The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities

Characterization of Airborne Bacteria at a Subway Station: Implications for Testing and Evaluation of Biological Detection, Identification, and Monitoring Systems

Biological detection, identification, and monitoring (BioDIM) systems that are able to provide rapid and reliable early-warning in the event of a bioterrorism attack may contribute to reduce the impact of such incidents. Currently, few if any available BioDIM systems have been able to meet all the users’ requirements with respect to reliable, sensitive, and selective detect-towarn capabilities in different operational environments. BioDIM efforts at most real life sites must be accomplished against a naturally occurring biological aerosol (bioaerosol) background. The bioaerosol background may be both complex and variable, and could challenge the operational performance of BioDIM systems, potentially resulting in the triggering of false alarms, or even worse, the failure to respond to a real incident. One way to improve the operational performance of BioDIM systems is to increase our understanding of relevant bioaerosol backgrounds. Subway stations are enclosed and crowded public environments which may be regarded as potential bioterrorism targets, and therefore also as a relevant operating environment for BioDIM systems. In order to improve our understanding of the bioaerosol background at subway stations, and especially how it may challenge the operational performance of BioDIM systems, the airborne bacterial background at the Nationaltheatret subway station in Oslo, Norway, was characterized in this study. Information about the concentration level, diversity, size distribution, and temporal variability of the airborne bacterial background was obtained. In addition various virulence- and survival-associated airborne bacterial characteristics such as hemolytic activity, antibiotic resistance, pigmentation, and spore fraction were investigated. The obtained bioaerosol background characteristics were consolidated with similar and different types of existing characteristics from other subway stations, and used to define a set of realistic subway station background characteristics. Such background characteristics may be valuable when applied in a BioDIM context for several reasons. The information may be used to improve the operational performance of BioDIM systems (e.g. by optimizing alarm algorithms), but also to develop more-realistic methods for testing and evaluation (T&E) of BioDIM systems that take into account the real life background. The defined background characteristics may be used to guide the construction of realistic synthetic subway station bioaerosol backgrounds that can be recreated together with a biological threat agent aerosol challenge during simulated operational T&E of BioDIM systems in aerosol chambers. While the airborne bacterial background information mainly was intended for use in a BioDIM context in this study, it may also be relevant when viewed in the context of public and occupational health as well as microbial ecology. An important part of this study also involved testing and implementation of sampling and analysis methods for airborne bacteria. Based on the recognized need for air samplers with well-defined performance criteria, comparative T&E of air samplers was performed in an aerosol chamber to establish their physical and biological sampling efficiencies. The obtained results revealed significant differences between the samplers, which were used to assess their suitability for various bioaerosol sampling applications. A matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) bacterial identification method (MALDI Biotyper) was evaluated and implemented as a rapid and cost-effective screening tool for airborne bacterial isolate collections. The identification results obtained with the MALDI Biotyper were shown to correspond well with 16S rRNA gene sequencing-based results. However, the MALDI Biotyper failed to obtain reliable identifications when the reference database did not contain library entries at the corresponding species or genus level, and it was suggested that the coverage of environmental airborne bacterial taxa in the reference database should be increased. Another BioDIM-relevant topic addressed as part of this study was rapid identification methods for Bacillus anthracis spores in suspicious powders (e.g. letters). A MALDI-TOF MS-based identification method for B. anthracis spores in powders was developed and validated. The observed performance of the analysis method demonstrated its potential applicability as a rapid, specific, sensitive, robust, and cost-effective analysis tool for resolving incidents involving suspicious powders in less than 30 min. The work presented in this thesis contributes to a deeper understanding of the bioaerosol background, especially at subway stations. It similarly highlights the potential importance of the bioaerosol background in a BioDIM context, and emphasizes the need for increased research efforts to close existing knowledge gaps. This thesis may also serve to highlight the research efforts that will be needed before real life bioaerosol background information may be fully exploited in a BioDIM context

Ear close to mouth : conversations between film and philosophy

Doktorandprojektet är en studie i och genom filmiska samtal. Det genomförs i relation till samtalets roll i lärandet av filosofi. Medan filosofi oftast antar individuellt skriven form studeras hur filmiska samtal kan fungera som filosofiskt uttryck, främst utifrån filmen Samtal om samtal som är projektets huvudmaterial. Filmen börjar i ett försök att prata om hur vi pratar med varandra på seminariet, och i en förlängning hur det kan bestämma vilken filosofi som alls blir möjlig: Vem talar och vem lyssnar? Vilka erfarenheter räknas och vilka idéer är välkomna? Samtidigt är samtalet inte bara av intresse som praktik utan också som uttryck. Ibland sägs något i samtalet som inte skulle bli sagt annars. Vad skulle hända om samtal, som ett slags gemensamt sägande, kunde utgöra ett filosofiskt uttryck i egen rätt, liksom den individuellt skrivna texten? Hur skulle ett sådant uttryck i så fall alls kunna ta form? Skulle det kunna göras med film? I och genom studiens filmiska samtal leder detta också vidare till frågor om representation och ansvar: Vad är det att göra film om eller med någon? Hur påverkas de som är del av en film och vad gör den på egen hand? Vad är det att ta ansvar i det filmiska arbetet och för den film som blir till? Utöver Samtal om samtal läggs texten Eftertext fram. Den försätter studien kring samma frågeställningar, men försöker därigenom också svara an till det filmiska arbetet i Samtal om samtal. Eftertext hänvisar även till filmerna Ett jag som säger vi och Rehearsals samt dokumentet Transkription. Dessa ingår som appendix då de utgör delstudier i arbetet med Samtal om samtal.This PhD project is a study in and through filmic conversations. The project addresses the role of conversation in philosophy education. While philosophy often is manifested in individually written form, this is a study of how filmic conversation can act as philosophical expression, mainly based on the film Samtal om samtal which is the principal material of this PhD project. The film begins by addressing the manner of which we speak to one another in a seminar; and by extension how that manner decides which philosophy is at all made possible: Who is speaking and who is listening? Whose experiences count and whose ideas are welcome? Yet, conversation is not only of interest as practice but also as expression. Sometimes something is said through/as conversation that could not have been expressed in any other form. What would happen if conversation, as a communal way of saying things, would constitute a form of philosophical expression in its own right, on par with the individually written text? What form would such an expression be allowed to take? Could philosophy be expressed through the medium of film? In and through the filmic conversation of this study, these queries also lead on to issues of representation and responsibility: What signifies the practice of making a film about or with someone? How are those involved in a film project affected, and how can the film act (in the world) independently? How could responsibility be understood in the process of making a film and regarding the final result? In addition to Samtal om samtal, the text Eftertext is submitted. The text further explores the previously mentioned questions, but adds another layer in commenting on the filmic work of Samtal om samtal. Eftertext also refers to the films Ett jag som säger vi and Rehearsals, as well as the document Transkription. These works are included as appendices, forming sub studies of the Samtal om samtal project. DOCUMENTED ARTISTIC RESEARCH PROJECT (DOCTORAL THESIS)consisting of1. Förtext (text)2. Samtal om samtal (film)3. Eftertext (text)Appendices: Ett jag som säger vi (film), Rehearsals (film), Transkription (text/image-document)</p

Characterization of airborne bacteria at an underground subway station

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Temporal variability of the bioaerosol background at a subway station: Concentration level, size distribution, and diversity of airborne bacteria

Naturally occurring bioaerosol environments may present a challenge to biological detection-identification-monitoring (BIODIM) systems aiming at rapid and reliable warning of bioterrorism incidents. One way to improve the operational performance of BIODIM systems is to increase our understanding of relevant bioaerosol backgrounds. Subway stations are enclosed public environments which may be regarded as potential bioterrorism targets. This study provides novel information concerning the temporal variability of the concentration level, size distribution, and diversity of airborne bacteria in a Norwegian subway station. Three different air samplers were used during a 72-h sampling campaign in February 2011. The results suggested that the airborne bacterial environment was stable between days and seasons, while the intraday variability was found to be substantial, although often following a consistent diurnal pattern. The bacterial levels ranged from not detected to 103 CFU m3 and generally showed increased levels during the daytime compared to the nighttime levels, as well as during rush hours compared to non-rush hours. The airborne bacterial levels showed rapid temporal variation (up to 270-fold) on some occasions, both consistent and inconsistent with the diurnal profile. Airborne bacterium-containing particles were distributed between different sizes for particles of >1.1 m, although 50% were between 1.1 and 3.3 m. Anthropogenic activities (mainly passengers) were demonstrated as major sources of airborne bacteria and predominantly contributed 1.1- to 3.3-m bacterium-containing particles. Our findings contribute to the development of realistic testing and evaluation schemes for BIODIM equipment by providing information that may be used to simulate operational bioaerosol backgrounds during controlled aerosol chamber-based challenge tests with biological threat agents

Characterization of airborne bacteria at an underground subway station

The reliable detection of airborne biological threat agents depends on several factors, including the performance criteria of the detector and its operational environment. One step in improving the detector's performance is to increase our knowledge of the biological aerosol background in potential operational environments. Subway stations are enclosed public environments, which may be regarded as potential targets for incidents involving biological threat agents. In this study, the airborne bacterial community at a subway station in Norway was characterized (concentration level, diversity, and virulence- and survival-associated properties). In addition, a SASS 3100 high-volume air sampler and a matrix-assisted laser desorption ionization–time of flight mass spectrometry-based isolate screening procedure was used for these studies. The daytime level of airborne bacteria at the station was higher than the nighttime and outdoor levels, and the relative bacterial spore number was higher in outdoor air than at the station. The bacterial content, particle concentration, and size distribution were stable within each environment throughout the study (May to September 2010). The majority of the airborne bacteria belonged to the genera Bacillus, Micrococcus, and Staphylococcus, but a total of 37 different genera were identified in the air. These results suggest that anthropogenic sources are major contributors to airborne bacteria at subway stations and that such airborne communities could harbor virulence- and survival-associated properties of potential relevance for biological detection and surveillance, as well as for public health. Our findings also contribute to the development of realistic testing and evaluation schemes for biological detection/surveillance systems by providing information that can be used to mimic real-life operational airborne environments in controlled aerosol test chambers

Quantification of aerosol dispersal from suspected aerosol-generating procedures

Background Oxygen-delivering modalities like humidified high-flow nasal cannula (HFNC) and noninvasive positive-pressure ventilation (NIV) are suspected of generating aerosols that may contribute to transmission of disease such as coronavirus disease 2019. We sought to assess if these modalities lead to increased aerosol dispersal compared to the use of non-humidified low-flow nasal cannula oxygen treatment (LFNC). Methods Aerosol dispersal from 20 healthy volunteers using HFNC, LFNC and NIV oxygen treatment was measured in a controlled chamber. We investigated effects related to coughing and using a surgical face mask in combination with the oxygen delivering modalities. An aerodynamic particle sizer measured aerosol particles (APS3321, 0.3–20 µm) directly in front of the subjects, while a mesh of smaller particle sensors (SPS30, 0.3–10 µm) was distributed in the test chamber. Results Non-productive coughing led to significant increases in particle dispersal close to the face when using LFNC and HFNC but not when using NIV. HFNC or NIV did not lead to a statistically significant increase in aerosol dispersal compared to LFNC. With non-productive cough in a room without air changes, there was a significant drop in particle levels between 100 cm and 180 cm from the subjects. Conclusions Our results indicate that using HFNC and NIV does not lead to increased aerosol dispersal compared to low-flow oxygen treatment, except in rare cases. For a subject with non-productive cough, NIV with double-limb circuit and non-vented mask may be a favourable choice to reduce the risk for aerosol spread

SARS-CoV-2 in the Air Surrounding Patients during Nebulizer Therapy

Nebulizer therapy is commonly used for patients with obstructive pulmonary disease or acute pulmonary infections with signs of obstruction. It is considered a “potential aerosol-generating procedure,” and the risk of disease transmission to health care workers is uncertain. The aim of this pilot study was to assess whether nebulizer therapy in hospitalized COVID-19 patients is associated with increased dispersion of SARS-CoV-2. Air samples collected prior to and during nebulizer therapy were analyzed by RT-PCR and cell culture. Total aerosol particle concentrations were also quantified. Of 13 patients, seven had quantifiable virus in oropharynx samples, and only two had RT-PCR positive air samples. For both these patients, air samples collected during nebulizer therapy had higher SARS-CoV-2 RNA concentrations compared to control air samples. Also, for particle sizes 0.3–5 µm, particle concentrations were significantly higher during nebulizer therapy than in controls. We were unable to cultivate virus from any of the RT-PCR positive air samples, and it is therefore unknown if the detected virus were replication-competent; however, the significant increase in smaller particles, which can remain airborne for extended periods of time, and increased viral RNA concentrations during treatment may indicate that nebulizer therapy is associated with increased risk of SARS-CoV-2 transmission.publishedVersio