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Vol 42 Iss S1 April 2021 Vol 42 | Iss S1 | April 2021 Abstracts
Vol 42 Iss S1 April 2021 Vol Vol 42 | Iss S1 | April | 2021 Abstracts Top Six Abstracts T2 One Year Follow up Results of the DETECT Enzymatic Debridement Multicenter RCT T1 Initial Results of the American Burn Association (ABA) Multi-Center Evaluation William L. Hickerson, MD, Jeremy Goverman, MD, on the Effectiveness of the Burn Navigator Sigrid A. Blome-Eberwein, MD, Adam Singer, MD, Lucy Wibbenmeyer, MD, Nicholas Meyer, MD, Julie A. Rizzo, MD FACS, Maria L. Serio-Melvin, Joshua S. Carson, MD, FACS, James Gallagher, MD, MSN RN, Elsa Coates, MS, RN, CCRN, FACS, Steven Kahn, MD, Dhaval Bhavsar, MBBS, Nehemiah T. Liu, MS, Jose Salinas, PhD David Mozingo, MD, Tam N. Pham, MD, FACS, United States Army Institute of Surgical Research, Nicole S. Gibran, MD, FACS, Jeffrey W. Shupp, Fort Sam Houston, Texas MD, FACS, Kevin N. Foster, MD, MBA, FACS, Giavonni M. Lewis, MD, FACS, Julie Caffrey, DO, Introduction: The Burn Navigator (BN) is an FDA-cleared MS, FACOS, Yaron Shoham, MD clinical decision support tool used to aid fluid resuscitation Firefighters’ Regional Burn Center, Memphis, Tennes- after major burn injury. The BN provides users with hourly see; Massachusetts General Hospital, Boston, Massa- recommendations for fluid titration during the initial resus- chusetts; LVHN, Allentown, Pennsylvania; Renais- citation based on various factors. The objective of this multi- sance School of Medicine at Stony Brook University, center observational study was to evaluate the resuscitation Stony Brook, New York; University of Iowa Hospitals volumes and related outcomes of patients admitted to five & Clinics, Iowa City, Iowa; Columbia-St. Mary’s ABA verified burn centers who underwent intravenous fluid Milwaukee Campus, Milwaukee, Wisconsin; UF resuscitation utilizing the BN. -
Thesis Entire.Pdf (12.90Mb)
Faculty OF Science AND TECHNOLOGY Department OF Computer Science TOWARD ReprODUCIBLE Analysis AND ExplorATION OF High-ThrOUGHPUT Biological Datasets — Bjørn Fjukstad A DISSERTATION FOR THE DEGREE OF Philosophiae Doctor – 2018 This thesis document was typeset using the UiT Thesis LaTEX Template. © 2018 – http://github.com/egraff/uit-thesis “Ta aldri problemene på forskudd, for da får du dem to ganger, men ta gjerne seieren på forskudd, for hvis ikke er det altfor sjelden du får oppleve den.” –Ivar Tollefsen AbstrACT There is a rapid growth in the number of available biological datasets due to the advent of high-throughput data collection instruments combined with cheap compute infrastructure. Modern instruments enable the analysis of biological data at different levels, from small DNA sequences through larger cell structures, and up to the function of entire organs. These new datasets have brought the need to develop new software packages to enable novel insights into the underlying biological mechanisms in the development and progression of diseases such as cancer. The heterogeneity of biological datasets require researchers to tailor the explo- ration and analyses with a wide range of different tools and systems. However, despite the need for their integration, few of them provide standard inter- faces for analyses implemented using different programming languages and frameworks. In addition, because of the many tools, different input parame- ters, and references to databases, it is necessary to record these correctly. The lack of such details complicates reproducing the original results and the reuse of the analyses on new datasets. This increases the analysis time and leaves unrealized potential for scientific insights. -
Opening Reproducible Research: Research Project Website and Blog Blog Post Authors
Opening Reproducible Research: research project website and blog Blog post authors: Daniel Nüst Lukas Lohoff Marc Schutzeichel Markus Konkol Matthias Hinz Rémi Rampin Vicky Steeves Opening Reproducible Research | doi:10.5281/zenodo.1485438 Blog posts Demo server update 14 Aug 2018 | By Daniel Nüst We’ve been working on demonstrating our reference-implementation during spring an managed to create a number of example workspaces. We now decided to publish these workspaces on our demo server. Screenshot 1: o2r reference implementation listing of published Executable Research Compendia . The right-hand side shows a metadata summary including original authors. The papers were originally published in Journal of Statistical Software or in a Copernicus Publications journal under open licenses. We have created an R Markdown document for each paper based on the included data and code following the ERC specification for naming core files, but only included data, an R Markdown document and a HTML display file. The publication metadata, the runtime environment description (i.e. a Dockerfile ), and the runtime image (i.e. a Docker image tarball) were all created during the ERC creation process without any human interaction (see the used R code for upload), since required metadata were included in the R Markdown document’s front matter. The documents include selected figures or in some cases the whole paper, if runtime is not extremely long. While the paper’s authors are correctly linked in the workspace metadata (see right hand side in Screenshot 1), the “o2r author” of all papers is o2r team member Daniel since he made the uploads. -
Imagej2: Imagej for the Next Generation of Scientific Image Data Curtis T
Rueden et al. BMC Bioinformatics (2017) 18:529 DOI 10.1186/s12859-017-1934-z SOFTWARE Open Access ImageJ2: ImageJ for the next generation of scientific image data Curtis T. Rueden1, Johannes Schindelin1,2, Mark C. Hiner1, Barry E. DeZonia1, Alison E. Walter1,2, Ellen T. Arena1,2 and Kevin W. Eliceiri1,2* Abstract Background: ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software’s ability to handle the requirements of modern science. Results: We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called “ImageJ2” in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. -
Jsr223: a Java Platform Integration for R with Programming Languages Groovy, Javascript, Jruby, Jython, and Kotlin by Floid R
CONTRIBUTED RESEARCH ARTICLES 440 jsr223: A Java Platform Integration for R with Programming Languages Groovy, JavaScript, JRuby, Jython, and Kotlin by Floid R. Gilbert and David B. Dahl Abstract The R package jsr223 is a high-level integration for five programming languages in the Java platform: Groovy, JavaScript, JRuby, Jython, and Kotlin. Each of these languages can use Java objects in their own syntax. Hence, jsr223 is also an integration for R and the Java platform. It enables developers to leverage Java solutions from within R by embedding code snippets or evaluating script files. This approach is generally easier than rJava’s low-level approach that employs the Java Native Interface. jsr223’s multi-language support is dependent on the Java Scripting API: an implementation of “JSR-223: Scripting for the Java Platform” that defines a framework to embed scripts in Java applications. The jsr223 package also features extensive data exchange capabilities and a callback interface that allows embedded scripts to access the current R session. In all, jsr223 makes solutions developed in Java or any of the jsr223-supported languages easier to use in R. Introduction About the same time Ross Ihaka and Robert Gentleman began developing R at the University of Auckland in the early 1990s, James Gosling and the so-called Green Project Team was working on a new programming language at Sun Microsystems in California. The Green Team did not set out to make a new language; rather, they were trying to move platform-independent, distributed computing into the consumer electronics marketplace. As Gosling explained, “All along, the language was a tool, not the end” (O’Connell, 1995). -
C L I N T E T T I N G
1 C L I N T E T T I N G E R AN ALPHABET OF REINVENTION by Clint Ettinger 1. A - E is for Exchange 2. F - K is for Kimmy 3. L - T is for Trio 4. U - Z is for Zap ONE A) The Oxford American Dictionary defines ‘reinventing oneself’ as taking up a radically new job or way of life. The Macmillan Dictionary defines it as changing the way you behave or the things you do so that people think of you as a different kind of person. Quite a difference. B) So, must we really change? Or should we just wear a veneer of change so that others perceive us as having changed? C) is for Change or Die Writer and entrepreneur John Mashni firmly believes there are only three types of reinvention 1. Reactive Reinvention - when an external event occurs and forces you to change. 2. Proactive Reinvention - when you intentionally change to capitalize on an opportunity. 3. Reflective Reinvention - when you fail at something but still have a strong desire to continue in that particular endeavor. D) “Make reinvention your lifestyle, and you’ll stay young at heart no matter your chronological age. Keep on reinventing yourself, and death becomes nothing more significant than the period at the end of this sentence.”1 E) is for Exchange Last week during my second-year writing class, I asked everyone what they thought about the topic ‘reinventing oneself.’ “These two words bring both happiness and fear,” Apple said. “It’s more complex than that. -
Downloaded Using Standard HTTP Mechanics
UCLA UCLA Electronic Theses and Dissertations Title Embedded Scientific Computing: A Scalable, Interoperable and Reproducible Approach to Statistical Software for Data-Driven Business and Open Science Permalink https://escholarship.org/uc/item/4q6105rw Author Ooms, Jeroen Publication Date 2014 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California University of California Los Angeles Embedded Scientific Computing: A Scalable, Interoperable and Reproducible Approach to Statistical Software for Data-Driven Business and Open Science A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Statistics by Jeroen Ooms 2014 c Copyright by Jeroen Ooms 2014 Abstract of the Dissertation Embedded Scientific Computing: A Scalable, Interoperable and Reproducible Approach to Statistical Software for Data-Driven Business and Open Science by Jeroen Ooms Doctor of Philosophy in Statistics University of California, Los Angeles, 2014 Professor Frederick Paik Schoenberg, Co-chair Professor Mark Hansen, Co-chair Methods for scientific computing are traditionally implemented in specialized soft- ware packages assisting the statistician in all facets of the data analysis process. A single product typically includes a wealth of functionality to interactively manage, explore and analyze data, and often much more. However, increasingly many users and organizations wish to integrate statistical computing into third party software. Rather than working in a specialized statistical environment, methods to analyze and visualize data get incorporated into pipelines, web applications and big data infrastructures. This way of doing data analysis requires a different approach to statistical software which emphasizes interoperability and programmable in- terfaces rather than user interaction. We refer to this branch of computing as embedded scientific computing. -
Héctor Corrada Bravo CMSC498T Spring 2015 University of Maryland Computer Science
Intro to R Héctor Corrada Bravo CMSC498T Spring 2015 University of Maryland Computer Science http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html?_r=2&pagewanted=1 http://www.forbes.com/forbes/2010/0524/opinions-software-norman-nie-spss-ideas-opinions.html http://www.theregister.co.uk/2010/05/06/revolution_commercial_r/ Some history • John Chambers and others started developing the “S” language in 1976 • Version 4 of the language definition(currently in use) was settled in 1998 • That year, “S” won the ACM Software System Award Some history • Ihaka and Gentleman (of NYTimes fame) create R in 1991 • They wanted lexical scoping (see NYTimes pic) • Released under GNU GPL in 1995 • Maintained by R Core Group since1997 2011 Languages used in Kaggle (prediction competition site) http://blog.kaggle.com/2011/11/27/kagglers-favorite-tools/ 2013 http://www.kdnuggets.com/polls/2013/languages-analytics-data-mining-data-science.html • Freely available: http://www.r-project.org/ • IDEs: • [cross-platform] http://rstudio.org/ • [Windows and Linux] http:// www.revolutionanalytics.com/ • Also bindings for emacs [http://ess.r- project.org/] and plugin for eclipse [http:// www.walware.de/goto/statet] • Resources: • Manuals from r-project http://cran.r-project.org/ manuals.html • Chambers (2008) Software for Data Analysis, Springer. • Venables & Ripley (2002) Modern Applied Statistics with S, Springer. • List of books: http://www.r-project.org/doc/bib/R- books.html • Uses a package framework (similar to Python) • Divided into two -
R Or Python: a Programmer’S Response
PhUSE US Connect 2018 Paper AB04 R or Python: A Programmer’s Response Jiangtang Hu, d-Wise, Morrisville, NC, USA ABSTRACT We hear lots of requests on porting R to Clinical Computing Platform besides SAS. Before R really touches the ground, I’d like to share some thoughts on why R is a not a good choice, considering there is a strong alternative, Python. In this paper, I will compare the strength and weakness of R and Python, on various tasks like data manipulation, statistical analysis, system integration. Although R is well known in our industry and has some good things, I argue that Python is a better fit: 1. Python is a better designed programming language; 2. For various programming tasks, Python offers more consistent and unified packages stack, while in R, the packages are scattered; 3. Python is better at system integration due to its reputation as glue language; 4. Considering its elegant syntax and unified ecosystem, Python is easier to learn for SAS programmers. Introduction It’s not a language war between R and Python. The argument was settled long ago in programmer world. The requests on R are mostly from statisticians inside clinical development units. Statisticians are not programmers; they might prefer R for some statistical tasks, like sample size estimate and visualization. But for heavy users for the Clinical Computing Platform, aka, clinical/statistical programmers, they need good language(s) to import data, clean data, transform data and do analysis and reporting. In this type of programming, I’d argue Python is far way better than R, from a programmer’s perspective. -
The Principles of Self- Restraint, Effort, Frugality, and Resourcefulness
TZUTZU CHI CHI USA USA Hosts / 主持人: Hosts / 主持人: Angela Chen Braden Ho 陳玟妤 何譜譜 Performers / 表演嘉賓: Paul Beaubrun Ximena Ibarra David D’or Chyi Yu Shou Chuan Lee 保羅.波本 希梅娜.伊貝瑞 大衛.迪歐 齊豫 李壽全 Austin Ku Ya Han Chang Charles Wang HsinYa Choir 顧忠光 張雅涵 王守謙 新芽合唱團 月 日 Saturday 2020 1 0.1 7 星期六 pm PST pm CST pm EST Tzu Chi Great Love Preschool and 4 晚上 美西 6 晚上 美中 7 晚上 美東 Tzu Chi Sign Language Team Walnut Elementary School Students 慈濟手語隊 慈濟大愛幼兒園和核桃市慈濟小學小朋友 LIVE 雲端直播 www.tzuchi.us/concert The principles of self- restraint, effort, frugality, and resourcefulness. 克 己、克 勤、克 儉、克 難 The monastics at the Jing Si Abode follow a life of self-restraint, diligence, frugality, and resourcefulness. This is the practice of simple life advocated by Master Cheng Yen. They not only make a living for themselves but also offer support for Tzu Chi's global operations to practice the Buddha's teachings. 靜思精舍的生活至今,常住師父克己、克勤、 克儉、克難的精神,是來自靜思法脈的樸實家 風;不僅要自力更生,還支撐著廣大的如來家 業,成為全球慈濟人堅強的後盾。 Those who are content with few desires are capable of practicing the teachings of Pu-Shien Bodhisattva. 是人少欲知足,能修普賢之行。 Those who have faith and follow the Lotus Sutra teachings of the Bodhisattva will have purity of mind, lack desire and gain contentment and joy of practice. Consequently, they have the right character and mindfulness to eventually achieve the merits equal to those of the Pu-Shien Bodhisattva. One of TIME Magazine’s 100 For over fifty years, Master Cheng Yen and her nuns have lived a life of subsistence, Most Influential People of 2011 following an ancient Buddhist monastic tradition of self-reliance called "no work, no meals". -
Indie Pop Duo Collaborates with Singers of 1980S and 1990S
18 YOUTH | Art Wednesday, October 31, 2018 CHINA DAILY HONG KONG EDITION CROSSOVER KING Chinese musician Zhang Yixing is eyeing the US market with his latest album featuring future bass, electronic and hiphop elements, Chen Nan reports. hang Yixing didn’t sleep well the previ ous night. Although you can detect his lack Z of rest, the 27yearold pop singersongwriter, clad in a white Tshirt and a pair of loose pants, vibrates with energy and cheer as he talks about his third studio album, Namanana, which was released on Oct 19. In less than 12 hours, the album sold more than 550,000 copies on the online streaming service, QQ Music. “I sleep three to four hours every day. When I made the album, I practically lived in the recording studio,” says Zhang. One of the most promising and talented musicians to emerge from China’s pop music scene in recent years, Zhang is poised to make his first foray into the American market with his third album, which includes both an English and a Mandarin ver sion of each of his 11 new songs. By working with an interna Zhang Yixing with Norwegian record producer and DJ Alan Walker. Zhang made his US debut alongside Walker in August while giving a tional team, including US performance at the Lollapalooza music festival in Chicago. PHOTOS PROVIDED TO CHINA DAILY singersongwriter Andrew Bazzi and Los Angelesbased Grammynominated producer came from the title song of On his birthday, Oct 7, audi ed to film, TV drama and reali duo Rice ’n’ Peas, Zhang com the new album, Namanana, ence members from all walks ty shows, which greatly posed, arranged and produced which Zhang wrote a year of life and different ages gath broadened his fan base. -
Efficient R Programming: a Practical Guide to Smarter Programming
Efficient R Programming A Practical Guide to Smarter Programming Colin Gillespie and Robin Lovelace Efficient R Programming by Colin Gillespie and Robin Lovelace Copyright © 2017 Colin Gillespie, Robin Lovelace. All rights reserved. Printed in the United States of America. Published by O’Reilly Media, Inc., 1005 Gravenstein Highway North, Sebastopol, CA 95472. O’Reilly books may be purchased for educational, business, or sales promotional use. Online editions are also available for most titles (http://oreilly.com/safari). For more information, contact our corporate/institutional sales department: 800-998-9938 or [email protected]. Editor: Nicole Tache Production Editor: Nicholas Adams Copyeditor: Gillian McGarvey Proofreader: Christina Edwards Indexer: WordCo Indexing Services Interior Designer: David Futato Cover Designer: Randy Comer Illustrator: Rebecca Demarest December 2016: First Edition Revision History for the First Edition 2016-11-29: First Release See http://oreilly.com/catalog/errata.csp?isbn=9781491950784 for release details. The O’Reilly logo is a registered trademark of O’Reilly Media, Inc. Efficient R Programming, the cover image, and related trade dress are trademarks of O’Reilly Media, Inc. While the publisher and the authors have used good faith efforts to ensure that the information and instructions contained in this work are accurate, the publisher and the authors disclaim all responsibility for errors or omissions, including without limitation responsibility for damages resulting from the use of or reliance on this work. Use of the information and instructions contained in this work is at your own risk. If any code samples or other technology this work contains or describes is subject to open source licenses or the intellectual property rights of others, it is your responsibility to ensure that your use thereof complies with such licenses and/or rights.