Showing papers by "Swedish Defence Research Agency published in 2018"

Bioconda: sustainable and comprehensive software distribution for the life sciences.

Abstract: We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.

Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells

Abstract: Persistence is a reversible and low-frequency phenomenon allowing a subpopulation of a clonal bacterial population to survive antibiotic treatments. Upon removal of the antibiotic, persister cells ...

Impact of Fire Suit Ensembles on Firefighter PAH Exposures as Assessed by Skin Deposition and Urinary Biomarkers

Abstract: Over the past 10 years, a number of safety measures for reducing firefighters' exposure to combustion particles have been introduced in Sweden. The most important measure was the reduction in the time firefighters wear suits and handle contaminated equipment after turn-outs involving smoke diving. This study was divided into two parts, those being to investigate the level of protection obtained by multiple garment layers and to assess exposure during a standardized smoke diving exercise. First, realistic work protection factors (WPFs) were calculated by comparing air concentrations of the full suite of gaseous and particle-bound polycyclic aromatic hydrocarbons (PAHs) inside and outside structural ensembles, including jacket and thick base layer, during a tough fire extinguishing exercise using wood as the fuel. Second, during a standardized smoke diving exercise, exposure was assessed by measuring PAH skin deposition and levels of eight urinary PAH metabolites in 20 volunteer student firefighters before and after the exercise. The average WPF for the sum of 22 PAHs was 146 ± 33 suggesting a relatively high protective capacity but also indicating a substantial enrichment of contaminants with a risk of prolonged dermal exposure. Accordingly, in the second exercise, the median levels of skin-deposited Σ14-PAHs and urinary 1-hydroxypyrene significantly increased 5-fold (21 to 99 ng/wipe) and 8-fold (0.14 to 1.1 µmol mol-1 creatinine), respectively, post exposure. Among the PAH metabolites investigated, 1-hydroxypyrene proved to be the most useful indicator of exposure, with significantly elevated urinary levels at both 6 h and 20 h after the exercise and with the strongest correlation to dermal exposure. Metabolites from two-ring and three-ring PAHs were eliminated faster while levels of 3-hydroxy-benzo[a]pyrene did not meet the detection criteria. The results from correlation studies indicated that dermal uptake was a major route of exposure in accordance with previous findings. To summarize, this study shows that some of the newly adopted protective measures were correctly implemented, and should continue to be followed and be more widely adopted.

Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest

Abstract: Interactions between Norway spruce trees and bacteria and fungi in nutrient limited boreal forests can be beneficial for tree growth and fitness Tree-level effects of anthropogenic nutrient additi

Political Bots and the Swedish General Election

Abstract: In this paper we present a study of political bots on Twitter and their influence on the Swedish general election in September 2018. We have not restricted our study to bots that are a software program, instead we are interested in any type of bot-like automated behaviour. This includes a human being manually copying or retweeting content repeatedly in a robot-like way with the aim of influencing the interaction between a user and content or with other users. We examined how bots influence discussions about the Swedish general election on Twitter during a three month period starting half a year before the election. For this purpose we trained a machine learning model to recognize automatic behaviour and studied accounts that tweet about the Swedish election. Our results show, among other things, that bot activity is at a similar level to that found in other studies, and that distinctive clusters, for example among right-wing Twitter accounts, can be identified.

Assessment of uncertainties in hot-wire anemometry and oil-film interferometry measurements for wall-bounded turbulent flows

Abstract: Assessment of uncertainties in hot-wire anemometry and oil-film interferometry measurements for wall-bounded turbulent flows

Informing crisis alerts using social media: Best practices and proof of concept

Abstract: Social media has become an integrated part of human communication, both as a means to establish and maintain social relationships, and as a means of sharing and co-creating information. Social media comes with an array of possibilities for individuals as well as organizations, corporations, and authorities. Within the field of crisis communication, social media possibilities such as online sharing and social networking have had an impact on the way crisis information is disseminated and updated. This paper addresses the issues related to using social media for communicating crisis information and broadcasting alert messages to the general population, discusses the role of social media in future pan-European crisis alerting, and presents a prototype system demonstrating the possibilities. An extensive systematic literature review was carried out to identify factors that affect the use of social media for alerting and warning. These factors were mirrored in experiences, collected through interviews, obtained by emergency management organizations in three European countries (Sweden, Czech Republic, and Spain). The factors finally form the basis for suggestions and recommendations regarding the design of technological tools for both communication and information collection to serve as an integral part of a future pan-European crisis alerting system.

The angloval tactical military scenario and experimentation environment

Abstract: The Anglova scenario is designed to support experimentation with tactical networking environments and provides node mobility and network connectivity for a realistic battalion-sized military operation consisting of three vignettes, including the deployment of armored vehicles, surveillance of the maritime domain and an urban operation with a naval component. Altogether, the scenario includes 283 nodes and lasts over four hours with detailed mobility and pathloss data for each node. Also included with the scenario are radio models for the different radios that would be part of a heterogeneous network. The scenario has been developed by the NATO IST-124 Research Task Group and released into the public domain in order to facilitate experimentation with networking protocols and algorithms by the community at large. While primarily designed for the Extendable Mobile Ad-hoc Network Emulator (EMANE), the scenario can also be adapted to other experimentation environments.

Recommendations for Next-Generation Ground Magnetic Perturbation Validation

Abstract: Data-model validation of ground magnetic perturbation forecasts, specifically of the time rate of change of surface magnetic field, dB/dt, is a critical task for model development and for mitigatio ...

Peak detection approaches for time-correlated single-photon counting three-dimensional lidar systems

Abstract: Time-correlated single-photon counting lidar provides very high-resolution range measurements, making the technology interesting for 3D imaging of objects behind foliage or other obscuration. We study six peak detection approaches and compare their performance from several perspectives: detection of double surfaces within the instantaneous field of view, range accuracy, performance under sparse sampling, and the number of outliers. The results presented are based on reference measurements of a characterization target. Special consideration is given to the possibility of resolving two surfaces closely separated in range within the field of view of a single pixel. An approach based on fitting a linear combination of impulse response functions to the collected data showed the best overall performance.

Less fibrosis in elderly subjects supplemented with selenium and coenzyme Q10-A mechanism behind reduced cardiovascular mortality?

Abstract: BACKGROUND: In an intervention study where 221 healthy elderly persons received selenium and coenzyme Q10 as a dietary supplement, and 222 received placebo for 4 years we observed improved cardiac ...

Photon-counting panoramic three-dimensional imaging using a Geiger-mode avalanche photodiode array

Abstract: A lidar system based on a photon-counting Geiger-mode avalanche photodiode (GmAPD) array can provide high range resolution three-dimensional imaging. The small number of pixels in the GmAPD array limits the size of measured scenes compared to passive cameras. Here, the performance of rapid panoramic imaging of larger scenes is investigated. Controlled environment indoor measurement at up to 24 m range is used to validate the principle. Outdoor daylight measurements of natural targets at 230 to 340 m range are performed to test the capability of the measurement system. A 20 deg by 1.8 deg scene is imaged with 0.25-mrad lateral resolution in 4 s. The standard deviation of point to plane distances for a flat wall in the outdoor measurement is 10.6 mm, giving an estimate of the achievable relative range accuracy, even if this will depend on the signal-to-noise ratio. A radiometric model is used to estimate the performance of an upgraded optimized system and the necessary laser power for imaging at longer ranges in both day and night conditions.

Predators and nutrient availability favor protozoa-resisting bacteria in aquatic systems

Abstract: The long co-existence of bacteria and protozoa has led to the development of bacterial protozoa resistance strategies, which are suggested to serve as drivers for the evolution of pathogenic bacteria. However, the ecological mechanisms underpinning selection for protozoa-resistance in aquatic bacteria are poorly known. To assess the role of nutrient availability and predation-pressure on selection for protozoa-resisting bacteria (PRB), an enrichment-dilution experiment was designed using laboratory microcosms containing natural lake water. PRB was monitored by screening 16S rRNA amplicon sequence data for reads assigned to bacteria that previously has been shown to resist degradation by amoebae. To estimate the effects of the microbial food web dynamics (microscopy of; heterotrophic bacteria, phytoplankton, protozoa and rotifers) and physicochemical variables on the PRB abundance in the study system, a joint species distribution modelling approach was used. The predation-pressure (ratio between predator and bacterial biomass) had a positive effect on the abundance of the PRB genus Mycobacterium, while perturbation (enrichment and dilution) favored the PRB genus Pseudomonas that dominated the bacterial community in the disturbed systems. Our results show that PRB with different ecological strategies can be expected in water of high and intermediate nutrient levels and after major disturbances of an aquatic system.

Two-scale cut-and-projection convergence; homogenization of quasiperiodic structures

Abstract: We demonstrate how the problem of finding the effective property of quasiperiodic constitutive relations can be simplified to the periodic homogenization setting by transforming the original quasiperiodic material structure to a periodic heterogeneous material in a higher dimensional space. The characterization of two-scale cut-and-projection convergence limits of partial differential operators is presented.

Cytotoxic lymphocytes in COPD airways: increased NK cells associated with disease, iNKT and NKT-like cells with current smoking

Abstract: Cytotoxic lymphocytes are increased in the airways of COPD patients. Whether this increase is driven primarily by the disease or by smoking is not clear, nor whether it correlates with the rate of decline in lung function. Bronchoscopy with BAL was performed in 52 subjects recruited from the longitudinal OLIN COPD study according to pre-determined criteria; 12 with COPD and a rapid decline in lung function (loss of FEV1 ≥ 60 ml/year), 10 with COPD and a non-rapid decline in lung function (loss of FEV1 ≤ 30 ml/year), 15 current and ex-smokers and 15 non-smokers with normal lung function. BAL lymphocyte subsets were determined using flow cytometry. In BAL fluid, the proportions of NK, iNKT and NKT-like cells all increased with pack-years. Within the COPD group, NK cells – but not iNKT or NKT-like cells – were significantly elevated also in subjects that had quit smoking. In contrast, current smoking was associated with a marked increase in iNKT and NKT-like cells but not in NK cells. Rate of lung function decline did not significantly affect any of the results. In summary, increased proportions of NK cells in BAL fluid were associated with COPD; iNKT and NKT-like cells with current smoking but not with COPD. Interestingly, NK cell percentages did not normalize in COPD subjects that had quit smoking, indicating that these cells might play a role in the continued disease progression seen in COPD even after smoking cessation. Clinicaltrials.gov identifier NCT02729220 .

Accounting for bacterial overlap between raw water communities and contaminating sources improves the accuracy of signature-based microbial source tracking

Abstract: Microbial source tracking (MST) analysis is essential to identifying and mitigating the fecal pollution of water resources. The signature-based MST method uses a library of sequences to identify co ...

Galleria mellonella Reveals Niche Differences Between Highly Pathogenic and Closely Related Strains of Francisella spp.

Abstract: Francisella tularensis, a highly virulent bacteria that causes the zoonotic disease tularemia, is considered a potential agent of biological warfare and bioterrorism. Although the host range for several species within the Francisella is known, little is known about the natural reservoirs of various Francisella species. The lack of knowledge regarding the environmental fates of these pathogens greatly reduces the possibilities for microbial risk assessments. The greater wax moth (Galleria mellonella) is an insect of the order Lepidoptera that has been used as an alternative model to study microbial infection during recent years. The aim of this study was to evaluate G. mellonella as a model system for studies of human pathogenic and closely related opportunistic and non-pathogenic strains within the Francisella genus. The employed G. mellonella larvae model demonstrated differences in lethality between human pathogenic and human non-pathogenic or opportunistic Francisella species. The F. novicida, F. hispaniensis and F. philomiragia strains were significantly more virulent in the G. mellonella model than the strains of human pathogens F. t. holarctica and F. t. tularensis. Our data show that G. mellonella is a possible in vivo model of insect immunity for studies of both opportunistic and virulent lineages of Francisella spp., that produces inverse results regarding lethality in G. mellonella and incapacitating disease in humans. The results provide insight into the potential host specificity of F. tularensis and closely related members of the same genus, thus increasing our present understanding of Francisella spp. ecology.

On the application of ICP-MS techniques for measuring uranium and plutonium: a Nordic inter-laboratory comparison exercise

Abstract: Inductively coupled plasma mass spectrometry (ICP-MS) techniques are widely used for determination of long-lived radionuclides and their isotopic ratios in the nuclear fields. Uranium (U) and Plutonium (Pu) isotopes have been determined by many researchers with ICP-MS due to its relatively high sensitivity and short measurement time. In this work, an inter-laboratory comparison exercise among the Nordic countries was performed, focusing on the measurement of U and Pu isotopes in certified reference materials by ICP-MS. The performance and characters of different ICP-MS instruments are evaluated and discussed in this paper.

Validation guidelines for PCR workflows in bioterrorism preparedness, food safety and forensics

Abstract: The polymerase chain reaction (PCR) is the backbone of contemporary DNA/RNA analysis, ideally enabling detection of one or just a few target molecules. However, when analysing food or forensic samples the analytical procedure is often challenged by low amounts of poor quality template molecules and complex matrices. Applying optimised and validated methods in all steps of the analysis workflow, i.e. sampling, sample treatment, DNA/RNA extraction and PCR (including reverse transcription for RNA analysis), is thus necessary to ensure the reliability of analysis. In this paper, we describe how in-house validation can be performed for the different modules of the diagnostic PCR process, providing practical examples as tools for laboratories in their planning of validation studies. The focus is analysis of heterogeneous samples with interfering matrices, with relevance in food testing, forensic DNA analysis, bioterrorism preparedness and veterinary medicine. Our objective is to enable rational in-house validation for reliable and swift quality assurance when results are urgent, for example in the event of a crisis such as a foodborne outbreak or a crime requiring the analysis of a large number of diverse samples. To that end, we explain the performance characteristics associated with method validation from a PCR and biological sample matrix perspective and suggest which characteristics to investigate depending on the type of method to be validated. Also, we include a modular approach to validation within the PCR workflow, aiming at efficient validation and a flexible use of methods.

Gamma spectrometry in the ITWG CMX-4 exercise.

Abstract: Low enriched uranium samples of unknown origin were analyzed by 16 laboratories in the context of a Collaborative Materials Exercise (CMX), organized by the Nuclear Forensics International Technical Working Group (ITWG). The purpose was to compare and prioritize nuclear forensic methods and techniques, and to evaluate attribution capabilities among participants. This paper gives a snapshot of the gamma spectrometric capabilities of the participating laboratories and summarizes the results achieved by gamma spectrometry.

Comparing results of X-ray diffraction, µ-Raman spectroscopy and neutron diffraction when identifying chemical phases in seized nuclear material, during a comparative nuclear forensics exercise

Abstract: This work presents the results for identification of chemical phases obtained by several laboratories as a part of an international nuclear forensic round-robin exercise In this work powder X-ray diffraction (p-XRD) is regarded as the reference technique Neutron diffraction produced a superior high-angle diffraction pattern relative to p-XRD Requiring only small amounts of sample, µ-Raman spectroscopy was used for the first time in this context as a potentially complementary technique to p-XRD The chemical phases were identified as pure UO2 in two materials, and as a mixture of UO2, U3O8 and an intermediate species U3O7 in the third material