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1,168 results on '"Logan, Robert A."'

1. Index

Author

Logan, Robert A.

Published
2018

11. Contents

Author

Logan, Robert A.

Published
2018

13. Interpreting Sequence-Levenshtein distance for determining error type and frequency between two embedded sequences of equal length

Author

Logan, Robert, Wehe, Amy W., Woods, Dori C., Tilly, Jon, and Khrapko, Konstantin

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Levenshtein distance is a commonly used edit distance metric, typically applied in language processing, and to a lesser extent, in molecular biology analysis. Biological nucleic acid sequences are often embedded in longer sequences and are subject to insertion and deletion errors that introduce frameshift during sequencing. These frameshift errors are due to string context and should not be counted as true biological errors. Sequence-Levenshtein distance is a modification to Levenshtein distance that is permissive of frameshift error without additional penalty. However, in a biological context Levenshtein distance needs to accommodate both frameshift and weighted errors, which Sequence-Levenshtein distance cannot do. Errors are weighted when they are associated with a numerical cost that corresponds to their frequency of appearance. Here, we describe a modification that allows the use of Levenshtein distance and Sequence-Levenshtein distance to appropriately accommodate penalty-free frameshift between embedded sequences and correctly weight specific error types., Comment: 10 pages, 8 figures

Published
2023

21. MEDIACY: A Way to Enrich Media Literacy

Author

Berger, Eva, Logan, Robert K., Miroshnichenko, Audrey, and Ringel, Anat

Abstract

We propose that the discipline or practice of media literacy defined as the ability to access, analyze, evaluate and create media in a variety of forms can be enriched and made more effective by incorporating two of Marshall McLuhan's insights into the nature of media. The first insight is that the effects of media that are independent of their content and intended function are subliminal and they are important because they "shape and control the scale and form of human association and action." The second insight is that the notion of media includes not just communication media but also all forms of human technology, tools and artifacts. We define "mediacy" as the study, understanding and consideration of these two key insights from McLuhan, and that mediacy compliments, and enriches, the traditional media literacy approach.

Published
2019

22. Hyperlinking in the Spheres: The Physiosphere, Biosphere, Technosphere, Sociosphere and Econosphere

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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23. Hypertext in the Digital Domain of Cyberspace

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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24. Life Is a Spiral and It Is Cyclic: The Spiral Structures of the Biosphere

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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25. Spiral Thought Structures in History and Philosophy

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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26. Spiral and Cyclic Structures in the Abiotic Inorganic Material World

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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27. Pre-digital Forms of Hypertext

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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28. Spirals and the Arts

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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29. The Mathematical Structure of Cyclic Phenomena: Spirals, Helixes, Revolutions, Waves and Oscillations

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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30. Mathematics, Deductive Logic and Abstract Science

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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31. The Spiral Structure of Marshall McLuhan’s Thinking

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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32. Mathematics, the Human Mind, Verbal Language: Mathematics in Mind

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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33. Computing and the Internet: The Six Languages of Speech, Writing, Math, Science, Computing and the Internet

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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34. Mathematics, Writing and Notation

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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35. The Origin of Mathematics in the Mind

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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36. Evolving urban agroecology with deep democracy : action research in London, UK

Author

Logan, Robert, Tornaghi, Chiara, Schmutz, Ulrich, and Chang, Marina

Abstract

The aim of this thesis is to evolve urban agroecology with a central feature of 'deep democracy' whilst surviving and thriving in the neoliberal city. Urban agriculture has many social and environmental benefits but has experienced issues of viability and also faced criticism for entrenching social inequities in movement practice and discourse. With theoretical frameworks such as alternative food networks failing to fully answer questions posed by the limitations of urban agriculture, urban agroecology has been pointed to as a holistic and political framework to develop emancipatory urban food systems. With a need for empirical research to connect theory to on-the-ground empirics and the emerging praxis far from meeting its potential, this thesis contributes strategic and practical learnings towards developing economically viable urban agroecologies with transformative relationships and democratic practices. This thesis draws on insider action research from 2017-2019 based in a surfacing urban agroecology movement in London, UK. Two distinct organisational processes iteratively emerged within a young food hub at the Wolves Lane Horticultural Centre (WLHC), and a new entrant agroecological workers' co-operative, London Grown Workers' Cooperative (LGWC), both based on public land. The former enquiry focused on developing a community-led food policy for the food hub as a democratic intervention, and the latter explored issues of viability in relation to generating anti-capitalist livelihoods within the neoliberal city coupled with evaluation of the workers' co-operative as an elevating model for urban agroecology. The enquiries combined engaged with 67 people and implemented eight different participatory and qualitative methods: photovoice, community mapping, graphic harvest, document analysis, focus groups, auto-ethnography, community cookery, and semi-structured interviews. Based on findings in the organisational enquiries, the thesis argues that the joint development of diálogos de saberes (dialogue among different knowledges and ways of knowing) and a 'prefigurative compromise' with the market, to generate viable place-making transformations in inequitable neoliberal contexts, is necessary to evolve urban agroecology with deep food democracy. I propose that accompanying research findings can support this strategic relationship, these being: a 'critical lovingness' embedded in organisational structures underpinned by an anti-oppression framework; creative popular education included in a transformative agroecological learning framework for Europe; and extending cooperative membership beyond worker identities. Overall, the thesis argues that securing long-term financial investment must be a short-term strategic aim over gifting economies, in order to create more stable, equitable foundations from which to develop autonomous commons-to-commons economies in the medium to long term.

Published
2021

37. Automated, miniaturized, and scalable screening of healthcare workers, first responders, and students for SARS-CoV-2 in San Diego County

Author

Morgan, Sydney C, Aigner, Stefan, Anderson, Catelyn, Belda-Ferre, Pedro, De Hoff, Peter, Marotz, Clarisse A, Sathe, Shashank, Zeller, Mark, Ahmed, Noorsher, Audhya, Xaver, Baer, Nathan A, Barber, Tom, Barrick, Bethany, Batachari, Lakshmi, Betty, Maryann, Blue, Steven M, Brainard, Brent, Buckley, Tyler, Case, Jamie, Castro-Martinez, Anelizze, Chacón, Marisol, Cheung, Willi, Chong, LaVonnye, Coufal, Nicole G, Crescini, Evelyn S, DeGrand, Scott, Dimmock, David P, Donofrio-Odmann, J Joelle, Eisner, Emily R, Estaki, Mehrbod, Vargas, Lizbeth Franco, Freddock, Michele, Gallant, Robert M, Galmozzi, Andrea, Gao, Nina J, Gilmer, Sheldon, Grzelak, Edyta M, Hakim, Abbas, Hart, Jonathan, Hobbs, Charlotte, Humphrey, Greg, Ilkenhans, Nadja, Jacobs, Marni, Kahn, Christopher A, Kapadia, Bhavika K, Kim, Matthew, Kurian, Sunil, Lastrella, Alma L, Lawrence, Elijah S, Lee, Kari, Liang, Qishan, Liliom, Hanna, Sardo, Valentina Lo, Logan, Robert, Machnicki, Michal, Magallanes, Celestine G, Mah, Clarence K, Malacki, Denise, Marina, Ryan J, Marsh, Christopher, Martin, Natasha K, Matteson, Nathaniel L, Maunder, Daniel J, McBride, Kyle, McDonald, Bryan, McDonald, Daniel, McGraw, Michelle, Meadows, Audra R, Meyer, Michelle, Morey, Amber L, Mueller, Jasmine R, Ngo, Toan T, Nguyen, Julie, Nguyen, Viet, Nicholson, Laura J, Nouri, Alhakam, Nudell, Victoria, Nunez, Eugenio, O’Neill, Kyle, Ostrander, R Tyler, Pantham, Priyadarshini, Park, Samuel S, Picone, David, Plascencia, Ashley, Pratumchai, Isaraphorn, Quigley, Michael, Ragsac, Michelle Franc, Richardson, Andrew C, Robles-Sikisaka, Refugio, Ruiz, Christopher A, Ryan, Justin, Sacco, Lisa, Saraf, Sharada, Seaver, Phoebe, Sewall, Leigh, Smoot, Elizabeth W, Sweeney, Kathleen M, Tekkatte, Chandana, Tsai, Rebecca, and Valentine, Holly

Subjects
Pediatric, Infectious Diseases, Emerging Infectious Diseases, Prevention, Biodefense, Vaccine Related, Clinical Research, Pediatric Research Initiative, Good Health and Well Being
Abstract

Background Successful containment strategies for SARS-CoV-2, the causative virus of the COVID-19 pandemic, have involved widespread population testing that identifies infections early and enables rapid contact tracing. In this study, we developed a rapid and inexpensive RT- qPCR testing pipeline for population-level SARS-CoV-2 detection, and used this pipeline to establish a clinical laboratory dedicated to COVID-19 testing at the University of California San Diego (UCSD) with a processing capacity of 6,000 samples per day and next-day result turnaround times. Methods and findings Using this pipeline, we screened 6,786 healthcare workers and first responders, and 21,220 students, faculty, and staff from UCSD. Additionally, we screened 6,031 preschool-grade 12 students and staff from public and private schools across San Diego County that remained fully or partially open for in-person teaching during the pandemic. Between April 17, 2020 and February 5, 2021, participants provided 161,582 nasal swabs that were tested for the presence of SARS-CoV-2. Overall, 752 positive tests were obtained, yielding a test positivity rate of 0.47%. While the presence of symptoms was significantly correlated with higher viral load, most of the COVID-19 positive participants who participated in symptom surveys were asymptomatic at the time of testing. The positivity rate among preschool-grade 12 schools that remained open for in-person teaching was similar to the positivity rate at UCSD and lower than that of San Diego County, with the children in private schools being less likely to test positive than the adults at these schools. Conclusions Most schools across the United States have been closed for in-person learning for much of the 2020-2021 school year, and their safe reopening is a national priority. However, as there are no vaccines against SARS-CoV-2 currently available to the majority of school-aged children, the traditional strategies of mandatory masking, physical distancing, and repeated viral testing of students and staff remain key components of risk mitigation in these settings. The data presented here suggest that the safety measures and repeated testing actions taken by participating healthcare and educational facilities were effective in preventing outbreaks, and that a similar combination of risk-mitigation strategies and repeated testing may be successfully adopted by other healthcare and educational systems.

Published
2021

38. Hypermedia: Hyperlinking Cinema and Television

Author

Logan, Robert K., Pruska-Oldenhof, Izabella, Danesi, Marcel, Series Editor, Hounkonnou, Norbert, Editorial Board Member, Kauffman, Louis H., Editorial Board Member, Martinovic, Dragana, Editorial Board Member, Mitrović, Melanija, Editorial Board Member, Neuman, Yair, Editorial Board Member, Núñez, Rafael, Editorial Board Member, Sfard, Anna, Editorial Board Member, Tall, David, Editorial Board Member, Tanaka-Ishii, Kumiko, Editorial Board Member, Vinner, Shlomo, Editorial Board Member, Logan, Robert K., and Pruska-Oldenhof, Izabella

Published
2022
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39. Detecting conversation topics in primary care office visits from transcripts of patient-provider interactions

Author

Park, Jihyun, Kotzias, Dimitrios, Kuo, Patty, Logan, Robert L, Merced, Kritzia, Singh, Sameer, Tanana, Michael, Taniskidou, Efi Karra, Lafata, Jennifer Elston, Atkins, David C, Tai-Seale, Ming, Imel, Zac E, and Smyth, Padhraic

Subjects
Clinical Research, Bioengineering, Health Services, Generic health relevance, Good Health and Well Being, Aged, Communication, Datasets as Topic, Humans, Machine Learning, Medical Records, Middle Aged, Natural Language Processing, Neural Networks, Computer, Office Visits, Physician-Patient Relations, Primary Health Care, Tape Recording, classification, supervised machine learning, patient care, communication, Information and Computing Sciences, Engineering, Medical and Health Sciences, Medical Informatics
Abstract

ObjectiveAmid electronic health records, laboratory tests, and other technology, office-based patient and provider communication is still the heart of primary medical care. Patients typically present multiple complaints, requiring physicians to decide how to balance competing demands. How this time is allocated has implications for patient satisfaction, payments, and quality of care. We investigate the effectiveness of machine learning methods for automated annotation of medical topics in patient-provider dialog transcripts.Materials and methodsWe used dialog transcripts from 279 primary care visits to predict talk-turn topic labels. Different machine learning models were trained to operate on single or multiple local talk-turns (logistic classifiers, support vector machines, gated recurrent units) as well as sequential models that integrate information across talk-turn sequences (conditional random fields, hidden Markov models, and hierarchical gated recurrent units).ResultsEvaluation was performed using cross-validation to measure 1) classification accuracy for talk-turns and 2) precision, recall, and F1 scores at the visit level. Experimental results showed that sequential models had higher classification accuracy at the talk-turn level and higher precision at the visit level. Independent models had higher recall scores at the visit level compared with sequential models.ConclusionsIncorporating sequential information across talk-turns improves the accuracy of topic prediction in patient-provider dialog by smoothing out noisy information from talk-turns. Although the results are promising, more advanced prediction techniques and larger labeled datasets will likely be required to achieve prediction performance appropriate for real-world clinical applications.

Published
2019

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