literature on research replication challenges. Results: While there is growing interest in re-analysis of existing data, experimental replication studies appear uncommon in informatics...
April 13, 2018: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29621832/identifying-associations-between-somatic-mutations-and-clinicopathologic-findings-in-lung-cancer-pathology-reports
#7
Nishant Kumar, Laura J Tafe, John H Higgins, Jason D Peterson, Francise Blumental de Abreu, Sophie J Deharvengt, Gregory J Tsongalis, Christopher I Amos, Saeed Hassanpour
OBJECTIVE: We aim to build an informatics methodology capable of identifying statistically significant associations between the clinical findings of non-small cell lung cancer (NSCLC) recorded in patient pathology reports and the various clinically actionable genetic mutations identified from next-generation sequencing (NGS) of patient tumor samples. METHODS: We built an information extraction and analysis pipeline to identify the associations between clinical findings in the pathology reports of patients and corresponding genetic mutations...
February 2018: Methods of Information in Medicine
https://www.readbyqxmd.com/read/29602854/acupuncture-for-constipation-in-patients-with-stroke-protocol-of-a-systematic-review-and-meta-analysis
#8
Jingbo Zhai, Wei Mu, Jinhua Si, Yan Li, Chen Zhao, Hongcai Shang, Huanan Li, Guihua Tian
INTRODUCTION: Constipation is one of the most common complications in patients with stroke. Acupuncture has gained increased popularity for the management of constipation. However, there is a lack of supportive evidence on the efficacy of acupuncture for poststroke constipation. This systematic review aims to collect and critically appraise all the available evidence about the efficacy and safety of the acupuncture for constipation in poststroke patients. METHODS AND ANALYSIS: A comprehensive search of Pubmed, Embase, Cochrane Central Register of Controlled Trials, Web of Science, four Chinese databases (National Knowledge Infrastructure (CNKI), Chinese Biomedical Literatures database (CBM), Wanfang Digital Periodicals (WANFANG) and Chinese Science and Technology Periodicals (VIP) database), one Japanese medical database (National Institute of Informatics, CiNii) and one Korean medical database (Oriental Medicine Advanced Searching Integrated System, OASIS) will be conducted to identify randomised controlled trials of acupuncture for constipation in poststroke patients...
March 30, 2018: BMJ Open
https://www.readbyqxmd.com/read/29596416/eleven-quick-tips-for-architecting-biomedical-informatics-workflows-with-cloud-computing
#9
Brian S Cole, Jason H Moore
Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more...
March 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29568713/translating-new-science-into-the-drug-review-process-the-us-fda-s-division-of-applied-regulatory-science
#10
Rodney Rouse, Naomi Kruhlak, James Weaver, Keith Burkhart, Vikram Patel, David G Strauss
In 2011, the US Food and drug Administration (FDA) developed a strategic plan for regulatory science that focuses on developing new tools, standards, and approaches to assess the safety, efficacy, quality, and performance of FDA-regulated products. In line with this, the Division of Applied Regulatory Science was created to move new science into the Center for Drug Evaluation and Research (CDER) review process and close the gap between scientific innovation and drug review. The Division, located in the Office of Clinical Pharmacology, is unique in that it performs mission-critical applied research and review across the translational research spectrum including in vitro and in vivo laboratory research, in silico computational modeling and informatics, and integrated clinical research covering clinical pharmacology, experimental medicine, and postmarket analyses...
March 2018: Therapeutic Innovation & Regulatory Science
https://www.readbyqxmd.com/read/29566172/biomedical-informatics-and-machine-learning-for-clinical-genomics
#11
James Diao, Isaac S Kohane, Arjun K Manrai
While tens of thousands of pathogenic variants are used in the myriad clinical applications of genomics, there remains limited quantitative risk information (i.e. penetrance) or consensus about the clinical utility of the majority of extant variants and tests. Relatedly, with the rising demand for genetic counseling, there is a need for computational approaches that scale the ability of counselors to interpret new and existing variants, whether by automating the determination of pathogenicity or filtering variants too common in the general population to be sufficiently penetrant...
March 16, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29551332/intelligent-and-effective-informatic-deconvolution-of-big-data-and-its-future-impact-on-the-quantitative-nature-of-neurodegenerative-disease-therapy
#12
REVIEW
Stuart Maudsley, Viswanath Devanarayan, Bronwen Martin, Hugo Geerts
Biomedical data sets are becoming increasingly larger and a plethora of high-dimensionality data sets ("Big Data") are now freely accessible for neurodegenerative diseases, such as Alzheimer's disease. It is thus important that new informatic analysis platforms are developed that allow the organization and interrogation of Big Data resources into a rational and actionable mechanism for advanced therapeutic development. This will entail the generation of systems and tools that allow the cross-platform correlation between data sets of distinct types, for example, transcriptomic, proteomic, and metabolomic...
March 15, 2018: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/29512494/a-novel-fuzzy-rough-selection-of-non-linearly-extracted-features-for-schizophrenia-diagnosis-using-fmri
#13
Akanksha Juneja, Bharti Rana, R K Agrawal
BACKGROUND AND OBJECTIVES: Schizophrenia is a severe brain disorder primarily diagnosed through externally observed behavioural symptoms due to the dearth of established clinical tests. Functional magnetic resonance imaging (fMRI) can capture the distortions caused by schizophrenia in the brain activation. Hence, it can be useful for developing a decision model that performs computer-aided diagnosis of schizophrenia. But, fMRI data is huge in dimension. Therefore dimension reduction is indispensable...
March 2018: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/29438494/artificial-intelligence-in-drug-combination-therapy
#14
Igor F Tsigelny
Currently, the development of medicines for complex diseases requires the development of combination drug therapies. It is necessary because in many cases, one drug cannot target all necessary points of intervention. For example, in cancer therapy, a physician often meets a patient having a genomic profile including more than five molecular aberrations. Drug combination therapy has been an area of interest for a while, for example the classical work of Loewe devoted to the synergism of drugs was published in 1928-and it is still used in calculations for optimal drug combinations...
February 9, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29431517/informatics-and-machine-learning-to-define-the-phenotype
#15
Anna Okula Basile, Marylyn DeRiggi Ritchie
For the past decade, the focus of complex disease research has been the genotype. From technological advancements to the development of analysis methods, great progress has been made. However, advances in our definition of the phenotype have remained stagnant. Phenotype characterization has recently emerged as an exciting area of informatics and machine learning. The copious amounts of diverse biomedical data that have been collected may be leveraged with data-driven approaches to elucidate trait-related features and patterns...
March 2018: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/29373850/machine-learning-takes-on-health-care-leonard-d-avolio-s-cyft-employs-big-data-to-benefit-patients-and-providers
#16
Leslie Mertz
When Leonard D'Avolio (Figure 1) was working on his Ph.D. degree in biomedical informatics, he saw the power of machine learning in transforming multiple industries; health care, however, was not among them. "The reason that Amazon, Netflix, and Google have transformed their industries is because they have embedded learning throughout every aspect of what they do. If we could prove that is possible in health care too, I thought we would have the potential to have a huge impact," he says.
January 2018: IEEE Pulse
https://www.readbyqxmd.com/read/29304188/drug-knowledge-bases-and-their-applications-in-biomedical-informatics-research
#17
Yongjun Zhu, Olivier Elemento, Jyotishman Pathak, Fei Wang
Recent advances in biomedical research have generated a large volume of drug-related data. To effectively handle this flood of data, many initiatives have been taken to help researchers make good use of them. As the results of these initiatives, many drug knowledge bases have been constructed. They range from simple ones with specific focuses to comprehensive ones that contain information on almost every aspect of a drug. These curated drug knowledge bases have made significant contributions to the development of efficient and effective health information technologies for better health-care service delivery...
January 3, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29302090/an-approach-for-some-in-advanced-pharmacy-informatics-education
#18
Allen Flynn, Brent I Fox, Kevin A Clauson, Terry L Seaton, Elizabeth Breeden
Computerization is transforming health care while the quantity and complexity of biomedical knowledge rapidly grows. Today, all clinicians use health information technology (HIT), but only some pharmacists need to be cross-trained in "all" that advanced informatics entails so they can devise new and better information systems to support the pharmacy practice of the future. We propose a dual approach to informatics education in pharmacy: incorporate fundamental informatics education into pharmacy curricula for all students; and train some students interested in becoming informatics experts to design, develop, implement, and evaluate novel HIT for pharmacy...
November 2017: American Journal of Pharmaceutical Education
https://www.readbyqxmd.com/read/29284909/evaluation-of-founding-members-of-the-international-academy-of-health-sciences-informatics-iahsi-based-on-google-scholar-and-scopus-parameters
#19
Izet Masic
Introduction: The International Academy of Health Sciences Informatics (IAHSI) is established by International Medical Informatics Association (IMIA) which is the world body for health and biomedical informatics. The Academy will serve as an honor society that recognizes expertise in biomedical and health informatics internationally. Academy membership will be one of the highest honors in the international field of biomedical and health informatics. Aim: To present scientometric analysis of founding members of the International Academy of Health Sciences Informatics, to evaluate members and their scientific rating...
December 2017: Acta Informatica Medica: AIM
https://www.readbyqxmd.com/read/29234465/ten-quick-tips-for-machine-learning-in-computational-biology
#20
REVIEW
Davide Chicco
Machine learning has become a pivotal tool for many projects in computational biology, bioinformatics, and health informatics. Nevertheless, beginners and biomedical researchers often do not have enough experience to run a data mining project effectively, and therefore can follow incorrect practices, that may lead to common mistakes or over-optimistic results. With this review, we present ten quick tips to take advantage of machine learning in any computational biology context, by avoiding some common errors that we observed hundreds of times in multiple bioinformatics projects...
2017: BioData Mining
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