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The National Healthcare Safety Network's digital quality measures: CDC's automated measures for surveillance of patient safety

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2024年第5期31卷 1199-1205页

作者： Shehab, Nadine Alschuler, Liora Mcilvenna, Sean Gonzaga, Zabrina Laing, Andrew deRoode, David Dantes, Raymund B. Betz, Kristina Zheng, Shuai Abner, Sheila Stutler, Elizabeth Geimer, Rick Benin, Andrea L. Lantana Consulting Grp East Thetford VT 05043 USA CDCP Div Healthcare Qual Promot CDC Atlanta GA 30333 USA Emory Univ Div Hosp Med Dept Med Sch Med Atlanta GA 30322 USA CDC Div Healthcare Qual Promot 1600 Clifton Rd NE MS H16-3 Atlanta GA 30333 USA

Objective This article presents the National Healthcare Safety Network (NHSN)'s approach to automation for public health surveillance using digital quality measures (dQMs) via an open-source tool (NHSNLink) and piloting of this approach using real-world data in a newly established collaborative program (NHSNCoLab). The approach leverages Health Level Seven Fast Healthcare Interoperability Resources (FHIR) application programming interfaces to improve data collection and reporting for public health and patient safety beginning with common, clinically significant, and preventable patient harms, such as medication-related hypoglycemia, healthcare facility-onset Clostridioides difficile infection, and healthcare-associated venous thromboembolism. Conclusions The NHSN's FHIR dQMs hold the promise of minimizing the burden of reporting, improving accuracy, quality, and validity of data collected by NHSN, and increasing speed and efficiency of public health surveillance.

关键词： National Healthcare Safety Network fast healthcare interoperability resources data modernization automation healthcare data exchange application programming interface digital quality measure healthcare-associated infections patient safety medication safety

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Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective

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BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014年第1期1844卷 63-76页

作者： Perez-Riverol, Yasset Wang, Rui Hermjakob, Henning Mueller, Markus Vesada, Vladimir Vizcaino, Juan Antonio European Bioinformat Inst EMBL Outstn Cambridge CB10 1SD England Ctr Genet Engn & Biotechnol Dept Prote Havana Cuba CMU Swiss Inst Bioinformat Proteome Informat Grp CH-1211 Geneva Switzerland

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. (C) 2013 Elsevier B.V. All rights reserved.

关键词： Proteomics Databases Bioinformatics Software libraries application programming interface Open source software

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An intelligent listening framework for capturing encounter notes from a doctor-patient dialog

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BMC MEDICAL INFORMATICS AND DECISION MAKING 2009年第1-Sup期9卷 S3-S3页

作者： Klann, Jeffrey G. Szolovits, Peter Regenstrief Inst Hlth Care Indianapolis IN 46202 USA Indiana Univ Indianapolis IN 46202 USA MIT Comp Sci & Artificial Intelligence Lab Clin Decis Making Grp Cambridge MA 02139 USA

Background: Capturing accurate and machine-interpretable primary data from clinical encounters is a challenging task, yet critical to the integrity of the practice of medicine. We explore the intriguing possibility that technology can help accurately capture structured data from the clinical encounter using a combination of automated speech recognition (ASR) systems and tools for extraction of clinical meaning from narrative medical text. Our goal is to produce a displayed evolving encounter note, visible and editable (using speech) during the encounter. Results: This is very ambitious, and so far we have taken only the most preliminary steps. We report a simple proof-of-concept system and the design of the more comprehensive one we are building, discussing both the engineering design and challenges encountered. Without a formal evaluation, we were encouraged by our initial results. The proof-of-concept, despite a few false positives, correctly recognized the proper category of single- and multi-word phrases in uncorrected ASR output. The more comprehensive system captures and transcribes speech and stores alternative phrase interpretations in an XML-based format used by a text-engineering framework. It does not yet use the framework to perform the language processing present in the proof-of-concept. Conclusion: The work here encouraged us that the goal is reachable, so we conclude with proposed next steps. Some challenging steps include acquiring a corpus of doctor-patient conversations, exploring a workable microphone setup, performing user interface research, and developing a multi-speaker version of our tools.

关键词： application programming interface Automate Speech Recognition Clinical Encounter Computerize Physician Order Entry Automate Speech Recognition System

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Evaluating client application status for V-World Open API service

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SPATIAL INFORMATION RESEARCH 2016年第4期24卷 367-376页

作者： Jang, Han-sol Kim, Dong-kyu Kim, Jung-min Jang, In-sung ICTWAY IT Res Lab Seoul South Korea SNA Global Mkt Dept Seoul South Korea ETRI Spatial Informat Technol Res Team Daejeon South Korea

Since the V-World, the spatial information open platform service, has introduced to public in 2012, V-World users have been continuously increased. Specifically, V-World provides Open API to public institution and various enterprises. Responding to the future demands and expanding the V-World's services systematically, it is necessary to understand specific status of the public users' applied fields and top contents in order to predict the future demands and to enhance the service efficiency. In this paper, we verified V-World's applied fields and top contents based on web server logs which collected from 16 different web servers in May 2015, we evaluated the status of V-World's usage and suggested further considerations for the future service and expansion of the Open API.

关键词： Client application status application programming interface Spatial information open platform V-World

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OpenFDA: an innovative platform providing access to a wealth of FDA's publicly available data

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2016年第3期23卷 596-600页

作者： Kass-Hout, Taha A. Xu, Zhiheng Mohebbi, Matthew Nelsen, Hans Baker, Adam Levine, Jonathan Johanson, Elaine Bright, Roselie A. US FDA Silver Spring MD USA Iodine Inc 34 Clyde St San Francisco CA 94107 USA

Objective The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs). Materials and Methods Using cutting-edge technologies deployed on FDA's new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets;open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas;and infrastructure that can be adopted for other public health big data challenges. Results Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event. Conclusion With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products.

关键词： openFDA drug safety adverse event API application programming interface open data open source

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Fast extraction of high-quality framework-specific models from application code

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AUTOMATED SOFTWARE ENGINEERING 2009年第1期16卷 101-144页

作者： Antkiewicz, Michal Bartolomei, Thiago Tonelli Czarnecki, Krzysztof Univ Waterloo Generat Software Dev Lab Waterloo ON N2L 3G1 Canada

Framework-specific models represent the design of application code from the framework viewpoint by showing how framework-provided concepts are instantiated in the code. Retrieving such models quickly and precisely is necessary for practical model-supported software engineering, in which developers use design models for development tasks such as code understanding, verifying framework usage rules, and round-trip engineering. Also, comparing models extracted at different times of the software lifecycle supports software evolution tasks. We describe an experimental study of the static analyses necessary to automatically retrieve framework-specific models from application code. We reverse engineer a number of applications based on three open-source frameworks and evaluate the quality of the retrieved models. The models are expressed using framework-specific modeling languages (FSMLs), each designed for an open-source framework. For reverse engineering, we use prototype implementations of the three FSMLs. Our results show that for the considered frameworks and a large body of application code rather simple code analyses are sufficient for automatically retrieving framework-specific models with high precision and recall. Based on the initial results, we refine the static analyses and repeat the study on a larger set of applications to provide more evidence and confirm the results. The refined static analyses provide precision and recall of close to 100% for the analyzed applications.

关键词： Reverse engineering Framework-specific models Framework-specific modeling languages Static analysis Object-oriented frameworks application programming interface API

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Designing sea ice web APIs for ice information services

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EARTH SCIENCE INFORMATICS 2015年第3期8卷 483-497页

作者： Liu, Xintao Li, Songnian Huang, Wei Gong, Jun Ryerson Univ Dept Civil Engn Toronto ON M5B 2K3 Canada Jiangxi Normal Univ Sch Software Nanchang 330022 Peoples R China

Due to climate change and global warming, sea ice studies have recently gained more and more attention from various fields. Despite previous work on sea ice data collection, digitalization and dissemination over the web, efficient sharing of ice data and information remains unsolved. Further, little has been done on analyzing specific sea ice data user requirements and developing flexible web-based processing and analytical services based on existing studies, which are useful for both sea ice and non-sea-ice data users. In this paper, we aim to develop a series of Google Maps-like sea ice web application programming interfaces (API) for JavaScript, which provide a flexible and easy-to-use way to enable online sea ice data sharing, visualization and spatio-temporal analyses. We identify sea ice data user requirements at different levels through investigating a group of interested Canadian northerners, and then we design and implement an online sea ice web APIs prototype. We also provide a web tool for registering and sharing other ice web services and an online web coding and debugging sandbox to facilitate and attract more sea ice users and developers. We believe this work will be a good example and potentially benefit the development of web APIs for sea ice data and information services as well as other relevant studies.

关键词： Sea ice Web application programming interface Sharing Service Climate

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Step Into the Digital Age with Python

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CHEMICAL ENGINEERING PROGRESS 2021年第9期117卷 47-53页

作者： Albrecht, Jacob Sage Bionetworks Benchmarking & Data Challenges Seattle WA 98109 USA

The Python programming language is free, is considered easy to learn, and offers flexibility for nearly any digital task. It is maintained by the nonprofit Python Software Foundation. Python was first released in 1991 as an easy-to-use programming language that would have broad appeal. The language is 30 years old, but Python has seen incredible growth in just the past decade, driven by some key application areas, such as data science and machine learning. Here, Albrecht describes the many ways Python can be used for chemical engineering work in the digital age.

关键词： Language Software Chemical engineering programming languages application programming interface Flexibility Automation Machine learning Popularity Engineers Skills

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A high performance message-passing system for network of workstations

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JOURNAL OF SUPERCOMPUTING 1997年第2期11卷 159-179页

作者： Park, SY Hariri, S Department of Electrical Engineering and Computer Science Syracuse University Syracuse

With the proliferation of Network of Workstations (NOW) environment, there has been a great demand for a high performance message-passing system to implement High Performance Distributed Computing (HPDC) applications over NOW environment. NYNET (ATM wide area network testbed in New York state) Communication System (NCS) is a multithreaded message-passing system developed at Syracuse University that provides low-latency and high-throughput communication services over the Asynchronous Transfer Mode (ATM) based HPDC environment. NCS provides High Performance application Communication interface (HPI) to support applications that demand high-throughput and low-latency communication services. This paper outlines the general architecture of NCS and presents the implementation approach of NCS HPI over an ATM network. This interface has been developed by modifying Fore Systems' ATM application programming interface (API) and its device driver. NCS HPI uses read/write trap routines to bypass traditional operating system calls and kernel-level communication interface (e.g., UNIX System V Streams). It reduces latency, data transfer time, and avoid using traditional communication protocols (e.g., TCP/IP). This substantially improves the communication performance.

关键词： application programming interface message-passing tool ATM Network of Workstations multithreading High Performance Distributed Computing

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Efficient metadata mining of web-accessible neural morphologies

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PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY 2022年 168卷 94-102页

作者： Akram, Masood A. Ljungquist, Bengt Ascoli, Giorgio A. George Mason Univ Ctr Neural Informat Struct & Plast Volgenau Sch Engn Krasnow Inst Adv Study Fairfax VA 22030 USA George Mason Univ Dept Bioengn Volgenau Sch Engn Fairfax VA 22030 USA

Advancements in neuroscience research have led to steadily accelerating data production and sharing. The online community repository of neural reconstructions *** grew from fewer than 1000 digitally traced neurons in 2006 to more than 140,000 cells today, including glia that now constitute 10.1% of the content. Every reconstruction consists of a detailed 3D representation of branch geometry and connectivity in a standardized format, from which a collection of morphometric features is extracted and stored. Moreover, each entry in the database is accompanied by rich metadata annotation describing the animal subject, anatomy, and experimental details. The rapid expansion of this resource in the past decade was accompanied by a parallel rise in the complexity of the available information, creating both opportunities and challenges for knowledge mining. Here, we introduce a new summary reporting functionality, allowing *** users to efficiently download digests of metadata and morphometrics from multiple groups of similar cells for further analysis. We demonstrate the capabilities of the tool for both glia and neurons and present an illustrative statistical analysis of the resulting data.

关键词： NeuroMorpho Org Digital reconstructions Neuron Glia Morphometry application programming interface Summary reporting

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