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1. Central mechanisms of real and sham electroacupuncture in the treatment of chronic low back pain: study protocol for a randomized, placebo-controlled clinical trial

Author

Jiang-Ti Kong, Brandon MacIsaac, Ruti Cogan, Amanda Ng, Christine Sze Wan Law, Joseph Helms, Rosa Schnyer, Nicholas Vasilis Karayannis, Ming-Chih Kao, Lu Tian, Beth D. Darnall, James J. Gross, Sean Mackey, and Rachel Manber

Subjects
Chronic, Low back pain, Electrical acupuncture, Electroacupuncture, Sham acupuncture, Quantitative sensory testing, Medicine (General), R5-920
Abstract

Abstract Background Chronic low back pain (CLBP) is the most common chronic pain condition and is often resistant to conventional treatments. Acupuncture is a popular alternative for treating CLBP but its mechanisms of action remain poorly understood. Evidence suggests that pain regulatory mechanisms (particularly the ascending and secondarily the descending pain modulatory pathways) and psychological mechanisms (e.g., expectations, pain catastrophizing and self-efficacy) may be involved in the pathogenesis of CLBP and its response to treatments. We will examine these mechanisms in the treatment of CLBP by electroacupuncture (EA). Methods We present the aims and methods of a placebo-controlled, participant-blinded and assessor-blinded mechanistic study. Adult patients with CLBP will be randomized to receiving 16 sessions of real (active) or sham (placebo) EA over the course of 8 weeks. The primary pain regulatory measure for which the study was powered is temporal summation (TS), which approximates ascending pain facilitation. Conditioned pain modulation (CPM), representing a descending pain modulatory pathway, will be our secondary pain regulatory measure. The primary psychological measure is expectations of benefit, and the secondary psychological measures are pain catastrophizing and self-efficacy in managing pain. Main clinical outcomes are back pain bothersomeness on a 0–100 visual analog scale (primary), Roland Morris Disability Questionnaire (secondary), and relevant items from the National Institutes of Health (NIH) Patient-Reported Outcome Measures Information System (secondary). We hypothesize that compared to sham, real EA will lead to greater reduction in TS after 8 treatment sessions (4 weeks); and that reduction in TS (and secondarily, increase in CPM) after 8 treatment sessions will mediate reduction in back pain bothersomeness from baseline to week 10 (clinical response) to EA. We also hypothesize that the three psychological factors are moderators of clinical response. With 100 treatment completers, the study is designed to have 80% power to detect a medium-sized between-group effect (d = 0.5) on temporal summation. Discussion To the best of our knowledge, this is the first appropriately powered, placebo-controlled clinical trial evaluating mechanisms of EA in the treatment of CLBP. Trial registration ClinicalTrials.gov, NCT02503475. Registered on 15 July 15 2015. Retrospectively registered.

Published
2018
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2. Effect of biodegradable and synthetic polymer combination on release behaviour of Nateglinide from matrix tablets.

Author

ASHOK KUMAR JANAKIRAMAN, Amanda Ng Thing Wei, Liew Kai Bin, Melbha Starlin, and Mohamed Ebrahim Habibur Rahman Shiek Abdul Kadhar

Subjects
Food processing and manufacture, TP368-456
Abstract

The present work was to study the effect of biodegradable and synthetic polymers on sustained release (SR) matrix tablets of Nateglinide by in vitro performance. The SR tablets were formulated with various concentrations of chitosan and/ or Eudragit RLPO or HPMC K100M via direct compression. The tablets were subjected to tests for drug-polymer interaction, weight variation, thickness, hardness, friability, drug content, in vitro drug release and stability studies. The NG06 SR matrix tablets formulated was able to sustain the release of the drug over 12 hours (CDR=98% ± 1.47) and shown optimum post-compression properties. In vitro release data of NG06 also showed a good linear relationship in the Korsmeyer-Peppas model (r2=0.9975) while n=0.750 indicated non-Fickian transport. The optimized formulation, NG06, which consisted of 12.5mg Chitosan and 12.5mg Eudragit RLPO, had the best characteristics to achieve the aims of this study.

Published
2019

8. How FAST are we? A systematic review and meta- analysis of the effectiveness of intervention done on paramedic services in increasing thrombolysis rate

Author

Amanda Ng Yuin Shan, Janice Iu Syuen Yin, Carissa Lee Xin Jin, Jamuna Appalasamy, null Md Golam Hasnain, and Shazwani Shaharuddin

Subjects
Neurology, Neurology (clinical)
Abstract

Objectives: The paramedics’ role is pivotal in ensuring eligible stroke patients reach the hospital within 4.5 hours, as this increases the chance of patients being treated with recombinant tissue plasminogen activator (rTPA) and improves their outcome. The lack of reviews on interventions done on paramedic services and the outcomes associated with them necessitates further investigation to enable policymakers to make guided decisions in improving the management of acute ischaemic strokes. Hence, our study aimed to identify interventions done and their impact on thrombolysis rate and onset-to-door (OTD) time. Methods: We searched PubMed, Embase, CINAHL and RCN to identify studies published between 1 January 2010 and 30 June 2020. The primary outcome of this study is investigating the impact of interventions done on paramedics services on the rTPA administration rate and OTD timing. Other outcomes include improvement in door-to-needle (DTN), door-to-imaging (DTI) and onset- to-needle (OTN) time. Random effect models were used to analyse the effects of the interventions carried out. Results: We gathered 621 papers, of which 11 met the eligibility criteria. The interventions carried out were bypass (n=3), education (n=2), pre-notification (n=4) and telemedicine (n=2). Based on the random effect model, rTPA administration was significantly higher in the intervention arm of ischemic stroke patients (n=7) with an OR of 1.45 (95%CI, 1.01-2.06). The trend was significantly higher with bypass intervention (OR 2.23 95%CI, 1.55-3.2), while the result with pre-notification (OR 0.53 95%CI, 0.09-2.95) and education (OR 1.51 95%CI, 0.87-2.60) were not significant. Conclusions: Paramedic interventions appear to have considerable effectiveness in improving the rates of rTPA, especially when the interventions used bypass mechanisms. This study provides detailed information on the net and quantitative benefits of the interventions and suggests the use of such interventions to reduce the pre-hospital delay of stroke patients and improve the rates of intravenous thrombolysis.

Published
2022
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13. Regular Bedtimes Among Children Aged 5–17 Years: United States, 2020

Author

Amanda Ng, Dzifa Adjaye-Gbewonyo, and Lindsey Black

Abstract

This report uses data from the 2020 National Health Interview Survey (NHIS) to describe regular bedtimes, defined as going to sleep at the same time most days or every day in a typical school week, among children aged 5–17 years. Estimates are presented by sociodemographic characteristics, family type, social vulnerability index (SVI), family income, and urbanicity of residence.

Published
2022
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14. Sleep Difficulties in Adults: United States, 2020

Author

Dzifa Adjaye-Gbewonyo, Amanda Ng, and Lindsey Black

Abstract

This report uses data from the 2020 National Health Interview Survey (NHIS) to describe the prevalence of sleep difficulties, defined here as trouble falling or staying asleep most days or every day in the past 30 days, among adults in the United States by sociodemographic and geographic characteristics.

Published
2022
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15. Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects

Author

Jonathan T. L. Kang, Jonathan Teo, Denis Bertrand, Amanda Ng, Aarthi Ravikrishnan, Melvin Yong, Ng Oon Tek, Kalisvar Marimuthu, Swaine Chen, Chng Kern Rei, Gan Yunn-Hwen, and Niranjan Nagarajan

Subjects
Microbiology (medical), Immunology, Cell Biology, Applied Microbiology and Biotechnology, Microbiology, beta-Lactamases, Anti-Bacterial Agents, Gastrointestinal Microbiome, Klebsiella pneumoniae, Carbapenem-Resistant Enterobacteriaceae, Bacterial Proteins, Genetics, Escherichia coli, Humans
Abstract

Long-term colonization of the gut microbiome by carbapenemase-producing Enterobacteriaceae (CPE) is a growing area of public health concern as it can lead to community transmission and rapid increase in cases of life-threatening CPE infections. Here, leveraging the observation that many subjects are decolonized without interventions within a year, we used longitudinal shotgun metagenomics (up to 12 timepoints) for detailed characterization of ecological and evolutionary dynamics in the gut microbiome of a cohort of CPE-colonized subjects and family members (n = 46; 361 samples). Subjects who underwent decolonization exhibited a distinct ecological shift marked by recovery of microbial diversity, key commensals and anti-inflammatory pathways. In addition, colonization was marked by elevated but unstable Enterobacteriaceae abundances, which exhibited distinct strain-level dynamics for different species (Escherichia coli and Klebsiella pneumoniae). Finally, comparative analysis with whole-genome sequencing data from CPE isolates (n = 159) helped identify substrain variation in key functional genes and the presence of highly similar E. coli and K. pneumoniae strains with variable resistance profiles and plasmid sharing. These results provide an enhanced view into how colonization by multi-drug-resistant bacteria associates with altered gut ecology and can enable transfer of resistance genes, even in the absence of overt infection and antibiotic usage.

Published
2022
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16. Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

Author

Gounot, Jean-Sebastien, primary, Minghao, Chia, additional, Bertrand, Denis, additional, Saw, Woei-Yuh, additional, Ravikrishnan, Aarthi, additional, Low, Adrian, additional, Ding, Yichen, additional, Qi Amanda, Ng Hui, additional, Lin Tan, Linda Wei, additional, Yik-Ying, Teo, additional, Seedorf, Henning, additional, and Nagarajan, Niranjan, additional

Published
2022
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17. Towards a cross-disciplinary framework for promoting youth wellbeing

Author

Amanda Ng and Dianne Vella-Brodrick

Subjects
Social Psychology, business.industry, Positive education, Cross disciplinary, 05 social sciences, Economics, Econometrics and Finance (miscellaneous), Psychological intervention, 050301 education, Public relations, Mental health, Youth studies, Coaching, 050106 general psychology & cognitive sciences, Quality of life (healthcare), 0501 psychology and cognitive sciences, business, Psychology, Positive Youth Development, 0503 education, Applied Psychology
Abstract

The youth wellbeing literature draws upon the fields of Positive Education, Positive Youth Development, Social and Emotional Learning, Coaching and Mentoring Psychology and Quality of Life, collectively referred to as the Youth Wellbeing Fives (YWB Fives). Despite their individual efforts to promote mental health and address mental health issues, no study to date has explored their collective contributions (intersections) towards this goal, nor has a framework been developed to understand the benefits of collaboration between youth wellbeing scholars from different fields. This paper develops a framework for promoting the cross-disciplinary study of youth wellbeing, and critically reviews the contributions of individual and collective YWB Fives to enhancing the wellbeing of young people. Given their complementary approaches and combined influence on successful interventions, we illuminate possibilities for intersections to exist among the YWB Fives. Insights gained have various research and practical applications; these include providing a rationale for future youth studies to empirically measure intersections among the YWB Fives, and encouraging the development, delivery and evaluation of cross-disciplinary interventions to ensure widespread access to wellbeing services by all young people.

Published
2019
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18. Does the Key Task Measure Prospective Memory? Cautionary Findings from Parallel Studies in HIV Disease and Older Adults

Author

Lara Fine, Amanda Ng, Erica Hodgson, Shayne Loft, Michael Weinborn, Steven Paul Woods, Kelli L. Sullivan, Michelle A Babicz, Maria Pushpanathan, Romola S. Bucks, and Denise Parker

Subjects
Adult, Male, 050103 clinical psychology, Memory, Episodic, HIV Infections, Neuropsychological Tests, Task (project management), Executive Function, 03 medical and health sciences, 0302 clinical medicine, Memory, Activities of Daily Living, Prospective memory, medicine, Humans, 0501 psychology and cognitive sciences, Neuropsychological assessment, Episodic memory, Aged, Face validity, medicine.diagnostic_test, 05 social sciences, Reproducibility of Results, Construct validity, General Medicine, Middle Aged, Psychiatry and Mental health, Clinical Psychology, Neuropsychology and Physiological Psychology, Socioeconomic Factors, Female, Psychology, Neurocognitive, Psychomotor Performance, 030217 neurology & neurosurgery, Hiv disease, Clinical psychology
Abstract

Objective Despite its brevity and face validity, little is known about the construct validity of the naturalistic “Key Task” of prospective memory (PM), in which an examinee is instructed to remind the examiner at a designated time to retrieve keys (or another belonging) placed out of sight. Method Study 1 included 162 HIV+ and 52 HIV− comparison participants who completed the Key Task alongside well-validated measures of PM and a comprehensive neuropsychological battery that included everyday functioning measures. Study 2 used broadly parallel methods in 168 older community-dwelling Australians. Results Overall, the Key Task was not reliably associated with neurocognitive functioning (including clinical and experimental measures of PM), PM symptoms, or everyday functioning in either sample. Conclusions The Key Task did not demonstrate compelling evidence of construct validity among persons living with HIV disease or older adults, which raises doubts regarding its clinical usefulness as a measure of PM.

Published
2019
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19. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author

Nadine Farhat, Tomoki Takeda, Astred Castro, Ken McGrath, Khaliun Sanchir, Iman Hajirasouliha, Eunice So, Laraib Zafar, Diana N. Nunes, Harun Mustafa, Amy Zhang, Priscilla Lisboa, Christian Schori, Marisano James, Jasna Chalangal, Sebastien Halary, Shahryar Rana, Yunmi Lee, Oli Schacher, Liliana Godoy, David A. Coil, Phanthira Pugdeethosal, Michelle D. Williams, German Marchandon, Angela Cantillo, Naoya Takahashi, Christopher Mozsary, Juana Gonzalez, Patrick K. H. Lee, Gerardo de Lamotte, Alessandro Robertiello, Steven Du, Fabienne Velter, Stefan G. Stark, Miguel Carbajo, Vincent Matthys, David A. Westfall, Julia Boeri, Irène Mauricette Mendy, Jonathan Cedillo, Francesco Oteri, Robert W. Crawford, Takayuki Ito, Tina Wunderlin, Maureen Muscat, David Paez-Espino, Carmen Urgiles, Aida Nesimi, Steffen Schaaf, Adan Ramirez-Rojas, Kunihiko Miyake, Christopher E. Mason, Anais Cardenas, Sharah Islam, Diego Benítez, Melissa Pool Pizzi, Kianna Ciaramella, Ciro Borrelli, Riham Islam, Dorottya Nagy-Szakal, Abd-Manaaf Bakere, Ait-hamlat Adel, Olha Lakhneko, Badamnyambuu Iderzorig, Ana Valeria Castro, Adam Phillips, Robert A. Petit, Flavia Corsi, Romain Conte, Krista Ryon, Soojin Jang, Joseph Benson, Fernanda de Souza Gomes Kehdy, Cindy Wang, Nicole Mathews, Jenn-Wei Chen, Rachel Paras, Paulina Pastuszek, Abigail Lyons, Paul Roldán, Muntaha Munia, Pierre Nicolas, Cassie L. Ettinger, Kyrylo Pyrshev, Katterinne N. Mendez, Eduardo Castro-Nallar, Valeriia Dotsenko, Michelle Tuz, Krizzy Mallari, Eileen Png, Yuya Sonohara, Tanja Miketic, Stéphane Delmas, Shu Zhang, Masaki Sato, Yuanting Zheng, Jifeng Zhu, Roland Häusler, Lucie Bittner, Savlatjon Rahmatulloev, Jonathan Foox, Bruno D'Alessandro, Alketa Plaku, Faisal Alquaddoomi, Yang Zhang, Kern Rei Chng, Juliana Lago, Allaeddine Chettouh, Tamera Henry, Houtan Noushmehr, Tranette Gregory, Sara Abdul Majid, Frank J. Kelly, Benjamin Pulatov, Laurie Casalot, Takema Kajita, Lennard Epping, Thais Fernanda Bartelli, Eftar Moniruzzaman, Renee Vivancos-Koopman, Thirumalaisamy P. Velavan, Tracy W. Liu, Yelyzaveta Tymoshenko, Alma Plaku, Nika Gurianova, Ambar Mendez, Anna Tomaselli, Sonia Dorado, Donato Giovannelli, Hira Choudhry, Synti Ng, Sheelta S. Kumar, Jennifer Q. Lu, Weijun Liang, Ellen Koag, Dennis Gankin, Maria João Amorim, Gwenola Simon, Kiyoshi Suganuma, Mikhail Karasikov, Christos A. Ouzounis, Madelyn May, Eran Elhaik, Stephan Ossowski, Kevin Bolzli, Matthew Arthur, Yuya Oto, Jananan Pathmanathan, Salah Mahmoud, Kou Takahashi, Brunna Marques, Kelly French, Felipe Sepúlveda, Shusei Yoshikawa, Paulo Thiago de Souza Santos, Andrew N. Gray, Juliana S Bernardes, Felipe Segato, Björn Brindefalk, George C. Yeh, Jhovana L. Velasco Flores, Jill Sullivan, Silva Baburyan, Denisse Flores, Russell Y. Neches, Sabrina Persaud, Rasheena Wright, Takumi Togashi, Verónica Antelo, Nao Kato, Skye Felice, Tatjana Mustac, Daisy Donnellan, Katerine Carrillo, Anna Litskevitch, Catalina García, Sota Ito, Naya Eady, Andrew Wan, Irene Meng, Sophie Guasco, Danilo Ercolini, Francesca De Filippis, Vincent Lemaire, Luice Fan, Lothar H. Wieler, Mariia Rybak, Jorge Sanchez, Jonathan S. Gootenberg, Itsuki Tomita, Maritza S Mosella, Laura Garcia, Natalka Makogon, Daisy Cheung, Hitler Francois Vasquez Arevalo, Freddy Asenjo, Gabriela P. Branco, Erika Cifuentes, Chloé Dequeker, Aspassia D. Chatziefthimiou, Alexis Terrero, Roy Meoded, Isabelle de Oliveira Moraes, Shaleni K. Singh, Orgil-Erdene Molomjamts, Karishma Miah, Laurent David, Wolfgang Haehr, Dao Phuong Giang, Romain Lannes, Prashanthi Ratnanandan, Ryota Yamanaka, Riccardo Vicedomini, Sadaf Ayaz, Oluwatosin M. Osuolale, Laura E. Vann, Gregory Chem, Andrea Gonzalez, Aszia Burrell, Ariel Chernomoretz, Sakura Ishizuka, Michelle Rivera, Avigdor Nosrati, Michelle B. Chen, Juliette Auvinet, Nils Ordioni, Tomoro Warashina, Guillaume Blanc, Tomislav Ivankovic, Christina Black, Lauren E. Hittle, David Hess-Homeier, Michael Kozhar, Hamood Suliman, Karobi Moitra, Saher Rahiel, Spyridon Gkotzis, Jenny Arevalo, Shaikh B. Iqbal, Beth Mutai, Mohammed Mohsin, Scott Tighe, Sylvie Collin, Yoshitaka Saito, Wayne Menary, Youping Deng, Lucy Lee, Esmeralda Jiminez, Ayuki Watanabe, Nikos C. Kyrpides, Natasha Mohan, Angelika Pupiec, Dedan Githae, Simone Cawthorne, Jonathan A. Eisen, Tomoki Iwashiro, Chiaki Homma, Thomas Saw Aung, Laura Molina, Marcus H. Y. Leung, Ophélie Da Silva, Yan Ling Wong, Hosna Noorzi, Mario Moreno, Alina Butova, Leming Shi, Brian W. Wong, Sarah S. Jackson, Moses Lin, Annabelle Meagher, Pujita Das, Catherine Burke, Mitsuki Ota, Maria Domenica Moccia, Nicolas Sprinsky, Catherine E. Pugh, David C. Green, Fazlina Fauzi, Erdenetsetseg Batdelger, Annie Geiger, Valeria Ventorino, Tolulope Oluwadare, Delisia Cuebas, Catalina Truong, Leonardo Posada, Michael Angelov, Tathiane M. Malta, Amanda Ng, Francesca Nadalin, Arya Hawkins-Zafarnia, Yuh Shiwa, Athena Mitsios, Milton Ozório Moraes, Manolo Laiola, Kalyn Ali, Jaden J.A. Hastings, Ikuto Saito, Maheen Shakil, Chisato Suzuki, Elena M. Vayndorf, Hubert Rehrauer, Ajay Menon, Kaitlan Russell, Aliyah Shari, Rebecca Smith, Gregorio Iraola, Max Priestman, Alan Briones, Silver A. Wolf, Camila Gonzalez-Poblete, Eleonora De Lazzari, Shirley Chiu, Michelle Ki, Irene Hoxie, Marianne Jaubert, Ayantu Jinfessa, Ryan J. King, Nghiem Xuan Hoan, Jalia Bynoe, Jacob Friedman, Aneisa Ramcharan, Pablo Fresia, Cristina Muñoz, Muhammad Afaq, Anyi Tang, Médine Benchouaia, Isabella Kuniko T. Takenaka, Anastasia Chasapi, Areeg Naeem, Hannah Benisty, Cecilia N. Cossio, Nathalie Hüsser, Mahfuza Sabina, Thais S. Sabedot, JoAnn Jacobs, Camila P. E. de Souza, Manuela Oliveira, Jean-Pierre Bouly, Mariko Usui, Wilson Miranda, Natalia Marciniak, Hiram Caballero, Samuel Weekes, Alexandra B. Graf, Emily Leong, Tatyana Nikolayeva, Dominique Thomas, Charlotte Greselle, Cecilia Salazar, Sreya Ray Chaudhuri, Kevin Becher, Sandra Roth, Ryusei Miura, Kari Oline Bøifot, Dimitri Manoir, Oliver Toth, Chandrima Bhattacharya, Manuel Perez, Isha Lamba, Takafumi Tsurumaki, Timothy D. Read, Anna-Lena M. Schinke, Ryan Sankar, Le Huu Song, Narasimha Rao Nedunuri, Emmanuel Dias-Neto, Ana Flávia Costa, Adiell Melamed, Christelle Desnues, Natalie R. Davidson, Aaron E. Darling, Hyung Jun Kim, Josephine Galipon, Jacqueline Orrego, Dimitar Vassilev, Michael Huber, Nur Hazlin Hazrin-Chong, Gaston H. Gonnet, Kaymisha Knights, Osman U. Sezerman, Dmitry Meleshko, Eunice Thambiraja, Jingcheng Yang, Aubin Fleiss, Gloria Nguyen, Katelyn Jackson, Nuria Aventin, Stephanie L. Hyland, Andrea Hässig, Catharine Aquino, Simona Lysakova, Israel O. Osuolale, Kasia Sluzek, Rania Siam, Alina Frolova, Samuel Hernandez, Yui Him Lo, Bazartseren Boldgiv, Ben Young, Maryna Korshevniuk, Majelia Ampadu, Yuk Man Tang, Amanda L. Muehlbauer, Sade Thomas, Gabriel Figueroa, Alexis Rivera, Lisbeth Pineda, Alexandra Dutan, Jennifer M. Tran, Chris K. Deng, Vedbar S. Khadka, Paola Florez de Sessions, Elizabeth Humphries, Hugues Richard, Hiba Naveed, Nora C. Toussaint, Mahshid Khavari, Maria del Mar Vivanco Ruiz, Antonin Thiébaut, Nicolás Rascovan, Marius Dybwad, Orhan Özcan, Lawrence Kwong, David Danko, Shaira Khan, Andrea Tassinari, Silvia Beurmann, Tsoi Ying Lai, Nanami Kubota, Tieliu Shi, Diana Chicas, Evan E. Afshin, Hirokazu Yano, Jonas Krebs, Mayuko Nakagawa, Hyun Jung Lee, Irene González Navarrete, Rachid Ounit, Lucia E. Alvarado-Arnez, Masaki Nasu, Allison Chan, Harilanto Andrianjakarivony, Jennifer Amachee, Mahdi Taye, Wan Chiew Ng, Kathryn O’Brien, Shino Ishikawa, Tristan Bitard-Feildel, Sora Takagi, Felix Hartkopf, Niamh B. O’Hara, Marcos A. S. Fonseca, Subhamitra Pakrashi, Amrit Kaur, Eva Hell, Patricia Vera-Wolf, Naimah Munim, Luiza Ferreira de Araújo, Mizuki Igarashi, Brianna Pompa-Hogan, Alessandra Carbone, Anne-Sophie Benoiston, Eric Helfrich, Michael A. Suarez-Villamil, Omar O. Abudayyeh, Natasha Abdullah, Jaime J. Fuentes, Juan Carlos Forero, Tetiana Yeskova, Denis Bertrand, Sambhawa Priya, Denisse Maldonado, Agier Nicolas, Ana Valeria B Castro, Starr Chatziefthimiou, André Kahles, Aaishah Francis, Fernanda Arredondo, Emilio Tarcitano, Irvind Buttar, Alex Alexiev, Jennifer Molinet, Sarah Shalaby, Itunu A. Oluwadare, Jason Sperry, Katrin Bakhl, Ana M. Cañas, Sofia Ahsanuddin, Miar Elaskandrany, Elodie Laine, Sven Bönigk, Johannes Werner, Stephen Eduard Boja Ruiz, Gargi Dayama, Paulina Buczansla, Brandon Valentine, Bharath Prithiviraj, Toni Bode, Stas Zubenko, Jake Cohen, Guilllaume Jospin, Zulena Saravi, Per O. Ljungdahl, Inderjit Kaur, Mauricio Moldes, Giuseppe KoLoMonaco, Denise Syndercombe Court, Sonia Bouchard, Sonia Losim, Sookwon Moon, Heba Shaaban, Suraj Patel, Sibo Zhu, Sarh Aly, Arif Asyraf Md Supie, LaShonda Dorsey, Juan Guerra, François Baudon, Rantimi A. Olawoyin, Alexia Bordigoni, Iqra Faiz, Mathilde Garcia, Gabriella Mason-Buck, María Gabriela Portilla, Niranjan Nagarajan, Fumie Takahara, Nancy Merino, Watson Andrew, Gina Kim, Yuma Sato, Hyenah Shim, Marie-Laure Jerier, Affifah Saadah Ahmad Kassim, Katerina Kuchin, Daniel Butler, Paweł P. Łabaj, Nadezhda Kobko-Litskevitch, Emmanuel F. Mongodin, Yuto Togashi, Paula Rodríguez, Pilar Lopez Hernandez, Xiaoqing Chen, Maria A. Sierra, Olga Nikolayeva, Manon Loubens, Colleen Conger, Hikaru Shirahata, Chenhao Li, Timothy Donahoe, Youngja Park, Lucia Elena Alvarado Arnez, Salama Chaker, Francisco Chavez, Alessandra Breschi, Jorge L. Sanchez, Kaung Myat San, Nayra Aguilar Rojas, Marcos Abraao, Kai Sasaki, Bryan Nazario, Olena Yemets, Klas I. Udekwu, Lynn M. Schriml, Anisia Peters, Aliaksei Holik, Mark Hernandez, Emile Faure, Malay Bhattacharyya, Josef W. Moser, Núria Andreu Somavilla, María Mercedes Zambrano, Kannan Rajendran, Gabriela E. Albuquerque, Tao Qing, Kazutoshi Tsuda, Ymke De Jong, Princess Osma, Mayra Arauco Livia, Javier Quilez Oliete, Carl Chrispin, Hyun Woo Joo, Ingrid Lafontaine, Nala An, Seisuke Sato, Felipe Segato Dezem, Andrew Maltez Thomas, Alexandre Desert, Xiao Wen Cai, O. Osuolale, Jun Wu, Coral Pardo-Esté, Courtney Robinson, Yuri Matsuzaki, Marina Nieto-Caballero, Cem Meydan, Ralph Schlapbach, Mark Menor, Sofia Castro, Rachel Kwong, Brittany Blyther, Olexandr Lykhenko, Jason R. Schriml, Christian Brion, Jenessa Orpilla, Juan A. Ugalde, Elsy Mankah Ngwa, Álvaro Aranguren, Lauren Mak, Matías Giménez, Ashanti Narce, Torsten Semmler, Stefan I. Tsonev, Abdollahi Nika, Katherine E. Dahlhausen, Monika Devi, Gunnar Rätsch, Oasima Muner, Carla Bello, Muhammad Al-Fath Amran, Anyelic Rosario, Melissa Ortega, Andrea Patrignani, Ante Peros, Elias McComb, Ryo Sato, Ireen Alam, Clara N. Dias, Soma Tanaka, Dayana Calderon, Ran Blekhman, Mathilde Mignotte, Alicia Boyd, Jochen Hecht, Thomas Neff, Xinzhao Tong, Josue Alicea, Kiara Olmeda, Sonia Marinovic, Carme Arnan, Kohei Ito, Samantha L. Goldman, Marianna S. Serpa, Renee Richer, Kaisei Sato, Jordana M. Silva, Akash Keluth Chavan, Sangwan Kim, Laís Pereira Ferreira, Sophie Vacant, Nowshin Sayara, Haruo Suzuki, Madeline Leahy, Juan C. Severyn, Sierra Vincent, Masaru Tomita, Maliha Mamun, Lucinda B. Davenport, Gabriella Oken, Dagmara Lewandowska, Gustavo Adolfo Malca Salas, Andrii Kuklin, Tyler Wong, Charlie Feigin, Eric Minwei Liu, Sonia L. Ghose, Daniela Bezdan, Antonietta La Storia, Juan P. Escalera-Antezana, Nuno Rufino de Sousa, Samuel M. Gerner, Weill Cornell Medicine [New York], Icahn School of Medicine at Mount Sinai [New York] (MSSM), Genome Institute of Singapore (GIS), Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), AUTRES, Massachusetts Institute of Technology (MIT), Indian Statistical Institute [Kolkata], University of Minnesota System, Universidad Andrés Bello [Santiago] (UNAB), California State University [Sacramento], University of Naples Federico II, University of Hawaii, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Medical Genomics Group, University College of London [London] (UCL)-UCL Cancer Institute, Norwegian Defence Research Establishment (FFI), Lund University [Lund], Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, University of Vienna [Vienna], King‘s College London, University of Colorado [Boulder], Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur Korea - Institut Pasteur de Corée, Fudan University [Shanghai], City University of Hong Kong [Hong Kong] (CUHK), Stockholm University, University of Maryland School of Medicine, University of Maryland System, Fundação Oswaldo Cruz (FIOCRUZ), University of São Paulo (USP), Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Barcelona Institute of Science and Technology (BIST), Elizade University, Acibadem Mehmet Ali Aydınlar University, Paléogénomique microbienne - Microbial paleogenomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Robert Koch Institute [Berlin] (RKI), East China Normal University [Shangaï] (ECNU), Cairo University, Vietnamese-German Center for Medical Research, Keio University, Université du Vermont, Universidad del Desarrollo, University of Sofia, University of Alaska [Fairbanks] (UAF), Universitätsklinikum Tübingen - University Hospital of Tübingen, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Corporación Corpogen-Research Center, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Weill Cornell Medicine [Cornell University], Cornell University [New York], University of Naples Federico II = Università degli studi di Napoli Federico II, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Universidade de São Paulo = University of São Paulo (USP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Софийски университет = Sofia University, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universidad Andrés Bello - UNAB (CHILE), Acibadem University Dspace, Danko, D., Bezdan, D., Afshin, E. E., Ahsanuddin, S., Bhattacharya, C., Butler, D. J., Chng, K. R., Donnellan, D., Hecht, J., Jackson, K., Kuchin, K., Karasikov, M., Lyons, A., Mak, L., Meleshko, D., Mustafa, H., Mutai, B., Neches, R. Y., Ng, A., Nikolayeva, O., Nikolayeva, T., Png, E., Ryon, K. A., Sanchez, J. L., Shaaban, H., Sierra, M. A., Thomas, D., Young, B., Abudayyeh, O. O., Alicea, J., Bhattacharyya, M., Blekhman, R., Castro-Nallar, E., Canas, A. M., Chatziefthimiou, A. D., Crawford, R. W., De Filippis, F., Deng, Y., Desnues, C., Dias-Neto, E., Dybwad, M., Elhaik, E., Ercolini, D., Frolova, A., Gankin, D., Gootenberg, J. S., Graf, A. B., Green, D. C., Hajirasouliha, I., Hastings, J. J. A., Hernandez, M., Iraola, G., Jang, S., Kahles, A., Kelly, F. J., Knights, K., Kyrpides, N. C., Labaj, P. P., Lee, P. K. H., Leung, M. H. Y., Ljungdahl, P. O., Mason-Buck, G., Mcgrath, K., Meydan, C., Mongodin, E. F., Moraes, M. O., Nagarajan, N., Nieto-Caballero, M., Noushmehr, H., Oliveira, M., Ossowski, S., Osuolale, O. O., Ozcan, O., Paez-Espino, D., Rascovan, N., Richard, H., Ratsch, G., Schriml, L. M., Semmler, T., Sezerman, O. U., Shi, L., Shi, T., Siam, R., Song, L. H., Suzuki, H., Court, D. S., Tighe, S. W., Tong, X., Udekwu, K. I., Ugalde, J. A., Valentine, B., Vassilev, D. I., Vayndorf, E. M., Velavan, T. P., Wu, J., Zambrano, M. M., Zhu, J., Zhu, S., Mason, C. E., Abdullah, N., Abraao, M., Adel, A. -H., Afaq, M., Al-Quaddoomi, F. S., Alam, I., Albuquerque, G. E., Alexiev, A., Ali, K., Alvarado-Arnez, L. E., Aly, S., Amachee, J., Amorim, M. G., Ampadu, M., Amran, M. A. -F., An, N., Andrew, W., Andrianjakarivony, H., Angelov, M., Antelo, V., Aquino, C., Aranguren, A., Araujo, L. F., Vasquez Arevalo, H. F., Arevalo, J., Arnan, C., Alvarado Arnez, L. E., Arredondo, F., Arthur, M., Asenjo, F., Aung, T. S., Auvinet, J., Aventin, N., Ayaz, S., Baburyan, S., Bakere, A. -M., Bakhl, K., Bartelli, T. F., Batdelger, E., Baudon, F., Becher, K., Bello, C., Benchouaia, M., Benisty, H., Benoiston, A. -S., Benson, J., Benitez, D., Bernardes, J., Bertrand, D., Beurmann, S., Bitard-Feildel, T., Bittner, L., Black, C., Blanc, G., Blyther, B., Bode, T., Boeri, J., Boldgiv, B., Bolzli, K., Bordigoni, A., Borrelli, C., Bouchard, S., Bouly, J. -P., Boyd, A., Branco, G. P., Breschi, A., Brindefalk, B., Brion, C., Briones, A., Buczansla, P., Burke, C. M., Burrell, A., Butova, A., Buttar, I., Bynoe, J., Bonigk, S., Boifot, K. O., Caballero, H., Cai, X. W., Calderon, D., Cantillo, A., Carbajo, M., Carbone, A., Cardenas, A., Carrillo, K., Casalot, L., Castro, S., Castro, A. V., Castro, A., Castro, A. V. B., Cawthorne, S., Cedillo, J., Chaker, S., Chalangal, J., Chan, A., Chasapi, A. I., Chatziefthimiou, S., Chaudhuri, S. R., Chavan, A. K., Chavez, F., Chem, G., Chen, X., Chen, M., Chen, J. -W., Chernomoretz, A., Chettouh, A., Cheung, D., Chicas, D., Chiu, S., Choudhry, H., Chrispin, C., Ciaramella, K., Cifuentes, E., Cohen, J., Coil, D. A., Collin, S., Conger, C., Conte, R., Corsi, F., Cossio, C. N., Costa, A. F., Cuebas, D., D'Alessandro, B., Dahlhausen, K. E., Darling, A. E., Das, P., Davenport, L. B., David, L., Davidson, N. R., Dayama, G., Delmas, S., Deng, C. K., Dequeker, C., Desert, A., Devi, M., Dezem, F. S., Dias, C. N., Donahoe, T. R., Dorado, S., Dorsey, L., Dotsenko, V., Du, S., Dutan, A., Eady, N., Eisen, J. A., Elaskandrany, M., Epping, L., Escalera-Antezana, J. P., Ettinger, C. L., Faiz, I., Fan, L., Farhat, N., Faure, E., Fauzi, F., Feigin, C., Felice, S., Ferreira, L. P., Figueroa, G., Fleiss, A., Flores, D., Velasco Flores, J. L., Fonseca, M. A. S., Foox, J., Forero, J. C., Francis, A., French, K., Fresia, P., Friedman, J., Fuentes, J. J., Galipon, J., Garcia, M., Garcia, L., Garcia, C., Geiger, A., Gerner, S. M., Ghose, S. L., Giang, D. P., Gimenez, M., Giovannelli, D., Githae, D., Gkotzis, S., Godoy, L., Goldman, S., Gonnet, G. H., Gonzalez, J., Gonzalez, A., Gonzalez-Poblete, C., Gray, A., Gregory, T., Greselle, C., Guasco, S., Guerra, J., Gurianova, N., Haehr, W., Halary, S., Hartkopf, F., Hawkins-Zafarnia, A., Hazrin-Chong, N. H., Helfrich, E., Hell, E., Henry, T., Hernandez, S., Hernandez, P. L., Hess-Homeier, D., Hittle, L. E., Hoan, N. X., Holik, A., Homma, C., Hoxie, I., Huber, M., Humphries, E., Hyland, S., Hassig, A., Hausler, R., Husser, N., Petit, R. A., Iderzorig, B., Igarashi, M., Iqbal, S. B., Ishikawa, S., Ishizuka, S., Islam, S., Islam, R., Ito, K., Ito, S., Ito, T., Ivankovic, T., Iwashiro, T., Jackson, S., Jacobs, J., James, M., Jaubert, M., Jerier, M. -L., Jiminez, E., Jinfessa, A., De Jong, Y., Joo, H. W., Jospin, G., Kajita, T., Ahmad Kassim, A. S., Kato, N., Kaur, A., Kaur, I., de Souza Gomes Kehdy, F., Khadka, V. S., Khan, S., Khavari, M., Ki, M., Kim, G., Kim, H. J., Kim, S., King, R. J., Kolomonaco, G., Koag, E., Kobko-Litskevitch, N., Korshevniuk, M., Kozhar, M., Krebs, J., Kubota, N., Kuklin, A., Kumar, S. S., Kwong, R., Kwong, L., Lafontaine, I., Lago, J., Lai, T. Y., Laine, E., Laiola, M., Lakhneko, O., Lamba, I., de Lamotte, G., Lannes, R., De Lazzari, E., Leahy, M., Lee, H., Lee, Y., Lee, L., Lemaire, V., Leong, E., Lewandowska, D., Li, C., Liang, W., Lin, M., Lisboa, P., Litskevitch, A., Liu, E. M., Liu, T., Livia, M. A., Lo, Y. H., Losim, S., Loubens, M., Lu, J., Lykhenko, O., Lysakova, S., Mahmoud, S., Majid, S. A., Makogon, N., Maldonado, D., Mallari, K., Malta, T. M., Mamun, M., Manoir, D., Marchandon, G., Marciniak, N., Marinovic, S., Marques, B., Mathews, N., Matsuzaki, Y., Matthys, V., May, M., Mccomb, E., Meagher, A., Melamed, A., Menary, W., Mendez, K. N., Mendez, A., Mendy, I. M., Meng, I., Menon, A., Menor, M., Meoded, R., Merino, N., Miah, K., Mignotte, M., Miketic, T., Miranda, W., Mitsios, A., Miura, R., Miyake, K., Moccia, M. D., Mohan, N., Mohsin, M., Moitra, K., Moldes, M., Molina, L., Molinet, J., Molomjamts, O. -E., Moniruzzaman, E., Moon, S., de Oliveira Moraes, I., Moreno, M., Mosella, M. S., Moser, J. W., Mozsary, C., Muehlbauer, A. L., Muner, O., Munia, M., Munim, N., Muscat, M., Mustac, T., Munoz, C., Nadalin, F., Naeem, A., Nagy-Szakal, D., Nakagawa, M., Narce, A., Nasu, M., Navarrete, I. G., Naveed, H., Nazario, B., Nedunuri, N. R., Neff, T., Nesimi, A., Ng, W. C., Ng, S., Nguyen, G., Ngwa, E., Nicolas, A., Nicolas, P., Nika, A., Noorzi, H., Nosrati, A., Nunes, D. N., O'Brien, K., O'Hara, N. B., Oken, G., Olawoyin, R. A., Oliete, J. Q., Olmeda, K., Oluwadare, T., Oluwadare, I. A., Ordioni, N., Orpilla, J., Orrego, J., Ortega, M., Osma, P., Osuolale, I. O., Osuolale, O. M., Ota, M., Oteri, F., Oto, Y., Ounit, R., Ouzounis, C. A., Pakrashi, S., Paras, R., Pardo-Este, C., Park, Y. -J., Pastuszek, P., Patel, S., Pathmanathan, J., Patrignani, A., Perez, M., Peros, A., Persaud, S., Peters, A., Phillips, A., Pineda, L., Pizzi, M. P., Plaku, A., Pompa-Hogan, B., Portilla, M. G., Posada, L., Priestman, M., Prithiviraj, B., Priya, S., Pugdeethosal, P., Pugh, C. E., Pulatov, B., Pupiec, A., Pyrshev, K., Qing, T., Rahiel, S., Rahmatulloev, S., Rajendran, K., Ramcharan, A., Ramirez-Rojas, A., Rana, S., Ratnanandan, P., Read, T. D., Rehrauer, H., Richer, R., Rivera, A., Rivera, M., Robertiello, A., Robinson, C., Rodriguez, P., Rojas, N. A., Roldan, P., Rosario, A., Roth, S., Ruiz, M., Boja Ruiz, S. E., Russell, K., Rybak, M., Sabedot, T. S., Sabina, M., Saito, I., Saito, Y., Malca Salas, G. A., Salazar, C., San, K. M., Sanchez, J., Sanchir, K., Sankar, R., de Souza Santos, P. T., Saravi, Z., Sasaki, K., Sato, Y., Sato, M., Sato, S., Sato, R., Sato, K., Sayara, N., Schaaf, S., Schacher, O., Schinke, A. -L. M., Schlapbach, R., Schori, C., Schriml, J. R., Segato, F., Sepulveda, F., Serpa, M. S., De Sessions, P. F., Severyn, J. C., Shakil, M., Shalaby, S., Shari, A., Shim, H., Shirahata, H., Shiwa, Y., Da Silva, O., Silva, J. M., Simon, G., Singh, S. K., Sluzek, K., Smith, R., So, E., Andreu Somavilla, N., Sonohara, Y., Rufino de Sousa, N., Souza, C., Sperry, J., Sprinsky, N., Stark, S. G., La Storia, A., Suganuma, K., Suliman, H., Sullivan, J., Supie, A. A. M., Suzuki, C., Takagi, S., Takahara, F., Takahashi, N., Takahashi, K., Takeda, T., Takenaka, I. K., Tanaka, S., Tang, A., Man Tang, Y., Tarcitano, E., Tassinari, A., Taye, M., Terrero, A., Thambiraja, E., Thiebaut, A., Thomas, S., Thomas, A. M., Togashi, Y., Togashi, T., Tomaselli, A., Tomita, M., Tomita, I., Toth, O., Toussaint, N. C., Tran, J. M., Truong, C., Tsonev, S. I., Tsuda, K., Tsurumaki, T., Tuz, M., Tymoshenko, Y., Urgiles, C., Usui, M., Vacant, S., Vann, L. E., Velter, F., Ventorino, V., Vera-Wolf, P., Vicedomini, R., Suarez-Villamil, M. A., Vincent, S., Vivancos-Koopman, R., Wan, A., Wang, C., Warashina, T., Watanabe, A., Weekes, S., Werner, J., Westfall, D., Wieler, L. H., Williams, M., Wolf, S. A., Wong, B., Wong, Y. L., Wong, T., Wright, R., Wunderlin, T., Yamanaka, R., Yang, J., Yano, H., Yeh, G. C., Yemets, O., Yeskova, T., Yoshikawa, S., Zafar, L., Zhang, Y., Zhang, S., Zhang, A., Zheng, Y., and Zubenko, S.

Subjects
Urban Population, Drug Resistance, Sequence assembly, Microbiologia, microbiome, global health, computer.software_genre, Medical and Health Sciences, shotgun sequencing, BGC, 0302 clinical medicine, Databases, Genetic, 11. Sustainability, Global health, AMR, 11 Medical and Health Sciences, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, built environment, metagenome, antimicrobial resistance, NGS, de novo assembly, biology, Shotgun sequencing, Microbiota, built Environment, Bacterial, Biodiversity, Biological Sciences, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infection, Biotechnology, Geospatial analysis, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Article, General Biochemistry, Genetics and Molecular Biology, Databases, 03 medical and health sciences, Antibiotic resistance, Genetic, Drug Resistance, Bacterial, International MetaSUB Consortium, Genetics, Humans, Microbiome, 030304 developmental biology, Human Genome, 06 Biological Sciences, 15. Life on land, biology.organism_classification, Resistènica als medicaments antiinfecciosos, SAÚDE PÚBLICA, Genòmica, 13. Climate action, Evolutionary biology, Metagenomics, Antimicrobial Resistance, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, 030217 neurology & neurosurgery, Archaea, Developmental Biology
Abstract

Summary We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities., Graphical abstract, Highlights • Cities possess a consistent “core” set of non-human microbes • Urban microbiomes echo important features of cities and city-life • Antimicrobial resistance genes are widespread in cities • Cities contain many novel bacterial and viral species, This systematic, worldwide catalog of urban microbiomes represents a metagenomic atlas important for understanding the ecology, virulence, and antibiotic resistance of city-specific microbial communities.

Published
2021
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20. Feasibility of smart glasses in supporting spinal surgical procedures in low- and middle-income countries: experiences from East Africa

Author

Fabian Sommer, Francois Waterkeyn, Ibrahim Hussain, Jacob L. Goldberg, Sertac Kirnaz, Rodrigo Navarro-Ramirez, Alaaeldin Azmi Ahmad, Massimo Balsano, Branden Medary, Hamisi Shabani, Amanda Ng, Pravesh Shankar Gadjradj, and Roger Härtl

Subjects
Feasibility Studies, Humans, Smart Glasses, Surgery, Neurology (clinical), General Medicine, Developing Countries, Tanzania, Spine
Abstract

OBJECTIVE Telemedicine technology has been developed to allow surgeons in countries with limited resources to access expert technical guidance during surgical procedures. The authors report their initial experience using state-of-the-art wearable smart glasses with wireless capability to transmit intraoperative video content during spine surgery from sub-Saharan Africa to experts in the US. METHODS A novel smart glasses system with integrated camera and microphone was worn by a spine surgeon in Dar es Salaam, Tanzania, during 3 scoliosis correction surgeries. The images were transmitted wirelessly through a compatible software system to a computer viewed by a group of fellowship-trained spine surgeons in New York City. Visual clarity was determined using a modified Snellen chart, and a percentage score was determined on the smallest line that could be read from the 8-line chart on white and black backgrounds. A 1- to 5-point scale (from 1 = unrecognizable to 5 = optimal clarity) was used to score other visual metrics assessed using a color test card including hue, contrast, and brightness. The same scoring system was used by the group to reach a consensus on visual quality of 3 intraoperative points including instruments, radiographs (ability to see pedicle screws relative to bony anatomy), and intraoperative surgical field (ability to identify bony landmarks such as transverse processes, pedicle screw starting point, laminar edge). RESULTS All surgeries accomplished the defined goals safely with no intraoperative complications. The average download and upload connection speeds achieved in Dar es Salaam were 45.21 and 58.89 Mbps, respectively. Visual clarity with the modified white and black Snellen chart was 70.8% and 62.5%, respectively. The average scores for hue, contrast, and brightness were 2.67, 3.33, and 2.67, respectively. Visualization quality of instruments, radiographs, and intraoperative surgical field were 3.67, 1, and 1, respectively. CONCLUSIONS Application of smart glasses for telemedicine offers a promising tool for surgical education and remote training, especially in low- and middle-income countries. However, this study highlights some limitations of this technology, including optical resolution, intraoperative lighting, and internet connection challenges. With continued collaboration between clinicians and industry, future iterations of smart glasses technology will need to address these issues to stimulate robust clinical utilization.

Published
2022
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21. Implementation of Laparoscopic Nissen Fundoplications in a Developing South African Pediatric Surgical Service

Author

Hansraj Mangray, Sanele Stanley Madziba, Amanda Ngobese, Yashlin Govender, and Damian L. Clarke

Subjects
laparoscopy, minimal access surgery, nissen fundoplication, pediatric surgery, teaching, Pediatrics, RJ1-570, Surgery, RD1-811
Abstract

Introduction: Pediatric laparoscopic Nissen fundoplication (LNF) has become the standard approach at many centers. We developed a minimal access surgery (MAS) training curriculum to enhance the delivery of MAS for pediatric patients in a resource-limited setting. We reviewed our 10-year experience in implementing and performing LNF at our institution. Methods: We described the challenges of implementing MAS training for LNF and how we addressed them. Beneficial technical considerations were described. A retrospective review was performed on all pediatric LNFs performed. Results: We performed 268 LNFs. Specialists or trainees under supervision performed all LNFs. The trainee group performed 43 LNFs (16%). The median operative time for the specialists was 94 min (interquartile range [IQR] 50), and the trainee group was 140 min (IQR 62.5). The median number of cases performed until we improved operative time amongst the trainees was nine (IQR 3). There were seven repeat LNFs, and 11 cases were converted to open. The overall complication rate was 8.9%. A reduction in complications among specialists occurred over the years. The 30-day mortality post-LNF was 0.7%. Conclusion: LNF can be successfully introduced at a tertiary training centre in South Africa with good outcomes. A comprehensive quality improvement program, including MAS training, supported this.

Published
2024
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23. Sleep disruption explains age-related prospective memory deficits: implications for cognitive aging and intervention

Author

Michael Weinborn, Amanda Ng, Yanqi Ryan Li, Belinda M. Brown, Erica Hodgson, Lara Fine, Shayne Loft, Ralph N. Martins, Denise Parker, Stephanie R. Rainey Smith, Hamid R. Sohrabi, and Romola S. Bucks

Subjects
Male, Sleep Wake Disorders, Cognitive aging, Aging, Memory, Episodic, Experimental and Cognitive Psychology, 050105 experimental psychology, Domain (software engineering), 03 medical and health sciences, Cognition, 0302 clinical medicine, Intervention (counseling), Age related, Prospective memory, Humans, 0501 psychology and cognitive sciences, Aged, Aged, 80 and over, Memory Disorders, High prevalence, 05 social sciences, Middle Aged, Sleep in non-human animals, Psychiatry and Mental health, Neuropsychology and Physiological Psychology, Cognitive Aging, Female, Self Report, Geriatrics and Gerontology, Sleep, Psychology, 030217 neurology & neurosurgery, Clinical psychology
Abstract

The high prevalence of sleep disruption among older adults may have implications for cognitive aging, particularly for higher-order aspects of cognition. One domain where sleep disruption may contribute to age-related deficits is prospective memory-the ability to remember to perform deferred actions at the appropriate time in the future. Community-dwelling older adults (55-93 years, N = 133) undertook assessment of sleep using actigraphy and participated in a laboratory-based prospective memory task. After controlling for education, sleep disruption (longer awakenings) was associated with poorer prospective memory. Additionally, longer awakenings mediated the relationship between older age and poorer prospective memory. Other metrics of sleep disruption, including sleep efficiency and wake after sleep onset, were not related to prospective memory, suggesting that examining the features of individual wake episodes rather than total wake time may help clarify relationships between sleep and cognition. The mediating role of awakening length was partially a function of greater depression and poorer executive function (shifting) but not retrospective memory. This study is among the first to examine the association between objectively measured sleep and prospective memory in older adults. Furthermore, this study is novel in suggesting sleep disruption might contribute to age-related prospective memory deficits; perhaps, with implications for cognitive aging more broadly. Our results suggest that there may be opportunities to prevent prospective memory decline by treating sleep problems.

Published
2018
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26. Six Recurrent Amyloid-Related Imaging Abnormality Episodes in a Patient Treated With Aducanumab

Author

Jacob N. Hall, Guido Davidzon, Athanasia Boumis, Sharon J. Sha, Elizabeth C. Mormino, Amanda Ng, and Jennifer L. Gaudioso

Subjects
Male, Amyloid, Pathology, medicine.medical_specialty, Vasogenic Brain Edema, business.industry, Brain, Antibodies, Monoclonal, Humanized, Magnetic Resonance Imaging, Article, Medical imaging, medicine, Humans, Neurology (clinical), Aducanumab, Abnormality, business, Aged
Published
2022
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28. Cerebral quantitative susceptibility mapping predicts amyloid-β-related cognitive decline

Author

David Ames, Patricia Desmond, Roger J. Ordidge, Ashley I. Bush, Amanda Ng, Christopher C. Rowe, Parnesh Raniga, Jurgen Fripp, Colin L. Masters, Ibrahima Diouf, Yen Ying Lim, Victor L. Villemagne, Paul Maruff, Shawna Farquharson, Olivier Salvado, Pierrick Bourgeat, Scott Ayton, Amir Fazlollahi, and James D. Doecke

Subjects
medicine.medical_specialty, medicine.diagnostic_test, Magnetic resonance imaging, Quantitative susceptibility mapping, medicine.disease, 030218 nuclear medicine & medical imaging, Temporal lobe, 03 medical and health sciences, 0302 clinical medicine, Neuroimaging, Frontal lobe, Positron emission tomography, Internal medicine, medicine, Cardiology, Neurology (clinical), Cognitive decline, Alzheimer's disease, Psychology, Neuroscience, 030217 neurology & neurosurgery
Abstract

See Derry and Kent (doi:10.1093/awx167) for a scientific commentary on this article.The large variance in cognitive deterioration in subjects who test positive for amyloid-β by positron emission tomography indicates that convergent pathologies, such as iron accumulation, might combine with amyloid-β to accelerate Alzheimer's disease progression. Here, we applied quantitative susceptibility mapping, a relatively new magnetic resonance imaging method sensitive to tissue iron, to assess the relationship between iron, amyloid-β load, and cognitive decline in 117 subjects who underwent baseline magnetic resonance imaging and amyloid-β positron emission tomography from the Australian Imaging, Biomarkers and Lifestyle study (AIBL). Cognitive function data were collected every 18 months for up to 6 years from 100 volunteers who were either cognitively normal (n = 64) or diagnosed with mild cognitive impairment (n = 17) or Alzheimer's disease (n = 19). Among participants with amyloid pathology (n = 45), higher hippocampal quantitative susceptibility mapping levels predicted accelerated deterioration in composite cognition tests for episodic memory [β(standard error) = -0.169 (0.034), P = 9.2 × 10-7], executive function [β(standard error) = -0.139 (0.048), P = 0.004), and attention [β(standard error) = -0.074 (0.029), P = 0.012]. Deteriorating performance in a composite of language tests was predicted by higher quantitative susceptibility mapping levels in temporal lobe [β(standard error) = -0.104 (0.05), P = 0.036] and frontal lobe [β(standard error) = -0.154 (0.055), P = 0.006]. These findings indicate that brain iron might combine with amyloid-β to accelerate clinical progression and that quantitative susceptibility mapping could be used in combination with amyloid-β positron emission tomography to stratify individuals at risk of decline.

Published
2017
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29. Abstract WP84: MRI Based Scores Outperform CTA Based Scores in Predicting Outcome After Basilar Artery Occlusion

Author

Ali Mahta, Katarina Dakay, Karen L. Furie, Mahesh V Jayaraman, Shawna Cutting, Justin F. Fraser, Bradford B Thompson, Michael E. Reznik, Linda C. Wendell, Shadi Yaghi, Anusha Boyanpally, Gaurav Jindal, Ryan A Mc Taggart, and Amanda Ng

Subjects
Advanced and Specialized Nursing, medicine.medical_specialty, Noninvasive imaging, medicine.diagnostic_test, business.industry, Basilar artery occlusion, Magnetic resonance imaging, Collateral circulation, medicine.disease, Internal medicine, Occlusion, Ischemic stroke, medicine, Cardiology, In patient, Neurology (clinical), Cardiology and Cardiovascular Medicine, business, Stroke
Abstract

Introduction: Clinical outcomes in patients with acute basilar occlusion (BAO) vary widely; several prognostic scores based on noninvasive imaging have been proposed. We aimed to compare the predictive value of several noninvasive neuroimaging scores in patients with BAO. Methods: We performed a single-center retrospective cohort study including all patients with acute BAO from 2015-2019. Using available clinical radiographic data, we calculated the following scores based on computed tomography (CT) and CT angiogram: Goyal posterior communicating artery score, posterior circulation collateral score, Basilar Artery on Computed Tomography Angiography (BATMAN) score, pc-ASPECTS score, and pons-midbrain index. We also calculated the following scores based on diffusion-weighted (DWI) magnetic resonance imaging (MRI): Bern DWI score, MRI pc-ASPECTS, and pons-midbrain index on DWI. We then used logistic regression with area under the ROC curve analysis to determine the accuracy of each score in predicting favorable 3-month outcome (modified Rankin Scale 0-2). Results: Of 39 patients in our cohort, 92.3% underwent endovascular treatment (n=36) and 35.8% (n=14) had a favorable 3-month outcome. The Bern DWI score (AUC 0.790, 95% CI 0.619-0.960), pc-ASPECTS on MRI (AUC 0.880, 95% CI 0.601-0.958), and pons-midbrain index on MRI (AUC 0.764, 95% CI 0.594-0.934) accurately predicted 3-month outcome when analyzed as raw scores (Figure 1).: Conclusion: MRI scores more strongly predict outcome in BAO as compared to CTA collateral scores. Larger prospective studies are needed to confirm our findings.

Published
2020
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32. Validity and reliability of the ten-item Connor-Davidson Resilience Scale (CD-RISC10) instrument in patients with axial spondyloarthritis (axSpA) in Singapore

Author

Julian Thumboo, Yu Heng Kwan, Truls Østbye, Jie Kie Phang, Ka Keat Lim, Nai Lee Lui, Amanda Ng, Warren Fong, Eng-Hui Chew, Chuen Seng Tan, and Ying Ying Leung

Subjects
Adult, Male, medicine.medical_specialty, Psychometrics, Intraclass correlation, Immunology, Validity, Structural equation modeling, 03 medical and health sciences, 0302 clinical medicine, Rheumatology, Cronbach's alpha, Surveys and Questionnaires, Spondylarthritis, medicine, Immunology and Allergy, Humans, Translations, 030212 general & internal medicine, Reliability (statistics), Face validity, Aged, 030203 arthritis & rheumatology, Singapore, business.industry, Construct validity, Reproducibility of Results, Middle Aged, Resilience, Psychological, Confirmatory factor analysis, Cross-Sectional Studies, Physical therapy, Female, business
Abstract

We aimed to assess the validity and reliability of the ten-item Connor–Davidson Resilience Scale (CD-RISC10) in patients with axial spondyloarthritis (axSpA) in Singapore. We used cross-sectional data from 108 patients with axSpA recruited from a dedicated axSpA clinic in a Singapore tertiary referral hospital from 2017 to 2018. Analyses were guided by the COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) framework. Face validity was assessed through cognitive debriefing interviews (CDIs). Internal consistency was assessed through Cronbach’s alpha. Test–retest reliability was assessed through intraclass correlation (ICC). Measurement error was assessed through smallest detectable change (SDC). Construct validity was assessed through six a priori hypotheses through correlation of the CD-RISC10 score with other patient-reported outcome measures. Structural validity was assessed using confirmatory factor analysis (CFA). Fit indices evaluated were root-mean-square error of approximation (RMSEA), comparative fit index (CFI), Tucker–Lewis index (TFI), and standardized root-mean-squared residual (SRMR). Ten patients completed the CDIs and face validity was supported. Among 108 patients (median age: 37(21–77), 81.5% males, 93.5% Chinese), the CD-RISC10 demonstrated good internal consistency (Cronbach’s alpha = 0.94), and excellent test–retest reliability [ICC = 0.964 (95% CI 0.937–0.980)]. SDC was calculated as 1.88. Construct validity was established by meeting five out of the six a priori hypotheses. Structural validity was supported as CFA confirmed a one-factor model, with adequate fit statistics after adding three covariances (RMSEA = 0.077; CFI = 0.975; TLI = 0.964; SRMR = 0.036). This study supports the CD-RISC10 as a valid and reliable measure of resilience for use in patients with axSpA.

Published
2018

33. Repeatable Battery for the Assessment of Neuropsychological Status (RBANS): Normative Data for Older Adults

Author

Michael Weinborn, Maria Pushpanathan, Erica Hodgson, Talitha Lowndes, Lara Fine, Amanda Ng, Denise Parker, Michelle Olaithe, Donna M. Bayliss, Romola S. Bucks, and Michael W. Anderson

Subjects
Male, 050103 clinical psychology, Repeatable Battery for the Assessment of Neuropsychological Status, Percentile, Younger age, media_common.quotation_subject, 050109 social psychology, Neuropsychological Tests, Healthy Aging, Cognition, Sex Factors, Reference Values, medicine, Humans, Mass Screening, 0501 psychology and cognitive sciences, Longitudinal Studies, Normality, media_common, Aged, Aged, 80 and over, medicine.diagnostic_test, 05 social sciences, Neuropsychology, Age Factors, Australia, General Medicine, Neuropsychological test, Middle Aged, Regression, Psychiatry and Mental health, Clinical Psychology, Neuropsychology and Physiological Psychology, Normative, Educational Status, Female, Independent Living, Psychology, Clinical psychology
Abstract

Objective Provide updated older adult (ages 60+) normative data for the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS), Form A, using regression techniques, and corrected for education, age, and gender. Method Participants (aged 60–93 years; N = 415) were recruited through the Healthy Ageing Research Program (HARP), University of Western Australia, and completed Form A of the RBANS as part of a wider neuropsychological test battery. Regression-based techniques were used to generate normative data rather than means-based methods. This methodology allows for the control of demographic variables using continuous data. To develop norms, the data were assessed for: (1) normality; (2) associations between each subtest score and age, education, and gender; (3) the effect of age, education, and gender on subtest scores; and (4) residual scores which were converted to percentile distributions. Results Differences were noted between the three samples, some of which were small and may not represent a clinically meaningful difference. Younger age, more years of education, and female gender were associated with better scores on most subtests. Frequency distributions, means, and standard deviations were produced using unstandardized residual scores to remove the effects of age, education, and gender. Conclusions These normative data expand upon past work by using regression-based techniques to generate norms, presenting percentiles, as well as means and standard deviations, correcting for the effect of gender, and providing a free-to-use Excel macro to calculate percentiles.

Published
2018

34. Mental and behavioral health problems among displaced Myanmar adults exhibiting suboptimal adherence to chronic disease medication treatment in Thailand

Author

Judith K Bass, Amanda Nguyen, Kittipong Sornlorm, Ye Htut Oo, Jarntrah Sappayabanphot, Catherine Lee, and Wongsa Laohasiriwong

Subjects
Chronic disease, Displaced populations, Mental health, Poor medication adherence, Public aspects of medicine, RA1-1270, Colonies and colonization. Emigration and immigration. International migration, JV1-9480
Abstract

Background: People living with non-communicable diseases (NCDs) such as hypertension and diabetes are at high risk for mental health and psychosocial problems. These problems, in turn, can lead to social isolation, lower quality of life, greater health needs, and poorer health outcomes. The prevalence of NCDs is rising in humanitarian settings, where residents are already at an increased risk of mental health problems due to trauma and stressful living conditions. Yet there has been limited focus on understanding experiences and intersections between these often-co-occurring health conditions in humanitarian settings. Improving this understanding holds promise for supporting integrated care and better patient health outcomes. Objective: To describe mental health problems of displaced Myanmar adults with current poor medication adherence for hypertension and/or type 2 diabetes mellitus and identify factors associated with poor mental health among this population. Methods: Cross-sectional analysis of 224 adults with poor medication adherence (

Published
2024
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35. Pre-course instructional videos and home-based laparoscopic suturing simulation enhances the educational impact of a laparoscopic training course

Author

Hansraj Mangray, Sanele Madziba, Shamaman Harilal, Yashlin Govender, Amanda Ngobese, and Damian L Clarke

Subjects
Minimal access surgery, Training, Laparoscopy, Intra-corporeal suturing, Psychomotor skills, Surgery, RD1-811
Abstract

Introduction: We developed a home-based laparoscopic suturing simulation (HBLSS) technique, which is intended to improve the impact of a structured laparoscopic training course. Method: A group of sixteen students were provided with the educational video, and after two weeks, all students were observed and timed performing a laparoscopic reef knot. The students were then randomized into two cohorts. The exclusive video group continued using the video for a further two weeks. The second group were shown the HBLSS technique and told to use this in conjunction with the video for a further two weeks. Results: The entire cohort had an initial median time to form an intracorporeal reef knot of 190 s (range 459, IQR 128). After two additional weeks of using the educational video exclusively, the median time was reduced to 85 s (range 282, IQR 125), whereas the HBLSS and educational video group had a median post-training time of 28.5 s (range 36, IQR 18.5). There was a clear statistical difference between the exclusive video group and the HBLSS and video group (P = 0.008). There was also an improvement from the movement of both instruments to one instrument, reduced crossing of instruments and reduced transverse movement in the HBLSS and video group. Conclusion: A combination of video-based teaching and HBLSS was associated with improved laparoscopic intra-corporeal knot-tying skills in comparison to the exclusive video-based teaching. This reflects the importance of imparting both cognitive and psychomotor skills to students practising laparoscopic surgery.

Published
2023
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36. [P1–444]: QUANTITATIVE SUSCEPTIBILITY MAPPING OF THE HIPPOCAMPUS PREDICTS HIPPOCAMPAL ATROPHY IN Aβ+ ELDERLY CONTROLS AND ALZHEIMER's DISEASE PATIENTS

Author

David Ames, Jurgen Fripp, Scott Ayton, Parnesh Raniga, Christopher C. Rowe, Vincent Dore, Victor L. Villemagne, Ibrahima Diouf, Amanda Ng, Amir Fazlollahi, Ashley I. Bush, Olivier Salvado, Colin L. Masters, and Pierrick Bourgeat

Subjects
Pathology, medicine.medical_specialty, Epidemiology, business.industry, Health Policy, 05 social sciences, Hippocampus, Quantitative susceptibility mapping, Disease, 050105 experimental psychology, Hippocampal atrophy, 03 medical and health sciences, Psychiatry and Mental health, Cellular and Molecular Neuroscience, 0302 clinical medicine, Developmental Neuroscience, medicine, 0501 psychology and cognitive sciences, Neurology (clinical), Geriatrics and Gerontology, business, 030217 neurology & neurosurgery
Published
2017
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37. Combining images and anatomical knowledge to improve automated vein segmentation in MRI

Author

David L. Dowe, Amanda Ng, David G. Barnes, Gary F. Egan, Phillip G. D. Ward, Parnesh Raniga, and Nicholas J. Ferris

Subjects
Male, Computer science, Cognitive Neuroscience, Image processing, Veins, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, Atlases as Topic, Imaging, Three-Dimensional, 0302 clinical medicine, Image Processing, Computer-Assisted, medicine, Humans, Segmentation, Computer vision, Vein, Anatomical location, medicine.diagnostic_test, Atlas (topology), business.industry, Brain, Magnetic resonance imaging, Pattern recognition, Image Enhancement, Magnetic Resonance Imaging, medicine.anatomical_structure, Neurology, Anatomical knowledge, cardiovascular system, Female, Artificial intelligence, business, 030217 neurology & neurosurgery
Abstract

PurposeTo improve the accuracy of automated vein segmentation by combining susceptibility-weighted images (SWI), quantitative susceptibility maps (QSM), and a vein atlas to produce a resultant image called a composite vein image (CV image).MethodAn atlas was constructed in common space from 1072 manually traced 2D-slices. The composite vein image was derived for each subject as a weighted sum of three inputs; a SWI image, a QSM image and the vein atlas. The weights for each input and each anatomical location, called template priors, were derived by assessing the accuracy of each input over an independent data set. The accuracy of venograms derived automatically from each of the CV image, SWI, and QSM image sets was assessed by comparison with manual tracings. Three different automated vein segmentation techniques were used, and ten performance metrics evaluated.ResultsVein segmentations using the CV image were comprehensively better than those derived from SWI or QSM images (mean Cohen’s d = 1.1). Sixty permutations of performance metric and automated segmentation technique were evaluated. Vein identification improvements that were both large and significant (Cohen’s d>0.80, pConclusionThe accuracy of automated venograms derived from the composite vein image was overwhelmingly superior to venograms derived from SWI or QSM alone.

Published
2017
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38. A normalisation framework for quantitative brain imaging; application to quantitative susceptibility mapping

Author

Amanda Ng, Jurgen Fripp, Pierrick Bourgeat, Olivier Salvado, David Ames, Victor L. Villemagne, Scott Ayton, Colin L. Masters, Ashley I. Bush, Christopher C. Rowe, Amir Fazlollahi, and Parnesh Raniga

Subjects
Normalization (statistics), medicine.diagnostic_test, business.industry, Computer science, Partial volume, Normalization (image processing), Magnetic resonance imaging, Pattern recognition, Quantitative susceptibility mapping, 030218 nuclear medicine & medical imaging, Intensity normalization, White matter, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, Neuroimaging, Region of interest, medicine, Medical imaging, Artificial intelligence, Reference Region, Nuclear medicine, business, 030217 neurology & neurosurgery
Abstract

Quantitative medical imaging often utilizes intensity normalization based on a signal from a neighboring region. The choice of this region can substantially affect the quantification, and is potentially confounded by the presence of pathology or other limitations such as partial volume effect. In this paper we outline the desirable list of criteria for selecting a normalization region of interest, and utilize this approach for quantitative susceptibility mapping (QSM) MRI in a study of neurodegeneration. The proposed criteria includes (i) association between reference region and demographics such as age, (ii) diagnostic group separation effect in the reference region, (iii) correlation between reference and target regions, (iv) local variance in the reference region, and (v) reduced cross-sectional variance within the diagnostic groups using the reference region. The intensity normalization was then evaluated using 119 subjects with normal cognition, mild cognitive impairment and Alzheimer's disease. For QSM applications in ageing we found that normalizing by the white matter regions not only satisfies the criteria but it also provides the best separation between clinical groups in the brain nuclei regions.

Published
2017
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39. Analysis of ADC model robustness in diffusion-weighted MRI

Author

David W. Wright, Amanda Ng, Syeda Warda Taqdees, Leigh A. Johnston, and Mary Tolcos

Subjects
medicine.diagnostic_test, Computer science, Experimental data, Magnetic resonance imaging, Upper and lower bounds, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Robustness (computer science), Parametric model, Statistics, medicine, Gamma distribution, Effective diffusion coefficient, Algorithm, 030217 neurology & neurosurgery, Diffusion MRI
Abstract

A variety of parametric models based on the Apparent Diffusion Coefficient (ADC) have been proposed to describe signal decay in the interpretation of diffusion weighted Magnetic Resonance Imaging data. In this work, we investigate the robustness of several of these models, including the exponential model, bi-exponential model and the recently proposed gamma distribution model, using a Cramer-Rao lower bound analysis. It is demonstrated that the parameters of all models are susceptible to significant estimation errors at the current gradient strengths of clinical scanners. To complement the theoretical analysis, the robustness of the models is compared through application to experimental ovine optic nerve and rat brain MRI data. Our results indicate that gamma distribution model fits experimental data better than the commonly employed bi-exponential model.

Published
2017
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40. Vein segmentation using shape-based Markov Random Fields

Author

Parnesh Raniga, Amanda Ng, David G. Barnes, Gary F. Egan, David L. Dowe, Nicholas J. Ferris, and Phillip G. D. Ward

Subjects
Cerebral veins, Computer science, Cerebral metabolic rate, computer.software_genre, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Voxel, Medical imaging, medicine, Segmentation, Computer vision, Vein, Markov random field, Random field, Markov chain, business.industry, Quantitative susceptibility mapping, Pattern recognition, Image segmentation, medicine.anatomical_structure, Artificial intelligence, business, computer, Perfusion, 030217 neurology & neurosurgery
Abstract

The magnetic susceptibility of haemoglobin is modulated by oxygen saturation, providing a mechanism to non-invasively measure oxygen extraction fraction. When combined with perfusion techniques, quantitative susceptibility mapping facilitates regional measurement of cerebral metabolic rate of oxygen consumption. However, accurate measurement requires a complete vein map to measure anatomical variance in the metabolic demands of tissue. In this work we present a novel shape-based Markov Random Field technique to segmentation the cerebral veins that provides accurate and complete vein maps. The shape-based graph underpinning the model controls the spatial relationships between voxels and enforces cylindrical geometry, allowing increased sensitivity with accurate vein boundaries.

Published
2017
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41. Improved Quantification of Cerebral Vein Oxygenation Using Partial Volume Correction

Author

Parnesh Raniga, David G. Barnes, Gary F. Egan, Phillip G. D. Ward, Amanda Ng, David L. Dowe, and Audrey P. Fan

Subjects
Cerebral veins, Materials science, Mean squared error, Partial volume, computer.software_genre, oxygen extraction fraction, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Voxel, vein, medicine, Methods, Psychology, partial volume, Vein, quantitative susceptibility mapping, medicine.diagnostic_test, OEF, business.industry, General Neuroscience, QSM, Neurosciences, Quantitative susceptibility mapping, Venous blood, medicine.anatomical_structure, Positron emission tomography, Cognitive Sciences, Nuclear medicine, business, computer, 030217 neurology & neurosurgery, Neuroscience, MRI
Abstract

Purpose: Quantitative susceptibility mapping (QSM) enables cerebral venous characterization and physiological measurements, such as oxygen extraction fraction (OEF). The exquisite sensitivity of QSM to deoxygenated blood makes it possible to image small veins; however partial volume effects must be addressed for accurate quantification. We present a new method, Iterative Cylindrical Fitting (ICF), to estimate voxel-based partial volume effects for susceptibility maps and use it to improve OEF quantification of small veins with diameters between 1.5 and 4 voxels. Materials and Methods: Simulated QSM maps were generated to assess the performance of the ICF method over a range of vein geometries with varying echo times and noise levels. The ICF method was also applied to in vivo human brain data to assess the feasibility and behavior of OEF measurements compared to the maximum intensity voxel (MIV) method. Results: Improved quantification of OEF measurements was achieved for vessels with contrast to noise greater than 3.0 and vein radii greater than 0.75 voxels. The ICF method produced improved quantitative accuracy of OEF measurement compared to the MIV approach (mean OEF error 7.7 vs. 12.4%). The ICF method provided estimates of vein radius (mean error

Published
2017

42. 7T-fMRI: Faster temporal resolution yields optimal BOLD sensitivity for functional network imaging specifically at high spatial resolution

Author

Nicholas L. Opie, Terence J. O'Brien, Yan T. Wong, Shawna Farquharson, Amanda Ng, Jon O. Cleary, Bradford A. Moffat, Sam E. John, Claire B. Mulcahy, Thomas J Oxley, Roger J. Ordidge, Peter E. Yoo, and David B. Grayden

Subjects
Adult, Male, Computer science, Cognitive Neuroscience, Image processing, computer.software_genre, Brain mapping, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Neuroimaging, Voxel, medicine, Image Processing, Computer-Assisted, Humans, Computer vision, Image resolution, Brain Mapping, Human Connectome Project, medicine.diagnostic_test, business.industry, Brain, Magnetic resonance imaging, Magnetic Resonance Imaging, medicine.anatomical_structure, Neurology, Temporal resolution, Female, Artificial intelligence, Nerve Net, Functional magnetic resonance imaging, business, computer, 030217 neurology & neurosurgery, Motor cortex
Abstract

Recent developments in accelerated imaging methods allow faster acquisition of high spatial resolution images. This could improve the applications of functional magnetic resonance imaging at 7 Tesla (7T-fMRI), such as neurosurgical planning and Brain Computer Interfaces (BCIs). However, increasing the spatial and temporal resolution will both lead to signal-to-noise ratio (SNR) losses due to decreased net magnetization per voxel and T1-relaxation effect, respectively. This could potentially offset the SNR efficiency gains made with increasing temporal resolution. We investigated the effects of varying spatial and temporal resolution on fMRI sensitivity measures and their implications on fMRI-based BCI simulations. We compared temporal signal-to-noise ratio (tSNR), observed percent signal change (%∆S), volumes of significant activation, Z-scores and decoding performance of linear classifiers commonly used in BCIs across a range of spatial and temporal resolution images acquired during an ankle-tapping task. Our results revealed an average increase of 22% in %∆S (p=0.006) and 9% in decoding performance (p=0.015) with temporal resolution only at the highest spatial resolution of 1.5×1.5×1.5mm3, despite a 29% decrease in tSNR (p 0.05) across spatial resolution specifically at the highest temporal resolution of 500ms. These results demonstrate that the overall BOLD sensitivity can be increased significantly with temporal resolution, granted an adequately high spatial resolution with minimal physiological noise level. This shows the feasibility of diffuse motor-network imaging at high spatial and temporal resolution with robust BOLD sensitivity with 7T-fMRI. Importantly, we show that this sensitivity improvement could be extended to an fMRI application such as BCIs.

Published
2016

43. P1‐312: Iron and Amyloid Depositions are Positively Related in Non‐Demented Individuals

Author

Scott Ayton, Vincent Dore, Jurgen Fripp, Amanda Ng, David Ames, Colin L. Masters, Olivier Salvado, Amir Fazlollahi, Christopher C. Rowe, Victor L. Villemagne, Parnesh Raniga, Pierrick Bourgeat, and Ashley I. Bush

Subjects
0301 basic medicine, medicine.medical_specialty, Epidemiology, business.industry, Health Policy, 03 medical and health sciences, Psychiatry and Mental health, Cellular and Molecular Neuroscience, 030104 developmental biology, 0302 clinical medicine, Endocrinology, Developmental Neuroscience, Internal medicine, medicine, Neurology (clinical), Geriatrics and Gerontology, business, Amyloid Depositions, 030217 neurology & neurosurgery
Published
2016
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44. Can skin microbes predispose you to eczema?

Author

Kern Rei Ng, Sri Anusha Matta, Fook Tim Chew, Andreas Wilm, Amanda Ng, John E.A. Common, Angeline Tay, Bani Kaur Suri, Chanhao Li, Colin Wong, Niranjan Nagaranjan, and Birgit Lane

Subjects
World Wide Web, Thesaurus (information retrieval), business.industry, Medicine, Dermatology, business, Molecular Biology, Biochemistry
Published
2017
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45. Compartment specific regulation of sleep by mushroom body requires GABA and dopaminergic signaling

Author

Margaret Driscoll, Steven N Buchert, Victoria Coleman, Morgan McLaughlin, Amanda Nguyen, and Divya Sitaraman

Subjects
Medicine, Science
Abstract

Abstract Sleep is a fundamental behavioral state important for survival and is universal in animals with sufficiently complex nervous systems. As a highly conserved neurobehavioral state, sleep has been described in species ranging from jellyfish to humans. Biogenic amines like dopamine, serotonin and norepinephrine have been shown to be critical for sleep regulation across species but the precise circuit mechanisms underlying how amines control persistence of sleep, arousal and wakefulness remain unclear. The fruit fly, Drosophila melanogaster, provides a powerful model system for the study of sleep and circuit mechanisms underlying state transitions and persistence of states to meet the organisms motivational and cognitive needs. In Drosophila, two neuropils in the central brain, the mushroom body (MB) and the central complex (CX) have been shown to influence sleep homeostasis and receive aminergic neuromodulator input critical to sleep–wake switch. Dopamine neurons (DANs) are prevalent neuromodulator inputs to the MB but the mechanisms by which they interact with and regulate sleep- and wake-promoting neurons within MB are unknown. Here we investigate the role of subsets of PAM-DANs that signal wakefulness and project to wake-promoting compartments of the MB. We find that PAM-DANs are GABA responsive and require GABAA-Rdl receptor in regulating sleep. In mapping the pathways downstream of PAM neurons innervating γ5 and β′2 MB compartments we find that wakefulness is regulated by both DopR1 and DopR2 receptors in downstream Kenyon cells (KCs) and mushroom body output neurons (MBONs). Taken together, we have identified and characterized a dopamine modulated sleep microcircuit within the mushroom body that has previously been shown to convey information about positive and negative valence critical for memory formation. These studies will pave way for understanding how flies balance sleep, wakefulness and arousal.

Published
2021
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46. Inhibition of itch by neurokinin 1 receptor (Tacr1) -expressing ON cells in the rostral ventromedial medulla in mice

Author

Taylor Follansbee, Dan Domocos, Eileen Nguyen, Amanda Nguyen, Aristea Bountouvas, Lauren Velasquez, Mirela Iodi Carstens, Keiko Takanami, Sarah E Ross, and Earl Carstens

Subjects
itch, descending modulation, pain, RVM, Medicine, Science, Biology (General), QH301-705.5
Abstract

The rostral ventromedial medulla (RVM) is important in descending modulation of spinal nociceptive transmission, but it is unclear if the RVM also modulates spinal pruriceptive transmission. RVM ON cells are activated by noxious algesic and pruritic stimuli and are pronociceptive. Many RVM-spinal projection neurons express the neurokinin-1 receptor (Tacr1), and ON-cells are excited by local administration of substance P (SP). We hypothesized that Tacr1-expressing RVM ON cells exert an inhibitory effect on itch opposite to their pronociceptive action. Intramedullary microinjection of SP significantly potentiated RVM ON cells and reduced pruritogen-evoked scratching while producing mild mechanical sensitization. Chemogenetic activation of RVM Tacr1-expressing RVM neurons also reduced acute pruritogen-evoked scratching. Optotagging experiments confirmed RVM Tacr1-expressing neurons to be ON cells. We conclude that Tacr1-expressing ON cells in RVM play a significant role in the modulation of pruriceptive transmission.

Published
2022
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47. Engineering an Enhanced EGFR Engager: Humanization of Cetuximab for Improved Developability

Author

Dennis R. Goulet, Soumili Chatterjee, Wai-Ping Lee, Andrew B. Waight, Yi Zhu, and Amanda Nga-Sze Mak

Subjects
cetuximab, antibody engineering, humanization, glycosylation, post-translational modifications, stability, Immunologic diseases. Allergy, RC581-607
Abstract

The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase whose proliferative effects can contribute to the development of many types of solid tumors when overexpressed. For this reason, EGFR inhibitors such as cetuximab can play an important role in treating cancers such as colorectal cancer and head and neck cancer. Cetuximab is a chimeric monoclonal antibody containing mouse variable regions that bind to EGFR and prevent it from signaling. Although cetuximab has been used clinically since 2004 to successfully control solid tumors, advances in protein engineering have created the opportunity to address some of its shortcomings. In particular, the presence of mouse sequences could contribute to immunogenicity in the form of anti-cetuximab antibodies, and an occupied glycosylation site in FR3 can contribute to hypersensitivity reactions and product heterogeneity. Using simple framework graft or sequence-/structure-guided approaches, cetuximab was humanized onto 11 new frameworks. In addition to increasing humanness and removing the VH glycosylation site, dynamic light scattering revealed increases in stability, and bio-layer interferometry confirmed minimal changes in binding affinity, with patterns emerging across the humanization method. This work demonstrates the potential to improve the biophysical and clinical properties of first-generation protein therapeutics and highlights the advantages of computationally guided engineering.

Published
2022
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48. Life stage impact on the human skin ecosystem: lipids and the microbial community

Author

Martin P. Pagac, Bala Davient, Luca Antonio Plado, Hilbert Yuen In Lam, Shi Mun Lee, Aarthi Ravikrishnan, Wee Ling Esther Chua, Sneha Muralidharan, Aishwarya Sridharan, Antony S. Irudayaswamy, Ramasamy Srinivas, Stephen Wearne, Ahmad Nazri Mohamed Naim, Eliza Xin Pei Ho, H. Q. Amanda Ng, Junmei Samantha Kwah, Eileen Png, Anne K. Bendt, Markus R. Wenk, Federico Torta, Niranjan Nagarajan, John Common, Yap Seng Chong, Elizabeth Huiwen Tham, Lynette Pei-Chi Shek, Evelyn Xiu Ling Loo, John Chambers, Yik Weng Yew, Marie Loh, and Thomas L. Dawson

Subjects
Microbial ecology, QR100-130
Abstract

Abstract Sebaceous free fatty acids are metabolized by multiple skin microbes into bioactive lipid mediators termed oxylipins. This study investigated correlations between skin oxylipins and microbes on the superficial skin of pre-pubescent children (N = 36) and adults (N = 100), including pre- (N = 25) and post-menopausal females (N = 25). Lipidomics and metagenomics revealed that Malassezia restricta positively correlated with the oxylipin 9,10-DiHOME on adult skin and negatively correlated with its precursor, 9,10-EpOME, on pre-pubescent skin. Co-culturing Malassezia with keratinocytes demonstrated a link between 9,10-DiHOME and pro-inflammatory cytokines IL-1β and IL-6 production. We also observed strong correlations between other skin oxylipins and microbial taxa, highlighting life stage differences in sebum production and microbial community composition. Our findings imply a complex host-microbe communication system mediated by lipid metabolism occurring on human skin, warranting further research into its role in skin health and disease and paving the way towards novel therapeutic targets and treatments.

Published
2025
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49. Structures and Ribosomal Interaction of Ribosome-Inactivating Proteins

Author

Wei-Wei Shi, Amanda Nga-Sze Mak, Kam-Bo Wong, and Pang-Chui Shaw

Subjects
ribosome-inactivating proteins, RNA N-glycosidases, ribosome, P proteins, ribosomal interaction, Organic chemistry, QD241-441
Abstract

Ribosome-inactivating proteins (RIPs) including ricin, Shiga toxin, and trichosanthin, are RNA N-glycosidases that depurinate a specific adenine residue (A-4324 in rat 28S ribosomal RNA, rRNA) in the conserved α-sarcin/ricin loop (α-SRL) of rRNA. RIPs are grouped into three types according to the number of subunits and the organization of the precursor sequences. RIPs are two-domain proteins, with the active site located in the cleft between the N- and C-terminal domains. It has been found that the basic surface residues of the RIPs promote rapid and specific targeting to the ribosome and a number of RIPs have been shown to interact with the C-terminal regions of the P proteins of the ribosome. At present, the structural basis for the interaction of trichosanthin and ricin-A chain toward P2 peptide is known. This review surveys the structural features of the representative RIPs and discusses how they approach and interact with the ribosome.

Published
2016
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50. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Author

Chng K. R., Li C., Bertrand D., Ng A. H. Q., Kwah J. S., Low H. M., Tong C., Natrajan M., Zhang M. H., Xu L., Ko K. K. K., Ho E. X. P., Av-Shalom T. V., Teo J. W. P., Khor C. C., Danko D., Bezdan D., Afshinnekoo E., Ahsanuddin S., Bhattacharya C., Butler D. J., De Filippis F., Hecht J., Kahles A., Karasikov M., Kyrpides N. C., Leung M. H. Y., Meleshko D., Mustafa H., Mutai B., Neches R. Y., Ng A., Nieto-Caballero M., Nikolayeva O., Nikolayeva T., Png E., Sanchez J. L., Shaaban H., Sierra M. A., Tong X., Young B., Alicea J., Bhattacharyya M., Blekhman R., Castro-Nallar E., Canas A. M., Chatziefthimiou A. D., Crawford R. W., Deng Y., Desnues C., Dias-Neto E., Donnellan D., Dybwad M., Elhaik E., Ercolini D., Frolova A., Graf A. B., Green D. C., Hajirasouliha I., Hernandez M., Iraola G., Jang S., Jones A., Kelly F. J., Knights K., Labaj P. P., Lee P. K. H., Shawn L., Ljungdahl P., Lyons A., Mason-Buck G., McGrath K., Mongodin E. F., Moraes M. O., Nagarajan N., Noushmehr H., Oliveira M., Ossowski S., Osuolale O. O., Ozcan O., Paez-Espino D., Rascovan N., Richard H., Ratsch G., Schriml L. M., Semmler T., Sezerman O. U., Shi L., Song L. H., Suzuki H., Court D. S., Thomas D., Tighe S. W., Udekwu K. I., Ugalde J. A., Valentine B., Vassilev D. I., Vayndorf E., Velavan T. P., Zambrano M. M., Zhu J., Zhu S., Mason C. E., Chen S. L., Ng O. T., Marimuthu K., Ang B., Genome Institute of Singapore (GIS), Singapore University of Technology and Design (SUTD), Singapore General Hospital, National University Hospital [Singapore] (NUH), Weill Cornell Medicine [Cornell University], Cornell University [New York], Nanyang Technological University [Singapour], Tan Tock Seng Hospital, Department of Computational and Systems Biology [Singapore], Funding for this work was provided by A*STAR (N.N.), and we are grateful for support from NMRC (NMRC CGAug16C005: O.T.N. and K.M.). C.E.M. acknowledges support from the WorldQuant Foundation, the Bill and Melinda Gates Foundation (OPP1151054) and the Alfred P. Sloan Foundation (G-2015-13964). The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript. We would like to thank J. Gilbert for insightful comments and feedback on this work., MetaSUB Consortium: David Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel J. Butler, Kern Rei Chng, Francesca De Filippis, Jochen Hecht, Andre Kahles, Mikhail Karasikov, Nikos C. Kyrpides, Marcus H. Y. Leung, Dmitry Meleshko, Harun Mustafa, Beth Mutai, Russell Y. Neches, Amanda Ng, Marina Nieto-Caballero, Olga Nikolayeva, Tatyana Nikolayeva, Eileen Png, Jorge L. Sanchez, Heba Shaaban, Maria A. Sierra, Xinzhao Tong, Ben Young, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro-Nallar, Ana M. Cañas, Aspassia D. Chatziefthimiou, Robert W. Crawford, Youping Deng, Christelle Desnues, Emmanuel Dias-Neto, Daisy Donnellan, Marius Dybwad, Eran Elhaik, Danilo Ercolini, Alina Frolova, Alexandra B. Graf, David C. Green, Iman Hajirasouliha, Mark Hernandez, Gregorio Iraola, Soojin Jang, Angela Jones, Frank J. Kelly, Kaymisha Knights, Paweł P. Łabaj, Patrick K. H. Lee, Levy Shawn, Per Ljungdahl, Abigail Lyons, Gabriella Mason-Buck, Ken McGrath, Emmanuel F. Mongodin, Milton Ozorio Moraes, Niranjan Nagarajan, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka O. Osuolale, Orhan Özcan, David Paez-Espino, Nicolas Rascovan, Hugues Richard, Gunnar Rätsch, Lynn M. Schriml, Torsten Semmler, Osman U. Sezerman, Leming Shi, Le Huu Song, Haruo Suzuki, Denise Syndercombe Court, Dominique Thomas, Scott W. Tighe, Klas I. Udekwu, Juan A. Ugalde, Brandon Valentine, Dimitar I. Vassilev, Elena Vayndorf, Thirumalaisamy P. Velavan, María M. Zambrano, Jifeng Zhu, Sibo Zhu & Christopher E. Mason, Weill Cornell Medicine [New York], Chng, K. R., Li, C., Bertrand, D., Ng, A. H. Q., Kwah, J. S., Low, H. M., Tong, C., Natrajan, M., Zhang, M. H., Xu, L., Ko, K. K. K., Ho, E. X. P., Av-Shalom, T. V., Teo, J. W. P., Khor, C. C., Danko, D., Bezdan, D., Afshinnekoo, E., Ahsanuddin, S., Bhattacharya, C., Butler, D. J., De Filippis, F., Hecht, J., Kahles, A., Karasikov, M., Kyrpides, N. C., Leung, M. H. Y., Meleshko, D., Mustafa, H., Mutai, B., Neches, R. Y., Ng, A., Nieto-Caballero, M., Nikolayeva, O., Nikolayeva, T., Png, E., Sanchez, J. L., Shaaban, H., Sierra, M. A., Tong, X., Young, B., Alicea, J., Bhattacharyya, M., Blekhman, R., Castro-Nallar, E., Canas, A. M., Chatziefthimiou, A. D., Crawford, R. W., Deng, Y., Desnues, C., Dias-Neto, E., Donnellan, D., Dybwad, M., Elhaik, E., Ercolini, D., Frolova, A., Graf, A. B., Green, D. C., Hajirasouliha, I., Hernandez, M., Iraola, G., Jang, S., Jones, A., Kelly, F. J., Knights, K., Labaj, P. P., Lee, P. K. H., Shawn, L., Ljungdahl, P., Lyons, A., Mason-Buck, G., Mcgrath, K., Mongodin, E. F., Moraes, M. O., Nagarajan, N., Noushmehr, H., Oliveira, M., Ossowski, S., Osuolale, O. O., Ozcan, O., Paez-Espino, D., Rascovan, N., Richard, H., Ratsch, G., Schriml, L. M., Semmler, T., Sezerman, O. U., Shi, L., Song, L. H., Suzuki, H., Court, D. S., Thomas, D., Tighe, S. W., Udekwu, K. I., Ugalde, J. A., Valentine, B., Vassilev, D. I., Vayndorf, E., Velavan, T. P., Zambrano, M. M., Zhu, J., Zhu, S., Mason, C. E., Chen, S. L., Ng, O. T., Marimuthu, K., Ang, B., and Acibadem University Dspace

Subjects
0301 basic medicine, Disease prevention, 030106 microbiology, Geographic Mapping, Drug resistance, Beds, Biology, Opportunistic Infections, Genome, General Biochemistry, Genetics and Molecular Biology, Article, Tertiary Care Centers, 03 medical and health sciences, Plasmid, Antibiotic resistance, Spatio-Temporal Analysis, Drug Resistance, Multiple, Bacterial, Drug Resistance, Bacterial, Patients' Rooms, Humans, Microbiome, Equipment and Supplies, Hospital, Genetics, Cross Infection, Infection Control, Singapore, Microbiota, General Medicine, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Resistome, Disinfection, 030104 developmental biology, Metagenomics, Biofilms, Equipment Contamination, Mobilome, Microbial genetics
Abstract

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections., Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.

Published
2020
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