Last data update: Nov 04, 2024. (Total: 48056 publications since 2009)
Records 1-12 (of 12 Records) |
Query Trace: Smith AC[original query] |
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Whole-genome sequencing resolves biochemical misidentification of Neisseria species from urogenital specimens
Smith AC , Shrivastava A , Cartee JC , Bélanger M , Sharpe S , Lewis J , Budionno S , Gomez R , Khubbar MK , Pham CD , Gernert KM , Schmerer MW , Raphael BH , Learner ER , Kersh EN , Joseph SJ . J Clin Microbiol 2024 e0070424 Neisseria meningitidis (Nm) and Neisseria gonorrhoeae (Ng) are human pathogens that sometimes occupy the same anatomical niche. Ng, the causative agent of gonorrhea, infects 87 million individuals annually worldwide and is an urgent threat due to increasing drug resistance. Ng is a pathogen of the urogenital tract and may infect the oropharyngeal or rectal site, often asymptomatically. Conversely, Nm is an opportunistic pathogen. While often a commensal in the oropharyngeal tract, it is also the leading cause of bacterial meningitis with 1.2 million cases globally, causing significant morbidity and mortality. Horizontal gene transfer (HGT) is likely to occur between Ng and Nm due to their shared anatomical niches and genetic similarity, which poses challenges for accurate detection and treatment. Routine surveillance through the Gonococcal Isolate Surveillance Project and Strengthening the U.S. Response to Resistant Gonorrhea detected six concerning urogenital Neisseria isolates with contradicting species identification in Milwaukee (MIL). While all six isolates were positive for Ng using nucleic acid amplification testing (NAAT) and matrix-assisted laser desorption/ionization time of flight identified the isolates as Ng, two biochemical tests, Gonochek-II and API NH, classified them as Nm. To address this discrepancy, we performed whole-genome sequencing (WGS) using Illumina MiSeq on all isolates and employed various bioinformatics tools. Species detection analysis using BMScan, which uses WGS data, identified all isolates as Ng. Furthermore, Kraken revealed over 98% of WGS reads mapped to the Ng genome and <1% to Nm. Recombination analysis identified putative HGT in all MIL isolates within the γ-glutamyl transpeptidase (ggt) gene, a key component in the biochemical tests used to differentiate between Nm and Ng. Further analysis identified Nm as the source of HGT event. Specifically, the active Nm ggt gene replaced the Ng pseudogenes, ggt1 and ggt2. Together, this study demonstrates that closely related Neisseria species sharing a niche underwent HGT, which led to the misidentification of species following biochemical testing. Importantly, NAAT accurately detected Ng. The misidentification highlights the importance of using WGS to continually evaluate diagnostic or bacterial identification tests. |
At-home specimen self-collection as an additional testing strategy for chlamydia and gonorrhoea: a systematic literature review and meta-analysis
Smith AC , Thorpe PG , Learner ER , Galloway ET , Kersh EN . BMJ Glob Health 2024 9 (8) INTRODUCTION: Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (Ng) infections are often asymptomatic; screening increases early detection and prevents disease, sequelae and further spread. To increase Ct and Ng testing, several countries have implemented specimen self-collection outside a clinical setting. While specimen self-collection at home is highly acceptable to patients and as accurate as specimens collected by healthcare providers, this strategy is new or not being used in some countries. To understand how offering at home specimen self-collection will affect testing uptake, test results, diagnosis and linkage to care, when compared with collection in clinical settings, we conducted a systematic literature review and meta-analysis of peer-reviewed studies. METHODS: We searched Medline, Embase, Global Health, Cochrane Library, CINAHL (EBSCOHost), Scopus and Clinical Trials. Studies were included if they directly compared specimens self-collected at home or in other non-clinical settings to specimen collection at a healthcare facility (self or clinician) for Ct and/or Ng testing and evaluated the following outcomes: uptake in testing, linkage to care, and concordance (agreement) between the two settings for the same individuals. Risk of bias (RoB) was assessed using Cochrane Risk of Bias (RoB2) tool for randomised control trials (RCTs). RESULTS: 19 studies, from 1998 to 2024, comprising 15 RCTs with a total of 62 369 participants and four concordance studies with 906 participants were included. Uptake of Ct or Ng testing was 2.61 times higher at home compared with clinical settings. There was a high concordance between specimens collected at home and in clinical settings, and linkage to care was not significantly different between the two settings (prevalence ratio 0.96 (95% CI 0.91-1.01)). CONCLUSION: Our meta-analysis and systematic literature review show that offering self-collection of specimens at home or in other non-clinical settings could be used as an additional strategy to increase sexually transmitted infection testing in countries that have not yet widely adopted this collection method. |
Some relevant parameters for assessing fire hazards of combustible mine materials using laboratory scale experiments
Litton CD , Perera IE , Harteis SP , Teacoach KA , DeRosa MI , Thomas RA , Smith AC . Fuel (Lond) 2018 218 306-315 When combustible materials ignite and burn, the potential for fire growth and flame spread represents an obvious hazard, but during these processes of ignition and flaming, other life hazards present themselves and should be included to ensure an effective overall analysis of the relevant fire hazards. In particular, the gases and smoke produced both during the smoldering stages of fires leading to ignition and during the advanced flaming stages of a developing fire serve to contaminate the surrounding atmosphere, potentially producing elevated levels of toxicity and high levels of smoke obscuration that render the environment untenable. In underground mines, these hazards may be exacerbated by the existing forced ventilation that can carry the gases and smoke to locations far-removed from the fire location. Clearly, materials that require high temperatures (above 1400 K) and that exhibit low mass loss during thermal decomposition, or that require high heat fluxes or heat transfer rates to ignite represent less of a hazard than materials that decompose at low temperatures or ignite at low levels of heat flux. In order to define and quantify some possible parameters that can be used to assess these hazards, small-scale laboratory experiments were conducted in a number of configurations to measure: 1) the toxic gases and smoke produced both during non-flaming and flaming combustion; 2) mass loss rates as a function of temperature to determine ease of thermal decomposition; and 3) mass loss rates and times to ignition as a function of incident heat flux. This paper describes the experiments that were conducted, their results, and the development of a set of parameters that could possibly be used to assess the overall fire hazard of combustible materials using small scale laboratory experiments. |
New improvements to MFIRE to enhance fire modeling capabilities
Zhou L , Smith AC , Yuan L . Min Eng 2016 68 (6) 45-50 NIOSH's mine fire simulation program, MFIRE, is widely accepted as a standard for assessing and predicting the impact of a fire on the mine ventilation system and the spread of fire contaminants in coal and metal/nonmetal mines, which has been used by U.S. and international companies to simulate fires for planning and response purposes. MFIRE is a dynamic, transient-state, mine ventilation network simulation program that performs normal planning calculations. It can also be used to analyze ventilation networks under thermal and mechanical influence such as changes in ventilation parameters, external influences such as changes in temperature, and internal influences such as a fire. The program output can be used to analyze the effects of these influences on the ventilation system. Since its original development by Michigan Technological University for the Bureau of Mines in the 1970s, several updates have been released over the years. In 2012, NIOSH completed a major redesign and restructuring of the program with the release of MFIRE 3.0. MFIRE's outdated FORTRAN programming language was replaced with an object-oriented C++ language and packaged into a dynamic link library (DLL). However, the MFIRE 3.0 release made no attempt to change or improve the fire modeling algorithms inherited from its previous version, MFIRE 2.20. This paper reports on improvements that have been made to the fire modeling capabilities of MFIRE 3.0 since its release. These improvements include the addition of fire source models of the t-squared fire and heat release rate curve data file, the addition of a moving fire source for conveyor belt fire simulations, improvement of the fire location algorithm, and the identification and prediction of smoke rollback phenomena. All the improvements discussed in this paper will be termed as MFIRE 3.1 and released by NIOSH in the near future. |
Modeling carbon monoxide spread in underground mine fires
Yuan L , Zhou L , Smith AC . Appl Therm Eng 2016 100 1319-1326 Carbon monoxide (CO) poisoning is a leading cause of mine fire fatalities in underground mines. To reduce the hazard of CO poisoning in underground mines, it is important to accurately predict the spread of CO in underground mine entries when a fire occurs. This paper presents a study on modeling CO spread in underground mine fires using both the Fire Dynamics Simulator (FDS) and the MFIRE programs. The FDS model simulating part of the mine ventilation network was calibrated using CO concentration data from full-scale mine fire tests. The model was then used to investigate the effect of airflow leakage on CO concentration reduction in the mine entries. The inflow of fresh air at the leakage location was found to cause significant CO reduction. MFIRE simulation was conducted to predict the CO spread in the entire mine ventilation network using both a constant heat release rate and a dynamic fire source created from FDS. The results from both FDS and MFIRE simulations are compared and the implications of the improved MFIRE capability are discussed. |
CFD modelling of nitrogen injection in a longwall gob area
Yuan L , Smith AC . Int J Min Miner Eng 2014 5 (2) 164-180 This paper describes computational fluid dynamics (CFD) simulations conducted to investigate the effectiveness of N2 injection in an active panel and a sealed longwall gob area to prevent and suppress spontaneous heating of coal using various injection locations and flow rates. In the active panel simulations, a single longwall panel with a bleederless ventilation system was simulated. The spontaneous heating of crushed coal from pillars was simulated and N2 was injected from different locations on the headgate side and through boreholes from the surface. The N2 injection rate at each location was varied between 0.18 m3/s and 0.94 m3/s (380 and 2000 cfm). In the sealed longwall simulations, seal leakage rate was varied to determine its effect on N2 injection effectiveness. The results of this study should aid mine ventilation engineers in developing more effective N2 injection strategies to prevent and control spontaneous heating of coal in underground coal mines. |
Numerical and experimental study on flame spread over conveyor belts in a large-scale tunnel
Yuan L , Mainiero RJ , Rowland JH , Thomas RA , Smith AC . J Loss Prev Process Ind 2014 30 55-62 Conveyor belt fires in an underground mine pose a serious life threat to the miners. This paper presents numerical and experimental results characterizing a conveyor belt fire in a large-scale tunnel. Acomputational fluid dynamics (CFD) model was developed to simulate the flame spread over the conveyor belt in a mine entry. Thermogravimetric analysis (TGA) tests were conducted for the conveyor belt and results were used to estimate the kinetic properties for modeling the pyrolysis process of the conveyor belt burning. The CFD model was calibrated using results from the large-scale conveyor belt fire experiments. The comparison between simulation and test results shows that the CFD model is able to capture the major features of the flame spread over the conveyor belt. The predicted maximum heat release rate, and maximum smoke temperature are in good agreement with the large-scale tunnel fire test results. The calibrated CFD model can be used to predict the flame spread over a conveyor belt in a mine entry under different physical conditions and ventilation parameters to aid in the design of improved fire detection and suppression systems, mine rescue, and mine emergency planning. |
CFD modelling of sampling locations for early detection of spontaneous combustion in long-wall gob areas
Yuan L , Smith AC . Int J Min Miner Eng 2012 4 (1) 50-62 In this study, computational fluid dynamics (CFD) modeling was conducted to optimize gas sampling locations for the early detection of spontaneous heating in longwall gob areas. Initial simulations were carried out to predict carbon monoxide (CO) concentrations at various regulators in the gob using a bleeder ventilation system. Measured CO concentration values at these regulators were then used to calibrate the CFD model. The calibrated CFD model was used to simulate CO concentrations at eight sampling locations in the gob using a bleederless ventilation system to determine the optimal sampling locations for early detection of spontaneous combustion. |
Experimental study on CO and CO2 emissions from spontaneous heating of coals at varying temperatures and O2 concentrations
Yuan L , Smith AC . J Loss Prev Process Ind 2013 26 (6) 1321-1327 Laboratory experiments were conducted to investigate carbon monoxide (CO) and carbon dioxide (CO2) emissions from spontaneous heating of three U.S. coal samples in an isothermal oven at temperatures between 50 and 110 °C. The oxygen (O2) concentration of an oxygen/nitrogen (N2) mixture flowing through the coal sample was 3, 5, 10, 15, and 21%, respectively. The temperature at the center of the coal sample was continuously monitored, while the CO, CO2, and O2 concentrations of the exit gas were continuously measured. The results indicate that the CO and CO2 concentrations and the CO/CO2 ratio increased when the initial temperature was increased. As the inlet O2 concentration increased, the CO and CO2 concentrations increased, while the CO/CO2 ratios tended to converge to the same value. The ratio of CO/CO2 was found to be independent of coal properties, approaching a constant value of 0.2. The maximum CO production rate correlated well with the maximum coal temperature rise. The apparent order of reaction for coal oxidation was estimated to be between 0.52 and 0.72. The experimental results in this study could be used for early detection and evaluation of a spontaneous heating in underground coal mines. |
CO and CO2 emissions from spontaneous heating of coal under different ventilation rates
Yuan L , Smith AC . Int J Coal Geol 2012 88 (1) 24-30 Carbon monoxide (CO) and carbon dioxide (CO2) emissions during a spontaneous heating event in a coal mine are important gases to monitor for detecting the spontaneous heating at an early stage. However, in underground coal mines, the CO and CO2 concentrations and their related fire ratios may be affected by mine ventilation. In this study, CO and CO2 emissions from spontaneous heating of a U.S. coal sample were evaluated in an isothermal oven under different airflow ventilation rates ranging from 100 to 500 cm3/min. Laboratory experiments were conducted at oven temperatures of 70, 90, and 100 °C. The temperature at the center of the coal sample was continually monitored, while the CO, CO2, and oxygen (O2) concentrations of the exit gas were continually measured. The results indicate that CO was generated immediately after the airflow passed through the coal, while CO2 was generated in a late phase. The amounts of CO generated under different airflow rates were approximately the same at the initial temperature of 70 °C, while the amounts of CO generated increased significantly as the airflow rates and initial temperatures increased. The ratio of CO/CO2 was found to be independent of airflow rate and initial temperature, approaching a constant value of 0.2 quickly if there was no thermal runaway. The value tended to decrease when a thermal runaway took place. The CO/O2 deficiency ratio was dependent on both airflow rates and the initial temperature. The experimental results are in qualitative agreement with some large-scale test and field monitoring results. |
Improvement of a mine fire simulation program – incorporation of smoke rollback into MFIRE 3.0
Zhou L , Smith AC . J Fire Sci 2011 30 (1) 29-39 Smoke rollback is a dangerous threat to miners and firefighters in an underground mine fire. The ability to predict smoke rollback can greatly improve the chances for safe miner evacuation and mine fire control and firefighting. A modified semi-empirical equation based on large-scale experiments conducted by the National Institute for Occupational Safety and Health (NIOSH) was developed to quantify smoke rollback during an underground mine fire. The equation was incorporated into a mine fire simulation program (MFIRE 3.0) to allow the user to predict the occurrence of smoke rollback and calculate the smoke rollback distance. This article describes the development of the equation and compares the experimental results with those predicted by MFIRE 3.0. The results indicate that the improved MFIRE 3.0 is capable of determining smoke rollback in a fire entry, not only to provide early warning for smoke rollback but also to verify the effectiveness of smoke rollback control efforts. |
Effect of longwall face advance on spontaneous heating in longwall gob area
Yuan L , Smith AC . Min Eng 2010 62 (3) 34-38 To reduce fire hazards from spontaneous combustion of coal in longwall gob areas, a series of computational fluid dynamics (CFD) simulations were conducted by the National Institute for Occupational Safety and Health (NIOSH) to model the spontaneous heating of coal in longwall gob areas. The previous modeling results demonstrate that spontaneous heating of coal usually occurred behind the longwall shields and along the face with a bleeder ventilation system. Assuming a stationary longwall face, the spontaneous heating could turn to a spontaneous fire in several days for the most reactive coal under favorable conditions. When the longwall face advances, the spontaneous heating process will be significantly affected. In this study, the effect of longwall face advance on the spontaneous heating in the gob area is investigated using the CFD model developed in previous studies. One longwall panel with a bleeder ventilation system is simulated. The width of the panel is 300 m (984 ft), while the length of the panel is changed between 1,000 to 2,000 m (3,280 to 6,560 ft). The same permeability and porosity profiles are used for gobs with different lengths. The spontaneous heating first develops in the gob when the longwall face is stationary. Then, the face advances at a certain rate. The face advance is simulated as a series of discrete movements, and the effect of the face advance on the maximum temperature developed during the face stoppage is examined. |
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