Last data update: May 13, 2024. (Total: 46773 publications since 2009)
Records 1-3 (of 3 Records) |
Query Trace: Kennedy PJ[original query] |
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Machine learning and applications in microbiology.
Goodswen SJ , Barratt JLN , Kennedy PJ , Kaufer A , Calarco L , Ellis JT . FEMS Microbiol Rev 2021 45 (5) To understand the intricacies of microorganisms at the molecular level requires making sense of copious volumes of data such that it may now be humanly impossible to detect insightful data patterns without an artificial intelligence application called machine learning. Applying machine learning to address biological problems is expected to grow at an unprecedented rate, yet it is perceived by the uninitiated as a mysterious and daunting entity entrusted to the domain of mathematicians and computer scientists. The aim of this review is to identify key points required to start the journey of becoming an effective machine learning practitioner. These key points are further reinforced with an evaluation of how machine learning has been applied so far in a broad scope of real-life microbiology examples. This includes predicting drug targets or vaccine candidates, diagnosing microorganisms causing infectious diseases, classifying drug resistance against antimicrobial medicines, predicting disease outbreaks and exploring microbial interactions. Our hope is to inspire microbiologists and other related researchers to join the emerging machine learning revolution. |
Implementation of influenza-like illness sentinel surveillance in Togo
Maman I , Badziklou K , Landoh ED , Halatoko AW , Nzussouo TN , Defang GN , Tamekloe TA , Kennedy PJ , Williams T , Kossi K , Issa Z , Kere AB . BMC Public Health 2014 14 981 BACKGROUND: The emergence of avian influenza A/H5N1 in 2003 as well as the pandemic influenza A (H1N1) pdm09 highlighted the need to establish influenza sentinel surveillance in Togo. The Ministry of Health decided to introduce Influenza to the list of diseases with epidemic potential. By April 2010, Togo was actively involved in influenza surveillance. This study aims to describe the implementation of ILI surveillance and results obtained from April 2010 to December 2012. METHODS: Two sites were selected based on their accessibility and affordability to patients, their adequate specimen storage capacity and transportation system. Patients with ILI presenting at sentinel sites were enrolled by trained medical staff based on the World Health Organization (WHO) case definitions. Oropharyngeal and nasopharyngeal samples were collected and they were tested at the National Influenza Reference Laboratory using a U.S. Centers for Disease Control and Prevention (CDC) validated real time RT-PCR protocol. Laboratory results and epidemiological data were reported weekly and shared with all sentinel sites, Ministry of Health, Division of Epidemiology, WHO and CDC/NAMRU-3. RESULTS: From April 2010 to December 2012, a total of 955 samples were collected with 52% of the study population aged between 0 and 4 years. Of the 955 samples, 236 (24.7%) tested positive for influenza viruses; with 136 (14.2%) positive for influenza A and 100 (10.5%) positive for influenza B. The highest influenza positive percentage (30%) was observed in 5-14 years old and patients aged 0-4 and >60 years had the lowest percentage (20%). Clinical symptoms such as cough and rhinorrhea were associated more with ILI patients who were positive for influenza type A than influenza type B. Influenza viruses circulated throughout the year with the positivity rate peaking around the months of January, May and again in October; corresponding respectively to the dry-dusty harmattan season and the long and then the short raining season. The pandemic A (H1N1) pdm09 was the predominantly circulating strain in 2010 while influenza B was the predominantly circulating strain in 2011. The seasonal A/H3N2 was observed throughout 2012 year. CONCLUSIONS: This study provides information on influenza epidemiology in the capital city of Togo. |
National inventory of core capabilities for pandemic influenza preparedness and response: results from 36 countries with reviews in 2008 and 2010
Moen A , Kennedy PJ , Cheng PY , Macdonald G . Influenza Other Respir Viruses 2013 8 (2) 201-8 BACKGROUND: Re-emergence in 2003 of human cases of avian H5N1 and the resultant spread of the disease highlighted the need to improve the capacity of countries to detect and contain novel viruses. To assess development in this capacity, the Centers for Disease Control and Prevention (CDC) produced a tool for assessing a country's capability in 12 critical areas related to pandemic preparedness, including monitoring and identifying novel influenza viruses. OBJECTIVES: Capabilities the CDC tool assesses range from how well a country has planned and is prepared for an outbreak to how prepared a country is to respond when a pandemic occurs. Included in this assessment tool are questions to determine whether a country has a detailed preparedness plan and the laboratory capacity to identify various strains of influenza quickly and accurately. METHODS: The tool was used first in 2008 when 40 countries in collaboration with CDC calculated baseline scores and used a second time in 2010 by 36 of the original 40 countries to determine whether they had improved their preparedness. Using basic mathematical comparison and statistical analyses, we compared data at the aggregate capability level as well as at the indicator and country levels. Additionally, we examined the comments of respondents to the assessment questionnaire for reasons (positive and negative) that would explain changes in scores from 2008 to 2010. RESULTS: Analysis of results of two assessments in 36 countries shows statistically significant improvement in all 12 capabilities on an aggregate level and 47 of 50 indicators. |
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