Radical collaboration during a global health emergency: development of the RDA COVID-19 data sharing recommendations and guidelines

Background: The coronavirus disease 2019 (COVID-19) global pandemic required a rapid and effective response. This included ethical and legally appropriate sharing of data. The European Commission (EC) called upon the Research Data Alliance (RDA) to recruit experts worldwide to quickly develop recommendations and guidelines for COVID-related data sharing. Purpose: The purpose of the present work was to explore how the RDA succeeded in engaging the participation of its community of scientists in a rapid response to the EC request. Methods: A survey questionnaire was developed and distributed among RDA COVID-19 work group members. A mixed-methods approach was used for analysis of the survey data. Results: The three constructs of radical collaboration (inclusiveness, distributed digital practices, productive and sustainable collaboration) were found to be well supported in both the quantitative and qualitative analyses of the survey data. Other social factors, such as motivation and group identity were also found to be important to the success of this extreme collaborative effort. Conclusions: Recommendations and suggestions for future work were formulated for consideration by the RDA to strengthen effective expert collaboration and interdisciplinary efforts.

Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group

The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such collaboration needs open research practices and the sharing of research outputs, such as data and code, thereby facilitating research and research reproducibility and timely collaboration beyond borders. The Research Data Alliance COVID-19 Working Group recently published a set of recommendations and guidelines on data sharing and related best practices for COVID-19 research. These guidelines include recommendations for clinicians, researchers, policy- and decision-makers, funders, publishers, public health experts, disaster preparedness and response experts, infrastructure providers from the perspective of different domains (Clinical Medicine, Omics, Epidemiology, Social Sciences, Community Participation, Indigenous Peoples, Research Software, Legal and Ethical Considerations), and other potential users. These guidelines include recommendations for researchers, policymakers, funders, publishers and infrastructure providers from the perspective of different domains (Clinical Medicine, Omics, Epidemiology, Social Sciences, Community Participation, Indigenous Peoples, Research Software, Legal and Ethical Considerations). Several overarching themes have emerged from this document such as the need to balance the creation of data adherent to FAIR principles (findable, accessible, interoperable and reusable), with the need for quick data release; the use of trustworthy research data repositories; the use of well-annotated data with meaningful metadata; and practices of documenting methods and software. The resulting document marks an unprecedented cross-disciplinary, cross-sectoral, and cross-jurisdictional effort authored by over 160 experts from around the globe. This letter summarises key points of the Recommendations and Guidelines, highlights the relevant findings, shines a spotlight on the process, and suggests how these developments can be leveraged by the wider scientific community.

Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group

The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such collaboration needs open research practices and the sharing of research outputs, such as data and code, thereby facilitating research and research reproducibility and timely collaboration beyond borders. The Research Data Alliance COVID-19 Working Group recently published a set of recommendations and guidelines on data sharing and related best practices for COVID-19 research. These guidelines include recommendations for researchers, policymakers, funders, publishers and infrastructure providers from the perspective of different domains (Clinical Medicine, Omics, Epidemiology, Social Sciences, Community Participation, Indigenous Peoples, Research Software, Legal and Ethical Considerations). Several overarching themes have emerged from this document such as the need to balance the creation of data adherent to FAIR principles (findable, accessible, interoperable and reusable), with the need for quick data release; the use of trustworthy research data repositories; the use of well-annotated data with meaningful metadata; and practices of documenting methods and software. The resulting document marks an unprecedented cross-disciplinary, cross-sectoral, and cross-jurisdictional effort authored by over 160 experts from around the globe. This letter summarises key points of the Recommendations and Guidelines, highlights the relevant findings, shines a spotlight on the process, and suggests how these developments can be leveraged by the wider scientific community.

Open government data and environmental science: a federal Canadian perspective

Governments worldwide are releasing data into the public domain via open government data initiatives. Many such data sets are directly relevant to environmental science and complement data collected by academic researchers to address complex and challenging environmental problems. The Government of Canada is a leader in open data among Organisation for Economic Co-operation and Development countries, generating and releasing troves of valuable research data. However, achieving comprehensive and FAIR (findable, accessible, interoperable, reusable) open government data is not without its challenges. For example, identifying and understanding Canada’s international commitments, policies, and guidelines on open data can be daunting. Similarly, open data sets within the Government of Canada are spread across a diversity of repositories and portals, which may hinder their discoverability. We describe Canada’s federal initiatives promoting open government data, and outline where data sets of relevance to environmental science can be found. We summarize research data management challenges identified by the Government of Canada, plans to modernize the approach to open data for environmental science and best practices for data discoverability, access, and reuse.

Determination of complex mixtures of volatile organic compounds in ambient air: an overview

This article reviews developments in the sampling and analysis of volatile organic compounds (VOCs) in ambient air since the 1970s, particularly in the field of environmental monitoring. Global monitoring of biogenic and anthropogenic VOC emissions is briefly described. Approaches used for environmental monitoring of VOCs and industrial hygiene VOC exposure assessments are compared. The historical development of the sampling and analytical methods used is discussed, and the relative advantages and disadvantages of sorbent and canister methods are identified. Overall, there is considerable variability in the reliability of VOC estimates and inventories. In general, canister methods provide superior precision and accuracy and are particulary useful for the analysis of complex mixtures of VOCs. Details of canister methods are reviewed in a companion paper.

Determination of complex mixtures of volatile organic compounds in ambient air: canister methodology

Canister methodology is applicable to 150 polar and nonpolar VOCs found in ambient air from parts-per-billion by volume (ppbv) to parts-per-million (ppmv) levels, and has been validated at parts-per-trillion (pptv) levels for a subset of these analytes. This article is a detailed review of techniques related to the collection of volatile organic compounds (VOCs) in evacuated Summa and fused-silica-lined canisters, and their analysis by gas chromatography/mass spectrometry (GC/MS). Emphasis is placed on canister cleaning, VOC stability in canisters, sample dilution, water management, and VOC cryogenic and sorbent preconcentration methods. A wide range of VOC preconcentration and water management methods are identified from the literature, and their relative merits and disadvantages are discussed. Examples of difficulties that commonly arise when processing canister samples are illustrated, and solutions to these problems are provided.

Cross-sensitivities of electrochemical detectors used to monitor worker exposures to airborne contaminants: False positive responses in the absence of target analytes

Ideally, the response of electrochemical detectors is proportional to the concentration of targeted airborne chemicals and is not be affected by concomitantly present substances. Manufacturers provide a limited list of cross-sensitivities but end-users have anecdotally reported unexpected interferences by other substances. Electrochemical detectors designed to measure airborne levels of CO, H(2)S, NO, NO(2), or SO(2), were challenged with potentially interfering substances in the absence of target analytes. Cross-sensitivities undocumented by the manufacturers were observed and were found to vary between different models of instruments for the same challenge chemical.

Municipal firefighter exposure groups, time spent at fires and use of self-contained-breathing-apparatus

BACKGROUND

Previous studies have found significant associations between firefighting and cancer.

METHODS

Fires, vehicle movement, and firefighter job assignment were determined, and storage and distribution of self-contained-breathing-apparatus (SCBAs) were tracked for 12 months. Time spent at fires and use of SCBAs were calculated.

RESULTS

Only 66% of fire department personnel were 1st-line combat firefighters. Number of runs was an unreliable surrogate for time spent at fires. Eight firefighter exposure groups were identified (based on job title, firehall assignment, and time spent at fires), ranging from no exposures to 3,244 min/year/firefighter. SCBAs appear to have been used for approximately 50% of the time at structural fires but for only 6% of the time at all fires.

CONCLUSIONS

Failure of previous studies to identify homogeneous exposure groups may have resulted in misclassification and underestimates of health risks. The approach used in this study may be used in epidemiological studies to identify exposure/response relationships.

Characterization of volatile organic compounds in smoke at municipal structural fires

The objective of this study was to characterize volatile organic compounds (VOCs) found at municipal structural fires in order to identify sources of long-term health risks to firefighters, which may be contributing factors in heart disease and cancer. Firefighters collected air into evacuated Summa canisters inside burning buildings at nine municipal structural fires under conditions where they judged that at least some firefighters might remove their self-contained breathing apparatus masks. Volatile organic compounds were identified and quantified for 144 target compounds using cryogenic preconcentration and gas chromatography/mass spectral detection (GC/MSD) methodology operating in selected ion monitoring mode. Samples were also analyzed in SCAN mode and examined for the appearance of substances that were not present in the instrument standard calibration mixture. The spectra of municipal structural fires were surprisingly similar and remarkable for their simplicity, which was largely due to the dominating presence of benzene along with toluene and naphthalene. Propene and 1,3-butadiene were found in all of the fires, and styrene and other alkyl-substituted benzene compounds were frequently identified. Similar "fingerprints" of the same 14 substances (propene, benzene, xylenes, 1-butene/2-methylpropene, toluene, propane, 1,2-butadiene, 2-methylbutane, ethylbenzene, naphthalene, styrene, cyclopentene, 1-methylcyclopentene, isopropylbenzene) previously identified at experimental fires burning various solid combustible materials were also found at municipal structural fires, accounting for 76.8% of the total VOCs measured. Statistically significant positive correlations were found between increasing levels of benzene and levels of propene, the xylenes, toluene, 1-butene/2-methylpropene, 1,3-butadiene, and naphthalene. Given the toxicity/carcinogenicity of those VOCs that were found in the highest concentrations, particularly benzene, 1,3-butadiene, and styrene, further investigation of VOC exposures of firefighters is warranted. Benzene, or its metabolic product s-phenylmercapturic acid in urine, was identified as a suitable chemical marker for firefighter exposure to combustion products.

Characterization of volatile organic compounds in smoke at experimental fires

Significant associations between firefighting and cancer have been reported; however, studies finding toxic products of combustion at municipal fires have been limited by (1) technical difficulties encountered at the scene of working fires, (2) the lack of a coherent sampling strategy, and (3) the absence of verified sampling methods. The objective of the present study was to characterize the presence of volatile organic compound (VOC) combustion products in fire smoke. Air samples from experimental fires burning various materials commonly found at structural fires were collected into evacuated Summa canisters and analyzed for 144 target VOCs using cryogenic preconcentration and gas chromatography/mass spectroscopy (GC/MSD) methodology. The resulting chromatograms were characterized by a small number of predominant peaks, with 14 substances (propene, benzene, xylenes, 1-butene/2-methylpropene, toluene, propane, 1,2-butadiene, 2-methylbutane, ethylbenzene, naphthalene, styrene, cyclopentene, 1-methylcyclopentene, isopropylbenzene) being found in proportionately higher concentrations in all experimental fires and accounting for 65% (SD = +/-12%) by mass of total measured VOCs. Benzene, toluene, 1,3-butadiene, naphthalene, and styrene were found at higher concentrations than most other VOCs and increased with the time of combustion together with increasing levels of carbon monoxide. Benzene was found in the highest concentrations, with peak levels ranging from 0.6 ppm to 65 ppm, while the levels of 1,3-butadiene, styrene, and naphthalene peaked at 0.1, 0.4, and 3 ppm, respectively. This study revealed that there were no new or novel, toxic nonpolar VOCs resulting from the burning of common building materials. This is important in view of the studies that have found associations between firefighting and various forms of cancer.

Application of a quantitative algorithm to restriction endonuclease analysis of Aujeszky's disease (pseudorabies) virus from a geographically localized outbreak

A retrospective epidemiologic study was conducted to evaluate the application of an objective quantitative algorithm for estimating genetic similarity from restriction endonuclease analysis data. The analysis was performed to assist the determination of chronologic trends in an Aujeszky's disease viral epidemic in a geographic region. DNA from each viral isolate obtained during the epidemic was digested with 4 restriction endonucleases and molar ratio labeled to generate separate fragment patterns that were simultaneously compared using the algorithm. The resultant estimates of genetic similarity were then used in conjunction with time of virus isolation and specific geographic location of the outbreaks to identify the probable sources of infection and the patterns of spread among swine herds. This type of quantitative analysis enabled a more precise and objective approach than previously has been applied to the interpretation of restriction endonuclease data, thereby demonstrating the benefit of this methodology for the investigation of infectious disease outbreaks.

C-mos, a nuclear marker useful for squamate phylogenetic analysis

Phylogenetic reconstruction in molecular systematics has largely been achieved using mitochondrial gene sequences and less frequently sequences of nuclear ribosomal RNA genes. At present few other nuclear genes have been identified that could be used to test these phylogenies. C-mos, a single-copy nuclear oncogene, has been identified as a candidate nuclear marker. Data are presented on the usefulness of c-mos sequences in the phylogenetic analysis of squamate reptile families. We obtained partial sequences of c-mos from 13 squamate reptile families and outgroup representatives from the orders Rhynchocephalia, Chelonia, and Crocodylia. Phylogenetic analysis reveals a high degree of phylogenetic information contained within the sequence for both the synonymous and nonsynonymous substitutions. Phylogenetic resolution was present at both the deepest and shallower divergences but relationships among the major squamate lineages were not resolved, possibly because rapid cladogenesis may have led to the diversification of these lineages.

Patterns of antimicrobial use and antimicrobial resistance among healthy children in Bolivia

OBJECTIVE

To determine the incidence of antimicrobial-resistant, nonpathogenic Escherichia coli among healthy children aged 6-72 months in Camiri town and a rural village, Javillo, in south-eastern Bolivia.

METHOD

A community-based survey: stool samples were obtained from 296 healthy children selected by modified cluster sampling in Camiri and all 25 eligible children in Javillo. E. coli isolates were tested for antimicrobial susceptibility according to the standard disc diffusion method. By a questionnaire survey of 12 pharmacies and by using simulated patients, we investigated the antimicrobial availability and the usage patterns in Camiri town.

RESULTS

In Camiri, over 90%, and in Javillo over 70% of children carried E. coli resistant to ampicillin, trimethoprim-sulphamethoxazole (TMP/SMX) or tetracycline. Overall, 63% of children carried E. coli with multiple resistance to ampicillin, TMP/SMX, tetracycline and chloramphenicol. In the simulated patients study, antimicrobials were dispensed inappropriately for 92% of adults and 40% of children with watery diarrhoea, and were under-prescribed for males with urethral discharge (67%) or females with fever and dysuria (58%). The dose and/or duration of antimicrobials dispensed was almost always too low.

CONCLUSION

Our study showed a disturbingly high prevalence of carriage of nonpathogenic E. coli resistant to antimicrobials. The prevalence of resistance to ampicillin and TMP/SMX was higher than that previously reported in developing countries. The existence of a large reservoir of resistance genes in healthy individuals in developing countries represents a threat to the success of antimicrobial therapy throughout the world. Programmes to improve rational and effective drug use in developing countries are urgently needed.

Carbon monoxide and water vapor contamination of compressed breathing air for firefighters and divers

Compressed breathing air, used in self-contained breathing apparatus (SCBA) by firefighters and other categories of workers as well as by recreational and commercial divers, is prepared with the aid of high-pressure compressors operating in the range of 5000 psig. There have been reports of unexplained deaths of SCUBA divers and anecdotal accounts of decreased time to exhaustion in firefighters using SCBAs. Compressed breathing air has been found to contain elevated levels of carbon monoxide (CO) and water vapor that are consistent with carboxyhemoglobin (COHb) poisoning and freezing of the user's regulator on the breathing apparatus. The Coburn-Forster-Kane equation (CFK equation) was used to estimate COHb levels at rest and at maximum exercise when exposed to different levels of CO in contaminated breathing air. The results demonstrated that, at maximum exercise, the COHb ranged from 6.0 to 17% with the use of 1 to 4 SCBA cylinders contaminated by 250 ppm CO. Standard operating procedures have been developed at the Montreal Fire Department to minimize the risk of compressed breathing air contamination. Results of the quality analysis/quality control program indicate that implementation of these procedures has improved the quality of the compressed breathing air. Recommendations are made for improvement of the air testing procedures mandated by the Canadian CAN3 180.1-M85 Standard on Compressed Breathing Air and Systems.

An outbreak of gastroenteritis and fever due to Listeria monocytogenes in milk

BACKGROUND

After an outbreak of gastroenteritis and fever among persons who attended a picnic in Illinois, chocolate milk served at the picnic was found to be contaminated with Listeria monocytogenes.

METHODS

In investigating this outbreak, we interviewed the people who attended the picnic about what they ate and their symptoms. Surveillance for invasive listeriosis was initiated in the states that receive milk from the implicated dairy. Stool and milk samples were cultured for L. monocytogenes. Serum samples were tested for IgG antibody to listeriolysin O.

RESULTS

Forty-five persons had symptoms that met the case definition for illness due to L. monocytogenes, and cultures of stool from 11 persons yielded the organism. Illness in the week after the picnic was associated with the consumption of chocolate milk. The most common symptoms were diarrhea (present in 79 percent of the cases) and fever (72 percent). Four persons were hospitalized. The median incubation period for infection was 20 hours (range, 9 to 32), and persons who became ill had elevated levels of antibody to listeriolysin O. Isolates from stool specimens from patients who became ill after the picnic, from sterile sites in three additional patients identified by surveillance, from the implicated chocolate milk, and from a tank drain at the dairy were all serotype 1/2b and were indistinguishable on multilocus enzyme electrophoresis, ribotyping, and DNA macrorestriction analysis.

CONCLUSIONS

L. monocytogenes is a cause of gastroenteritis with fever, and sporadic cases of invasive listeriosis may be due to unrecognized outbreaks caused by contaminated food.

A new method of bipolymerase sequencing prevents "stop-bands"

This article presents a relatively quick and cost-effective DNA sequencing method that prevents the formation of stop-bands. This method uses a combination of Taq and Sequenase that allows sequencing at both low and high temperatures. The ability to sequence at a high temperature appears to be the fundamental component in preventing stop-band formation in G+C rich regions.