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Sökning: WFRF:(Francisco Francisco 1985 )

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1.
  • Bender, Anke, et al. (författare)
  • Imaging-sonar observations of salmonid interactions with a vertical axis instream turbine
  • 2023
  • Ingår i: Rivers Research and Applications. - : John Wiley & Sons. - 1535-1459 .- 1535-1467.
  • Tidskriftsartikel (refereegranskat)abstract
    • Anthropogenic activities and their influences on aquatic systems is an important topic, especially considering the growing interest in using the earth's resources in a sustainable way. One of those anthropogenic activities is the introduction of renewable technologies into the aquatic environment such as instream turbines. Environmental studies around those technologies are often still ongoing due to their novelty. During the spring of 2018, juvenile individuals of two salmonid species, Atlantic salmon and brown trout were released upstream a vertical axis instream turbine in the river Dal (Dalälven) in eastern Sweden. The aim of this study was to investigate the swimming behavior of the salmonids around a small-scale prototype vertical axis instream turbine. The swimming pattern and the possible response of avoiding the vertical axis instream turbine were documented with a multi beam sonar. A control area, next to the turbine, was used as reference. No consistent results were shown for trout as they were passing the control area with a statistically high variation, and specimens were rarely observed in proximity of the turbine, neither if the turbine was operating nor at stand still. Salmon clearly avoided the operating turbine, but did not avoid the turbine when it was at stand still, and was often observed swimming straight through the turbine area. These findings indicate that operating this type of instream turbine in a river affects the swimming behavior of Atlantic salmon but is unlikely to affect its migration paths. For brown trout, the statistical results are inconclusive, although data indicate a response of avoiding the turbine. The species are in little risk to suffer physical harm as no fish entered the rotating turbine, despite very turbid water conditions.
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2.
  • Bender, Anke, et al. (författare)
  • A Review of Methods and Models for Environmental Monitoring of Marine Renewable Energy
  • 2017
  • Ingår i: Proceedings of the 12th European Wave and Tidal Energy Conference. - : EWTEC.
  • Konferensbidrag (refereegranskat)abstract
    • A continued expansion of the marine renewable energy sector will result in an increased demand in monitoring the natural marine environment. This may be due to a basic scientific interest but is foremost linked to the requirement of pre- and post-construction studies in relation to environmental impact assessments and consenting processes for marine renewable energy projects. With focus on wave and tidal power, but without attempting to provide a comprehensive list, we review methods, technologies and other scientific tools used for monitoring and predicting possible impacts from marine energy installations, on both population and behavioural levels. This includes traditional methods such as fishing gear, like nets and cages, modern technologies such as platforms with multi parameter equipment and the use of deterministic models. This paper is intended to serve as an overview for technology developers as well as authorities, regulators and decision makers with interests in general techniques, and naturally for scientists and consultants commonly being executors of studies and monitoring programs. By giving relevant and up to date references this paper may also be useful for finding more detailed information on study methods and variants. Finally, we give recommendations on where development of technologies is needed in order to face future requirements.
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3.
  • Costa, Joao, et al. (författare)
  • The burden of atherosclerosis in Portugal
  • 2021
  • Ingår i: European Heart Journal - Quality of Care and Clinical Outcomes. - : Oxford University Press. - 2058-5225 .- 2058-1742. ; 7:2, s. 154-162
  • Tidskriftsartikel (refereegranskat)abstract
    • Aims This article sought to estimate the burden of disease attributable to atherosclerosis in mainland Portugal in 2016.Methods and results The burden of atherosclerosis was measured in disability-adjusted life years following the latest 2010 Global Burden of Disease (GBD) methodology. Disability-adjusted life years were estimated as the sum of years of life lost (YLL) with years lived with disability (YLD). The following clinical manifestations of atherosclerosis were included: ischaemic heart disease (IHD) (including acute myocardial infarction, stable angina, and ischaemic heart failure), ischaemic cerebrovascular disease (ICVD), and peripheral arterial disease (PAD). Years of life lost were estimated based on all-cause mortality data for the Portuguese population and mortality due to IHD, ICVD, and PAD for the year 2016 sourced from national statistics. Standard life expectancy was sourced from the GBD study. Years lived with disability corresponded to the product of the number of prevalent cases by an average disability weight for all possible combinations of disease. Prevalence data for the different clinical manifestations of atherosclerosis were sourced from epidemiological studies. Disability weights were sourced from the published literature. In 2016, 15123 deaths were attributable to atherosclerosis, which corresponded to 14.3% of overall mortality in mainland Portugal. Disability-adjusted life years totalled 260943, 75% due to premature death (196438 YLL) and 25% due to disability (64505 YLD).Conclusion Atherosclerosis entails a high disease burden to society. A large part of this burden would be avoidable if evidence-based effective and cost-effective interventions targeting known risk factors, from prevention to treatment, were implemented.
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4.
  • Francisco, Francisco, 1985- (författare)
  • Adapting sonar systems for monitoring ocean energy technologies
  • 2018
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The global energy sector is under profound reforms aiming towards renewable energy sources, clean technologies and expansion of smart grids, all with the additional aim of providing affordable and dependable electricity for everyone. A reduction of carbon dioxide emissions is a priority on the global agenda, and to achieve that, cleaner energy technologies has to be more integrated into the energy mix. This thesis focus on a sustainable implementation of wave, tidal and offshore wind power, wherefore there is a need to investigate more about the prerequisites and consequences ocean energy can have on the marine environment. For that, reliable, cost effective and continuous environmental monitoring framework is necessary in order to support and safeguard ocean energy operations.The main objectives of the research presented in this thesis are to develop a multifunctional environmental monitoring platform based on sonar systems for ocean energy applications, by adapting high resolution multibeam, dual beam and split beam sonar systems and also underwater cameras; Propose data acquisition and processing protocols capable of decipher sonar data in order to provide continuous environmental monitoring and reporting; Conduct qualitative and quantitative observations of fish and marine mammals using the built monitoring platform; And investigate the feasibility of utilizing the Uppsala University wave energy converter technology to generate electricity worldwide. As a result, a multifunctional platform was designed, built and tested. This included the hardware, the data acquisition system, and a data analysis framework comprising new algorithms necessary to process the new acoustic data. The multibeam, dual beam, and split beam sonar systems and underwater cameras produced both qualitative and quantitative data of biomass, occurrence and behavior of fish and marine mammals in the vicinity of ocean energy devices. With this platform, it was also possible to conduct seabed and structural inspections within ocean energy devices, observe cavitating flows, etc. One of the most important results of this research was the possibility of extracting visual signatures of fish and marine mammals through acoustic images. This can be valuable for training algorithms for manual or automatic identification and classification of underwater targets through imaging sonar systems, a technique that can be widely used in the offshore activities. Regarding feasibility studies and wave power resource assessment, this study concluded that mild wave climates can provide enough energy to run reverse osmosis desalination systems as well as produce sufficient electricity to integrate into a national grid.In summary, this thesis concludes that the implementation of ocean energy can be facilitated by creating environmental monitoring, risk and resource assessment frameworks such as the presented research work that contribute to lowering the risks associated with subsea work and thereby costs of ocean energy projects.
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5.
  • Francisco, Francisco, 1985-, et al. (författare)
  • An alternative technique for ultra-high resolution bathymetry and seabed inspection for marine renewables
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Marine renewable energy technologies have a great potential in supplying clean electricity to millions of people across the globe, if technical and economic conditions are in right. So far, ocean energy projects are commonly started by SMEs or educational institutions with limited budgets. Therefore, any effort to reduce expenses is of great value. One of the areas involving substantial expenses are the inevitable seabed inspection prior to deployment of marine renewable energy device. Detailed seabed inspections can also reduce the risk of associated with deployment of structures on uneven seabed, especially marine renewable energy devices with gravity foundations. By reducing the costs and risks of such surveys prior and during the installation phases, the feasibility of marine renewable energy projects can be more favoured and competitive. In this perspective, this study proposes a cost and time effective technique for seabed surveys. The proposed technique involves the use of high precision and inexpensive sonar systems and underwater optical cameras integrated into a versatile and compact subsea monitoring platform. It also involves simple and practical data acquisition and processing protocols that do not requires hi expertise for operation. The results obtained showed that high resolution bathymetric maps and detailed seabed inspections imagery can be acquired. This study concludes that a simple and inexpensive subsea monitoring platform comprising a multibeam, dual beam and video cameras can be effective for high resolution seabed inspection and bathymetric measurements for marine energy applications.
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6.
  • Francisco, Francisco, 1985-, et al. (författare)
  • Detection of Visual Signatures of Marine Mammals and Fish within Marine Renewable Energy Farms Using Multibeam Imaging Sonar
  • 2019
  • Ingår i: Nutrients. - : MDPI. - 2072-6643. ; 7:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Techniques for marine monitoring have evolved greatly over the past decades, making the acquisition of environment data safer, reliable and more efficient. On the other hand, the exploration of marine renewable energy introduced dissimilar ways of exploring the oceans and with that arises the need for new techniques for environmental data acquisition, processing and analysis. Marine energy is mostly harvested in murky and high energetic places where conventional data acquisition techniques are impractical. Modern sonar systems, operating at high frequencies, can acquire detailed images of the underwater environment. Variables such as occurrence, size, class and behaviour of a variety of aquatic species of fish, birds, mammals, coexisting within marine energy sites can be gathered using imaging sonar systems. Although sonar images can provide high level of details, still in most of the cases they are difficult to decipher. Therefore, to facilitate the classification of targets through sonar images, this study introduces a framework of extracting visual features of marine targets that would serve as unique signatures. The acoustic measure of visibility (AVM) is here introduced as an indirect technique of identification and classification of targets by comparing the observed size with a standard value. This information can be used to instruct manual and automatic algorithms for identification and classification of underwater targets using imaging sonar systems. Using image processing algorithms embedded in Proviwer4 and FIJI software, this study found that acoustic images can be effectively used to classify cod, harbour and grey seals, and orcas through their size, shape and swimming behaviour. Data showed that cod occurred as bright, 0.9 m long, ellipsoidal targets shoaling in groups of up to 50 individuals. Harbour seals occurred as bright torpedo-like fast moving target, whereas grey seals occurred as bulky-ellipsoidal targets with serpentine movement. Orca or larger marine mammals occurred with relatively low visibility on the acoustic images compared to their body size which measured between 4 m and 7 m. This framework provide a new window of performing qualitative and quantitative observations of underwater targets, and with further improvements, this method can be useful for environmental studies within marine renewable energy farms and for other purposes.
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7.
  • Francisco, Francisco, 1985-, et al. (författare)
  • Evaluation of Underwater Acoustic and Optical Imaging for Structural Inspections for Marine Renewables
  • Ingår i: IEEE Journal of Oceanic Engineering.
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • Environmental monitoring and visual inspections are indispensable tasks in the marine renewable energy sector. Today, acoustic and electromagnetic instrumentation are used to observe the underwater environment. However, depending on the application, both electromagnetic and acoustic instruments have limitations mostly due to signal attenuation. For visual inspections, electromagnetic instruments e.g. optical cameras provide the best method of observation enabling an easy identification and classification of targets. However, electromagnetic radiation is more attenuated in water than sound, limiting the use of optical cameras to nearfield observations. In murky and turbid waters, acoustic imaging sonar systems can be used to observe underwater objects at much longer ranges up to 100 m away. Presumably, underwater optical images are mostly appropriate in clear waters or at nearfield, and acoustic images are suitable for murky and turbid waters. This study aimed to find the optimal ranges in which optical and acoustic images can be acquired in In Situ conditions. A multibeam imaging sonar and several different optical cameras were used to acquire underwater images of the surroundings of marine renewable energy devices. The results from observation showed that optical images were significantly affected by the decreasing of luminosity, increasing depth and water velocity. And acoustic images were mostly affected by water column stratification, bubbles and reverberation. In summary, optical cameras had superior performance for nearfield and high accuracy image acquisition, while imaging sonar provided superior performance at acquiring images at mid to long range.
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8.
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9.
  • Francisco, Francisco Gemo Albino, 1985-, et al. (författare)
  • Sonar for environmental monitoring : Configuration of a multifunctional active acoustics platform applied for marine renewables
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Marine renewable energy is emerging as one of the fast-growing industry in the last decades, as modern society pushes for technologies that can convert energy contained from winds, waves, tides and stream flows. The implementation of renewable energy technologies impose high demands on both structural and environmental engineering, as the energy converters have to work under extreme conditions where parameters such as sea-bottom configuration, water transparency and depth, sea-states and prevailing winds are harsh. Constant monitoring of the marine environment is crucial in order to keep this sector reliable. Active acoustics is becoming a standard tool to collect multi-dimensional data from physical, geological and biological properties of the marine environment. The Div. of Electricity of Uppsala University have been developing an environmental monitoring platform based on sonar (Sound Navigation And Raging) systems. This platform aims to monitor the installation, operation and decommissioning of marine renewable energy converters. The focus will be given the observations of behaviours of marine animals in vicinity of energy converters but also structural inspection and monitoring of MRETs. This paper describes how this multifunctional environmental monitoring platform come to existence from the design to the deployment phase.
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10.
  • Francisco, Francisco, 1985-, et al. (författare)
  • Sonar for Environmental Monitoring : Understanding the Functionality of Active Acoustics as a Method for Monitoring Marine Renewable Energy Devices
  • 2015
  • Konferensbidrag (refereegranskat)abstract
    • Active acoustics monitoring (AAM) systems can play an important role in the inspection and survey of the subsea environment around marine renewable energy devices, especially in murky and deep waters. Alternative methods comprising a multifunctional platform based on multibeam (MBS) and Dualbeam (DBS) sonar systems are being developed. The aim is to monitor the environmental impacts during installation, operation and maintenance of wave energy converters, marine current turbines, subsea substations and other offshore renewable energy technologies. At this initial phase, one of the specific objective is to understand the functionality of AAM systems. Field tests were done using the MBS and DBS systems. A platform is being tested at the Lysekil Wave Power Project test site and at the Söderfors Marine Current Project test site. Preliminary results show that the MBS produces better acoustic images when the platform is steady, and when in slow-moving waters such as in harbours and shallow rivers. At near field, the MBS is able to track targets < 20 cm such as fish swimming close to hard structures. The DBS can detect isolated targets at far field. Target dimensions estimated using the sonar match the real dimensions of the same´targets.
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11.
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12.
  • Francisco, Francisco, 1985- (författare)
  • Sonar for environmental monitoring of marine renewable energy technologies
  • 2016
  • Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Human exploration of the hydrosphere is ever increasing as conventional industries grow and new industries emerge. A new emerging and fast-growing industry is the marine renewable energy. The last decades have been characterized by an accentuated development rate of technologies that can convert the energy contained in stream flows, waves, wind and tides. This growth benefits from the fact that human society has become notably aware of the well-being of the environment that we all live in. This brings a human desire to implement technologies which cope better with the natural environment. Yet, this environmental awareness poses difficulties in approving new renewable energy projects such as offshore wind, wave and tidal energy farms. Lessons have been learned that lack of consistent environmental data can become an impasse when consenting permits for testing and deployments marine renewable energy technologies. An example is the European Union in which a majority of the member states requires rigorous environmental monitoring programs to be in place when marine renewable energy technologies are commissioned and decommissioned. To satisfy such high demands and to simultaneously boost the marine renewable sector, long-term environmental monitoring framework that gathers multi-variable data are needed to keep providing data to technology developers, operators as well as to the general public. Technologies based on active acoustics might be the most advanced tools to monitor the subsea environment around marine manmade structures especially in murky and deep waters where divining and conventional technologies are cost.The main objective of this PhD project has develop and test an active acoustic monitoring system for offshore renewable energy farms, by integrating a multitude of appropriate monitoring sonar, hydrophones and cameras systems to be developed with standards suitable for subsea environmental monitoring. In this project, a first task was to identify, secondly acquire and test sonar systems, then a platform was designed and built, a data acquisition device control systems were developed, finally additional instruments such as video cameras and sonars were added. This systems integration followed by calibration of devices was conducted. The sonar systems were used for quantitative measurements of the occurrence of e.g. large marine animals and schools of fish near marine renewable energy converters. The sonar systems were also used for seabed inspections, depth measurements and capitating flow observations.So far, the combination of multibeam and dual-beam sonar systems produced good results of target detection, bottom inspection, depth measurements and biomass estimation. The multibeam sonar system was capable of resolving isolated targets located near high acoustic retroreflective objects. Panoramic acoustic images of wave and instream energy converters were acquired using a multibeam sonar operating at frequencies near 1 GHz. The Dual-beam and split-beam sonar systems produced data referent to acoustic background intensity of targets that helps to classify targets according to its size, composition and 3-Dimensional location within the water column. The next phase of this project will deploy the platform for longer periods in order to gather consistent acoustic and optical backscattering data of marine animal behaviour within marine renewable energy farms.
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13.
  • Francisco, Francisco, 1985-, et al. (författare)
  • Use of Multibeam and Dual-Beam Sonar Systems to Observe Cavitating Flow Produced by Ferryboats : In a Marine Renewable Energy Perspective
  • 2017
  • Ingår i: Journal of Marine Science and Engineering. - : MDPI. - 2077-1312. ; 5:3
  • Tidskriftsartikel (refereegranskat)abstract
    • With the prospect to deploy hydrokinetic energy converters in areas with heavy boat traffic, a study was conducted to observe and assess the depth range of cavitating flow produced by ferryboats in narrow channels. This study was conducted in the vicinity of Finnhamn Island in Stockholm Archipelago. The objectives of the survey were to assess whether the sonar systems were able to observe and measure the depth of what can be cavitating flow (in a form of convected cloud cavitation) produced by one specific type of ferryboats frequently operating in that route, as well as investigate if the cavitating flow within the wake would propagate deep enough to disturb the water column underneath the surface. A multibeam and a dual-beam sonar systems were used as measurement instruments. The hypothesis was that strong and deep wake can disturb the optimal operation of a hydrokinetic energy converter, therefore causing damages to its rotors and hydrofoils. The results showed that both sonar system could detect cavitating flows including its strength, part of the geometrical shape and propagation depth. Moreover, the boat with a propeller thruster produced cavitating flow with an intense core reaching 4 m of depth while lasting approximately 90 s. The ferry with waterjet thruster produced a less intense cavitating flow; the core reached depths of approximately 6 m, and lasted about 90 s. From this study, it was concluded that multibeam and dual-beam sonar systems with operating frequencies higher than 200 kHz were able to detect cavitating flows in real conditions, as long as they are properly deployed and the data properly analyzed.
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14.
  • Francisco, Francisco, 1985-, et al. (författare)
  • Use of Multibeam Imaging Sonar for Observation Of Marine Mammals and Fish on a Marine Renewable Energy Site
  • 2022
  • Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 17:12
  • Tidskriftsartikel (refereegranskat)abstract
    • Environmental data is crucial for planning, permitting, execution and post construction monitoring of marine renewable energy projects. In harsh conditions in which marine renewable energy is harvested, integrated monitoring platforms comprising multibeam imaging sonar systems coupled with other sensors can provide multi-dimensional data of the marine environment surrounding marine renewable energy installations. The aim of this study was to test the possibilities of observing the occurrence of fish and marine mammals using a multibeam imaging sonar system deployed at a wave power test site. The results obtained from a ten-day data set proved the platform as suitable for long time underwater monitoring and also revealed that the occurrence of fish and marine mammals was distributed across characteristic time and space domains. Large fish [>0.4 m] frequently occurred at night-time and near the benthic zone. Small fish [<0.2 m] frequently occurred during daylight and within the pelagic zone. The occurrence of seals was periodically distributed along a daily cycle, with intervals of 1 – 2 hours between maxima and minima. In conclusion, the use of multibeam imaging sonar can be a reliable technique for the qualitative and quantitative observations of fish and marine mammals in general and at marine renewable energy sites specifically, including protected and economically important species.
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15.
  • Francisco, Francisco, 1985-, et al. (författare)
  • Wave Power as Solution for Off-Grid Water Desalination Systems : Resource Characterization for Kilifi-Kenya
  • 2018
  • Ingår i: Energies. - : MDPI. - 1996-1073. ; 11:4
  • Tidskriftsartikel (refereegranskat)abstract
    • Freshwater scarcity is one of humanity's reoccurring problems that hamper socio-economic development in many regions across the globe. In coastal areas, seawater can be desalinated through reverse osmosis (RO) and transformed into freshwater for human use. Desalination requires large amounts of energy, mostly in the form of a reliable electricity supply, which in many cases is supplied by diesel generators. The objective of this work is to analyze the wave power resource availability in Kilifi-Kenya and evaluate the possible use of wave power converter (WEC) to power desalination plants. A particular focus is given use of WECs developed by Uppsala University (UU-WEC). The results here presented were achieved using reanalysis-wave data revealed that the local wave climate has an approximate annual mean of 7 kW/m and mode of 5 kW/m. Significant wave height and wave mean period are within 0.8-2 m and 7-8 s respectively, with a predominant wave mean direction from southeast. The seasonal cycle appeared to be the most relevant for energy conversion, having the highest difference of 6 kW/m, in which April is the lowest (3.8 kW/m) and August is the peak (10.5 kW/m). In such mild wave climates, the UU-WEC and similar devices can be suitable for ocean energy harvesting for water desalination systems. Technically, with a capacity factor of 30% and energy consumption of 3 kWh/m(3), a coastal community of about five thousand inhabitants can be provided of freshwater by only ten WECs with installed capacity of 20 kW.
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16.
  • Francisco, Francisco, 1985-, et al. (författare)
  • Wave Power in the Electricity Generation Mix : a Case Study of Ghana
  • Ingår i: Energies. - 1996-1073.
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • The access and quality of electricity are key factors for sustainable development. Off grid areas across the globe, in particular the rural areas in Africa, are in the need of renewable energy technologies as reliable electricity providers. Dedicated investments and technical reforms are needed in the renewable energy sector in order to diversify, expand and proliferate technologies able to provide reliable and affordable electricity for all. A specific case is Ghana where the electrification rate is approximately 79 %, but the utilization rate is approximately 35 %. To improve the current situation, different renewable energy systems should be brought into the power generation mix, and wave power can substantially contribute to electricity generation in Ghana and other countries with wave power resources. The aim of this study was to evaluate the wave power resource availability in Ada, Ghana, where a 100 MW wave power farm is planned to be located, and estimate the quantity of electricity that can be generated using different capacity factors. The results show that the wave climate in Ghana is mild with annual mean values of significant wave height of ca. 1.3 m, energy period of ca. 12 s and wave power value of ca. 10 kW/m. The availability, capacity factors and electricity generation were estimated to be high during the most of the year with exceptions for May, November and December. Estimated annual electricity generation were 175 GWh, to 610 GWh, for capacity factors in the range of 25%, 50% and ca. 70%, respectively. This study conclude that the annual resource availability factor is ca. 80%, suggesting that a wave power farm would be able to produce electricity during the most of the annual cycle. If these result were to be confirmed, wave power will be considered a dependable technology for electricity generation in countries such as Ghana and possibly qualify as baseload in the electricity generation mix.
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17.
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18.
  • Karlsson, Roger, 1975, et al. (författare)
  • Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping
  • 2020
  • Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 19:3, s. 518-528
  • Tidskriftsartikel (refereegranskat)abstract
    • Mass spectrometry (MS) and proteomics offer comprehensive characterization and identification of microorganisms and discovery of protein biomarkers that are applicable for diagnostics of infectious diseases. The use of biomarkers for diagnostics is widely applied in the clinic and the use of peptide biomarkers is increasingly being investigated for applications in the clinical laboratory. Respiratory-tract infections are a predominant cause for medical treatment, although, clinical assessments and standard clinical laboratory protocols are time-consuming and often inadequate for reliable diagnoses. Novel methods, preferably applied directly to clinical samples, excluding cultivation steps, are needed to improve diagnostics of infectious diseases, provide adequate treatment and reduce the use of antibiotics and associated development of antibiotic resistance. This study applied nano-liquid chromatography (LC) coupled with tandem MS, with a bioinformatics pipeline and an in-house database of curated high-quality reference genome sequences to identify species-unique peptides as potential biomarkers for four bacterial pathogens commonly found in respiratory tract infections (RTIs): Staphylococcus aureus; Moraxella catarrhalis; Haemophilus influenzae and Streptococcus pneumoniae. The species-unique peptides were initially identified in pure cultures of bacterial reference strains, reflecting the genomic variation in the four species and, furthermore, in clinical respiratory tract samples, without prior cultivation, elucidating proteins expressed in clinical conditions of infection. For each of the four bacterial pathogens, the peptide biomarker candidates most predominantly found in clinical samples, are presented. Data are available via ProteomeXchange with identifier PXD014522. As proof-of-principle, the most promising species-unique peptides were applied in targeted tandem MS-analyses of clinical samples and their relevance for identifications of the pathogens, i.e. proteotyping, was validated, thus demonstrating their potential as peptide biomarker candidates for diagnostics of infectious diseases.
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19.
  • Matos, Francisco A., et al. (författare)
  • Deep learning for plasma tomography using the bolometer system at JET
  • 2017
  • Ingår i: Fusion engineering and design. - : ELSEVIER SCIENCE SA. - 0920-3796 .- 1873-7196. ; 114, s. 18-25
  • Tidskriftsartikel (refereegranskat)abstract
    • Deep learning is having a profound impact in many fields, especially those that involve some form of image processing. Deep neural networks excel in turning an input image into a set of high-level features. On the other hand, tomography deals with the inverse problem of recreating an image from a number of projections. In plasma diagnostics, tomography aims at reconstructing the cross-section of the plasma from radiation measurements. This reconstruction can be computed with neural networks. However, previous attempts have focused on learning a parametric model of the plasma profile. In this work, we use a deep neural network to produce a full, pixel-by-pixel reconstruction of the plasma profile. For this purpose, we use the overview bolometer system at JET, and we introduce an up-convolutional network that has been trained and tested on a large set of sample tomograms. We show that this network is able to reproduce existing reconstructions with a high level of accuracy, as measured by several metrics.
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20.
  • Potapenko, Tatiana, et al. (författare)
  • Renewable Energy Potential for Micro-Grid at Hvide Sande
  • 2023
  • Ingår i: Sustainability. - : MDPI. - 2071-1050. ; 15:3
  • Tidskriftsartikel (refereegranskat)abstract
    • Decarbonization of ports is a major goal to reduce their global carbon footprint. The port of Hvide Sande is located on the coast of the North Sea in Denmark and it has the potential to utilize various renewable energy sources. Wind and solar thermal parks are already installed there. Wave energy is an alternative to solar and wind energies and its advantage is the spatial concentration, predictability, and persistence. Heat to the town is provided by Hvide Sande Fjernvarme. In this work, it is investigated if the heat demand could be fully covered by renewable energies. Power profiles for each renewable energy resource were calculated using 30 years of re-analysis environmental data. Long, mid, and short term time series of power supply has been statistically and quantitatively examined. Considering the heat demand of Hvide Sande, the lowest frequency of zero occurrence in power generation can be ensured by the combination of wind, solar energy and wave. The article also estimated the capacity for Lithium-ion batteries. The optimal size of the battery is found by the bisection method. Finally, different combinations of renewable energy and demand as well as batteries are evaluated. The lowest zero occurrences in power production is met by the mix of three renewable energies. Also, the mix of three renewable energies significantly reduces the value of energy, required from the battery.
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21.
  • 2019
  • Tidskriftsartikel (refereegranskat)
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22.
  • Andersson, Svante, 1962-, et al. (författare)
  • Sustainable development—Direct and indirect effects between economic, social, and environmental dimensions in business practices
  • 2022
  • Ingår i: Corporate Social Responsibility and Environmental Management. - Oxford : John Wiley & Sons. - 1535-3958 .- 1535-3966. ; 29:5, s. 1158-1172
  • Tidskriftsartikel (refereegranskat)abstract
    • This study investigates the direct and indirect effects between economic, social and environmental dimensions of triple bottom line (TBL), based on a questionnaire survey and cross-industrial sample in Sweden. The analyses apply partial least squares structural equation models. The study tests the direct and indirect effects between economic, social, and environmental dimensions of TBL and offers additional validity and reliability to establish the measurement and structural properties between the dimensions of TBL. The study extends earlier findings by explicitly discussing how the three TBL goals relate to each other and shows how the dynamic capability view can be a fruitful lens to investigate business sustainability. Some differences in sustainability business practices caused by differences in national cultures are identified. Sustainability reporting in a strong uncertainty avoidance (UA) country happens in accordance with regulations and laws. Conversely, for weak UA cultures, reporting and compliance with regulations are ways to build trust with stakeholders. That is, reporting is more transparent and widespread in weak UA countries. The study also provides a foundation to guide companies' actions of business sustainability. The model shows companies how to establish the order of actions undertaken across economic, social, and environmental dimensions. In addition, it clarifies that the economic dimension exerts an effect on the social and environmental dimensions. The model also grasps long-term economic performance by including competitiveness and brand value, while earlier research mainly has focused on more short-term measurements as return on assets. © 2022 The Authors. Corporate Social Responsibility and Environmental Management published by ERP Environment and John Wiley & Sons Ltd.
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23.
  • Becerra Garcia, Marley, 1979-, et al. (författare)
  • High field conduction in mineral oil based zno nanofluids prior to negative streamer inception
  • 2021
  • Ingår i: Journal of Physics Communications. - : IOP Publishing. - 2399-6528. ; 5:4
  • Tidskriftsartikel (refereegranskat)abstract
    • The electric conduction under intense electric fields (up to ∼ 10 V/m) in nanofluids using surface-modified ZnO–C nanoparticles dispersed in mineral oil as host, is investigated with both experiments and numerical simulations. The measurements are used to estimate unknown parameters necessary to represent the generation and loss of electrons in an electrohydrodynamic model for mineral oil with and without ZnO–C nanoparticles in a needle-plane configuration. The model suggests that ZnO–C nanoparticles induce an enhanced field emission from negative needles, explaining the significantly larger conduction currents measured in the nanofluid compared with those in the host liquid. It is also found that the scavenging of electrons by ZnO–C nanoparticles is a process which is negligible compared with the loss of electrons due to attachment in mineral oil. It is shown that ZnO–C nanoparticles hinder the streamer initiation process by reducing the effective electric field at the tip of the needle. This electric field reduction is caused by the combined effect of enhanced electron injection through ZnO–C nanoparticles and strong electron attachment in mineral oil. Thus, the electric field on the needle tip reaches the same threshold value when the streamer is incepted in the nanofluid as in mineral oil, although at a larger voltage. Solid evidence indicating that the additional electron scavenging and the reduced electron mobility introduced by nanoparticles has no effect in the conduction currents and in the negative streamer inception in the tested ZnO–C nanofluids is shown.
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24.
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25.
  • Broman, Elias, 1985-, et al. (författare)
  • Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments
  • 2024
  • Ingår i: The ISME journal. - 1751-7370 .- 1751-7362. ; 18:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Coastal ecosystems dominate oceanic methane (CH4) emissions. However, there is limited knowledge about how biotic interactions between infauna and aerobic methanotrophs (i.e. CH4 oxidizing bacteria) drive the spatial-temporal dynamics of these emissions. Here, we investigated the role of meio- and macrofauna in mediating CH4 sediment-water fluxes and aerobic methanotrophic activity that can oxidize significant portions of CH4. We show that macrofauna increases CH4 fluxes by enhancing vertical solute transport through bioturbation, but this effect is somewhat offset by high meiofauna abundance. The increase in CH4 flux reduces CH4 pore-water availability, resulting in lower abundance and activity of aerobic methanotrophs, an effect that counterbalances the potential stimulation of these bacteria by higher oxygen flux to the sediment via bioturbation. These findings indicate that a larger than previously thought portion of CH4 emissions from coastal ecosystems is due to faunal activity and multiple complex interactions with methanotrophs.
  •  
26.
  • Broman, Elias, 1985-, et al. (författare)
  • Cyanophage Diversity and Community Structure in Dead Zone Sediments
  • 2021
  • Ingår i: mSphere. - : American Society for Microbiology. - 2379-5042. ; 6:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Up to 20% of prokaryotic organisms in the oceans are estimated to die every day due to viral infection and lysis. Viruses can therefore alter microbial diversity, community structure, and biogeochemical processes driven by these organisms. Cyanophages are viruses that infect and lyse cyanobacterial cells, adding bioavailable carbon and nutrients into the environment. Cyanobacteria are photosynthesizing bacteria, with some species capable of N-2 fixation, which are known to form large blooms as well as resistant resting cells known as akinetes. Here, we investigated cyanophage diversity and community structure plus cyanobacteria in dead zone sediments. We sampled surface sediments and sequenced DNA and RNA, along an oxygen gradient-representing oxic, hypoxic, and anoxic conditions-in one of the world's largest dead zones located in the Baltic Sea. Cyanophages were detected at all stations and, based on partial genome contigs, had a higher alpha diversity and different beta diversity in the hypoxic-anoxic sediments, suggesting that cyanobacteria in dead zone sediments and/or environmental conditions select for specific cyanophages. Some of these cyanophages can infect cyanobacteria with potential consequences for gene expression related to their photosystem and phosphate regulation. Top cyanobacterial genera detected in the anoxic sediment included Dolichospermum/Anabaena, Synechococcus, and Cyanobium. RNA transcripts classified to cyanobacteria were associated with numerous pathways, including anaerobic carbon metabolism and N-2 fixation. Cyanobacterial blooms are known to fuel oxygen-depleted ecosystems with phosphorus (so-called internal loading), and our cyanophage data indicate the potential for viral lysis of cyanobacteria which might explain the high nutrient turnover in these environments. IMPORTANCE Cyanophages are viruses that target cyanobacteria and directly control their abundance via viral lysis. Cyanobacteria are known to cause large blooms in water bodies, substantially contributing to oxygen depletion in bottom waters resulting in areas called dead zones. Our knowledge of cyanophages in dead zones is very scarce, and so far, no studies have assembled partial cyanophage genomes and investigated their associated cyanobacteria in these dark and anoxic sediments. Here, we present the first study using DNA and RNA sequencing to investigate in situ diversity of cyanophages and cyanobacteria in dead zones. Our study shows that dead zone sediments contain different cyanophages compared to oxic sediments and suggest that these viruses are able to affect cyanobacterial photosystem and phosphate regulation. Furthermore, cyanophage-controlled lysis of cyanobacteria might also increase the turnover of carbon, phosphorus, and nitrogen in these oxygen-free environments at the bottom of the sea.
  •  
27.
  • Broman, Elias, 1985-, et al. (författare)
  • Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities
  • 2023
  • Ingår i: Microbial Ecology. - : Elsevier. - 0095-3628 .- 1432-184X. ; 86, s. 2357-2372
  • Tidskriftsartikel (refereegranskat)abstract
    • Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.
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28.
  • Broman, Elias, 1985-, et al. (författare)
  • No evidence of light inhibition on aerobic methanotrophs in coastal sediments using eDNA and eRNA
  • 2023
  • Ingår i: Environmental DNA. - 2637-4943. ; 5:4, s. 766-781
  • Tidskriftsartikel (refereegranskat)abstract
    • It is estimated that up to half of global methane (CH4) emissions are derived from microbial processes in aquatic ecosystems. However, it is not fully understood which factors explain the spatial and temporal variability of these emissions. For example, light has previously been shown to both inhibit and stimulate aerobic methane-oxidizing bacteria (i.e., methanotrophs) in the water column. These contrasting results indicate that the mechanisms that light has on CH4 oxidation are not yet clearly known, even less so for benthic aerobic methanotrophs. Here, we tested whether light reaching the seafloor can inhibit methanotrophic activity on the sediment surface. We sampled and distributed over 40 intact sediment cores from two coastal sites (illuminated 10 m, and a dark site at 33 m water depth) into 0, 50, and 100 PAR light treatments. After 10 days, we found no difference between treatments for each site in pore-water CH4 concentrations, relative abundance of aerobic methanotrophs, or the number of RNA transcripts related to methane oxidation. Our results suggest that light attenuation in coastal waters does not significantly affect aerobic methanotrophs in coastal sediments.
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29.
  • Cao, Huizhong, 1996, et al. (författare)
  • VR Interaction for Efficient Virtual Manufacturing : Mini Map for Multi-User VR Navigation Platform
  • 2024
  • Ingår i: Sustainable Production through Advanced Manufacturing, Intelligent Automation and Work Integrated Learning. - : IOS Press. - 9781643685106 - 9781643685113 ; 52, s. 335-345
  • Konferensbidrag (refereegranskat)abstract
    • Over the past decade, the value and potential of VR applications in manufacturing have gained significant attention in accordance with the rise of Industry 4.0 and beyond. Its efficacy in layout planning, virtual design reviews, and operator training has been well-established in previous studies. However, many functional requirements and interaction parameters of VR for manufacturing remain ambiguously defined. One area awaiting exploration is spatial recognition and learning, crucial for understanding navigation within the virtual manufacturing system and processing spatial data. This is particularly vital in multi-user VR applications where participants' spatial awareness in the virtual realm significantly influences the efficiency of meetings and design reviews. This paper investigates the interaction parameters of multi-user VR, focusing on interactive positioning maps for virtual factory layout planning and exploring the user interaction design of digital maps as navigation aid. A literature study was conducted in order to establish frequently used technics and interactive maps from the VR gaming industry. Multiple demonstrators of different interactive maps provide a comprehensive A/B test which were implemented into a VR multi-user platform using the Unity game engine. Five different prototypes of interactive maps were tested, evaluated and graded by the 20 participants and 40 validated data streams collected. The most efficient interaction design of interactive maps is thus analyzed and discussed in the study. 
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30.
  • Cappelluti, Emmanuele, et al. (författare)
  • Flat-band optical phonons in twisted bilayer graphene
  • 2023
  • Ingår i: Physical Review B. - : American Physical Society (APS). - 2469-9950 .- 2469-9969. ; 108:12
  • Tidskriftsartikel (refereegranskat)abstract
    • Twisting bilayer sheets of graphene have been proven to be an efficient way to manipulate the electronic Dirac-like properties, resulting in flat bands at magic angles. Inspired by the electronic model, we develop a continuum model for the lattice dynamics of twisted bilayer graphene and we show that a remarkable band flattening applies to almost all the high-frequency in-plane lattice vibration modes, including the valley Dirac phonon, valley optical phonon, and zone-center optical phonon bands. Utilizing an approximate approach, we estimate small but finite magic angles at which a vanishing phonon bandwidth is expected. In contrast to the electronic case, the existence of a restoring potential prohibits the emergence of a magic angle in a more accurate modeling. The predicted phonon band flattening is highly tunable by the twist angle and this strong dependence is directly accessible by spectroscopic tools.
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31.
  • Dreos, Ambra, 1987, et al. (författare)
  • Investigating New Applications of a Photoswitchable Fluorescent Norbornadiene as a Multifunctional Probe for Delineation of Amyloid Plaque Polymorphism.
  • 2023
  • Ingår i: ACS sensors. - : American Chemical Society (ACS). - 2379-3694. ; 8:4, s. 1500-1509
  • Tidskriftsartikel (refereegranskat)abstract
    • Amyloid beta (Aβ) plaques are a major pathological hallmark of Alzheimer's disease (AD) and constitute of structurally heterogenic entities (polymorphs) that have been implicated in the phenotypic heterogeneity of AD pathology and pathogenesis. Understanding amyloid aggregation has been a critical limiting factor to gain understanding of AD pathogenesis, ultimately reflected in that the underlying mechanism remains elusive. We identified a fluorescent probe in the form of a turn-off photoswitchable norbornadiene derivative (NBD1) with several microenvironment-sensitive properties that make it relevant for applications within advanced fluorescence imaging, for example, multifunctional imaging. We explored the application of NBD1 for in situ delineation of structurally heterogenic Aβ plaques in transgenic AD mouse models. NBD1 plaque imaging shows characteristic broader emission bands in the periphery and more narrow emission bands in the dense cores of mature cored plaques. Further, we demonstrate in situ photoisomerization of NBD1 to quadricyclane and thermal recovery in single plaques, which is relevant for applications within both functional and super-resolution imaging. This is the first time a norbornadiene photoswitch has been used as a probe for fluorescence imaging of Aβ plaque pathology in situ and that its spectroscopic and switching properties have been studied within the specific environment of senile Aβ plaques. These findings open the way toward new applications of NBD-based photoswitchable fluorescent probes for super-resolution or dual-color imaging and multifunctional microscopy of amyloid plaque heterogeneity. This could allow to visualize Aβ plaques with resolution beyond the diffraction limit, label different plaque types, and gain insights into their physicochemical composition.
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32.
  • Fernández Reyes, Francisco Ramón, 1985- (författare)
  • Abstractions to Control the Future
  • 2021
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Multicore and manycore computers are the norm nowadays, and users have expectations that their programs can do multiple things concurrently. To support that, developers use concur- rency abstractions such as threads, promises, futures, and/or channels to exchange information. All these abstractions introduce trade-offs between the concurrency model and the language guarantees, and developers accept these trade-offs for the benefits of concurrent programming.Many concurrent languages are multi-paradigm, e.g., mix the functional and object-oriented paradigms. This is beneficial to developers because they can choose the most suitable approach when solving a problem. From the point of view of concurrency, purely functional programming languages are data-race free since they only support immutable data. Object-oriented languages do not get a free lunch, and neither do multi-paradigm languages that have imperative features.The main problem is uncontrolled concurrent access to shared mutable state, which may inadvertently introduce data-races. A data-race happens when two concurrent memory operations target the same location, at least one of them is a write, and there is no synchronisation operation involved. Data-races make programs to exhibit (unwanted) non-deterministic behaviour.The contribution of this thesis is two-fold. First, this thesis introduces new concurrent abstractions in a purely functional, statically typed programming language (Paper I – Paper III); these abstractions allow developers to write concurrent control- and delegation-based patterns. Second, this thesis introduces a capability-based dynamic programming model, named Dala, that extends the applicability of the concurrent abstractions to an imperative setting while maintaining data-race freedom (Paper IV). Developers can also use the Dala model to migrate unsafe programs, i.e., programs that may suffer data-races, to data-race free programs.
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33.
  • Garrison, Julie A., 1993-, et al. (författare)
  • Molecular diet analysis enables detection of diatom and cyanobacteria DNA in the gut of Macoma balthica
  • 2022
  • Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 17:11
  • Tidskriftsartikel (refereegranskat)abstract
    • Detritivores are essential to nutrient cycling, but are often neglected in trophic networks, due to difficulties with determining their diet. DNA analysis of gut contents shows promise of trophic link discrimination, but many unknown factors limit its usefulness. For example, DNA can be rapidly broken down, especially by digestion processes, and DNA provides only a snapshot of the gut contents at a specific time. Few studies have been performed on the length of time that prey DNA can be detected in consumer guts, and none so far using benthic detritivores. Eutrophication, along with climate change, is altering the phytoplankton communities in aquatic ecosystems, on which benthic detritivores in aphotic soft sediments depend. Nutrient-poor cyanobacteria blooms are increasing in frequency, duration, and magnitude in many water bodies, while nutrient-rich diatom spring blooms are shrinking in duration and magnitude, creating potential changes in diet of benthic detritivores. We performed an experiment to identify the taxonomy and quantify the abundance of phytoplankton DNA fragments on bivalve gut contents, and how long these fragments can be detected after consumption in the Baltic Sea clam Macoma balthica. Two common species of phytoplankton (the cyanobacteria Nodularia spumigena or the diatom Skeletonema marinoi) were fed to M. balthica from two regions (from the northern and southern Stockholm archipelago). After removing the food source, M. balthica gut contents were sampled every 24 hours for seven days to determine the number of 23S rRNA phytoplankton DNA copies and when the phytoplankton DNA could no longer be detected by quantitative PCR. We found no differences in diatom 18S rRNA gene fragments of the clams by region, but the southern clams showed significantly more cyanobacteria 16S rRNA gene fragments in their guts than the northern clams. Interestingly, the cyanobacteria and diatom DNA fragments were still detectable by qPCR in the guts of M. balthica one week after removal from its food source. However, DNA metabarcoding of the 23S rRNA phytoplankton gene found in the clam guts showed that added food (i.e. N. spumigena and S. marinoi) did not make up a majority of the detected diet. Our results suggest that these detritivorous clams therefore do not react as quickly as previously thought to fresh organic matter inputs, with other phytoplankton than large diatoms and cyanobacteria constituting the majority of their diet. This experiment demonstrates the viability of using molecular methods to determine feeding of detritivores, but further studies investigating how prey DNA signals can change over time in benthic detritivores will be needed before this method can be widely applicable to both models of ecological functions and conservation policy.
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34.
  • Gomes, Francisco, 1987, et al. (författare)
  • Evolution of statistical analysis in empirical software engineering research : Current state and steps forward
  • 2019
  • Ingår i: Journal of Systems and Software. - : Elsevier Inc.. - 0164-1212 .- 1873-1228. ; 156, s. 246-267
  • Tidskriftsartikel (refereegranskat)abstract
    • Software engineering research is evolving and papers are increasingly based on empirical data from a multitude of sources, using statistical tests to determine if and to what degree empirical evidence supports their hypotheses. To investigate the practices and trends of statistical analysis in empirical software engineering (ESE), this paper presents a review of a large pool of papers from top-ranked software engineering journals. First, we manually reviewed 161 papers and in the second phase of our method, we conducted a more extensive semi-automatic classification of papers spanning the years 2001–2015 and 5196 papers. Results from both review steps was used to: i) identify and analyse the predominant practices in ESE (e.g., using t-test or ANOVA), as well as relevant trends in usage of specific statistical methods (e.g., nonparametric tests and effect size measures) and, ii) develop a conceptual model for a statistical analysis workflow with suggestions on how to apply different statistical methods as well as guidelines to avoid pitfalls. Lastly, we confirm existing claims that current ESE practices lack a standard to report practical significance of results. We illustrate how practical significance can be discussed in terms of both the statistical analysis and in the practitioner's context. © 2019 Elsevier Inc.
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35.
  • Gonzales-Siles, Lucia, et al. (författare)
  • Mass Spectrometry Proteotyping of Streptococcus pneumoniae and commensal Streptococcus: identification of biomarkers for infectious strain characterization
  • 2016
  • Ingår i: 26th ECCMID 2016 Amsterdam, The Netherlands. 9 - 12 April 2016.
  • Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
    • Background: Streptococcus pneumoniae (pneumococcus) is the leading cause of community-acquired pneumonia, with morbidity and mortality worldwide. S. pneumoniae belongs to the S. mitis-Group (viridans streptococci), phenotypically and genotypically similar to commensal species of the upper respiratory tract, S. mitis, S. oralis, and S. pseudopneumoniae, causing problems for identifications in clinical laboratories. In this project, we apply state-of-the-art proteomics for Streptococcus spp. 'proteotyping'; identifying and characterizing protein biomarkers for species-level identification, antibiotic resistance, virulence and strain typing for epidemiological analyses (1). Material/methods: Bacterial proteins, from intact bacteria or cell fractions, are bound to a membrane surface, using patented (WO2006068619) FlowCell (LPITM) technology. Peptides are generated from the bound proteins, by enzymatic digestion, separated and analyzed, using LC-MS/MS. The mass spectra profiles are compared to reference peptide sequences and whole genome sequence (wgs) data of the NCBI RefSeq Database. The S. mitis-Group specie, S. pneumoniae, S. mitis, S. oralis, S. psedopneumoniae, as well as the more distantly-related, Group A Streptococcus (GAS) species, S. pyogenes , were analyzed individually and in mixtures, to demonstrate the resolution of proteotyping for differentiating bacteria. Results: Using proteotyping protocols, S. pneumoniae were detected and differentiated from other streptococci, S. mitis, S. oralis, S. psedopneumoniae and the more distant relative, S. pyogenes, by identification of unique discriminatory peptides. Metabolic protein biomarkers were identified, including for antibiotic resistance and virulence. It was possible to find discriminatory biomarkers for a target species when analyzing 1:1 mixes of S. pneumoniae and other species from the S. mitis-Group. The different strains of S. pneumoniae, analyzed in different ratio combinations, were successfully differentiated and identified. For successful proteotyping, a comprehensive and accurate genomic database was observed to be key for obtaining reliable peptide matching and proteotyping data. Importantly, because of observed high rates of misclassified wgs data in the public databases, the taxonomic classifications of genomes in GenBank were analyzed against reference type strain genomes of target species by calculating wgs similarities, using Average Nucleotide Identity with BLAST (ANIb). While wgs data for S. pneumoniae were confirmed to be classified correctly, approximately one-third of wgs data for other species of the S. mitis-Group were determined to be misclassified. Streptococci strains that could not be identified, using standard genotypic and phenotypic approaches, were characterized by proteotyping and genome sequencing to establish their taxonomy and biomarker features to enhance species database matching. Conclusions: Proteotyping enables differentiation, identification and characterization of pneumococcus from the most closely related species attaining, as well, strain-level discrimination from single LC-MS/MS analyses. The protocol enhances identification and characterization of pathogenic bacterial isolates through identifications of expressed biomarkers, ultimately for cultivation-independent analyses of clinical samples. 1) Karlsson et al., 2015. Syst Appl Microbiol. 38:246-257.
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36.
  • Gross, Susanna, 1982, et al. (författare)
  • Optimization of a high-throughput phenotyping method for chain-forming phytoplankton species
  • 2018
  • Ingår i: Limnology and Oceanography : Methods. - : Wiley. - 1541-5856. ; 16:2, s. 57-67
  • Tidskriftsartikel (refereegranskat)abstract
    • Modern equipment facilitates phenotyping of hundreds of strains of unicellular organisms by culturing and monitoring growth in microplates. However, in the field of phytoplankton ecology, automated monitoring of growth is not often done and this method has not been tested for many species. To meet the demand for a high-throughput technique for monitoring growth of chain-forming phytoplankton species, we have assessed and optimized a method commonly used for other microorganisms. Skeletonema marinoi is a pelagic chain-forming diatom, and we have acquired growth patterns in four different treatments (i.e., low and high light, low and high nutrient concentrations) when cultured in multi-well plates. Due to the unexpected heterogeneity in growth rates and maximum cell densities observed between wells (spatial) and runs (temporal), a set of models was fitted to the obtained phenotypic data to correct for these biases. Models were tested for robustness on two replicate multi-strain experiments including 23 different strains. Using the model accounting for temporal and spatial bias, we could reliably determine changes in growth rate caused by nutrient treatments as well as differences in cell density as a response to nutrient availability and light treatment. This method can facilitate high-throughput phenotyping of hundreds of strains, which is often a bottleneck in characterizing the ecology and capacity for adaptation of chain-forming phytoplankton.
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37.
  • Izquierdo Riera, Francisco Blas, 1988, et al. (författare)
  • Clipaha : A Scheme to Perform Password Stretching on the Client
  • 2023
  • Ingår i: Proceedings of the 9th International Conference on Information Systems Security and Privacy - ICISSP. - : Science and Technology Publications, Lda. - 2184-4356. - 9789897586248 ; , s. 58-69
  • Konferensbidrag (refereegranskat)abstract
    • Password security relies heavily on the choice of password by the user but also on the one-way hash functions used to protect stored passwords. To compensate for the increased computing power of attackers, modern password hash functions like Argon2, have been made more complex in terms of computational power and memory requirements. Nowadays, the computation of such hash functions is performed usually by the server (or authenticator) instead of the client. Therefore, constrained Internet of Things devices cannot use such functions when authenticating users. Additionally, the load of computing such functions may expose servers to denial of service attacks. In this work, we discuss client-side hashing as an alternative. We propose Clipaha, a client-side hashing scheme that allows using high-security password hashing even on highly constrained server devices. Clipaha is robust to a broader range of attacks compared to previous work and covers important and complex usage scenarios. Our evaluation discusses critical aspects involved in client-side hashing. We also provide an implementation of Clipaha in the form of a web library1 and benchmark the library on different systems to understand its mixed JavaScript and WebAssembly approach’s limitations. Benchmarks show that our library is 50% faster than similar libraries and can run on some devices where previous work fails. © 2023 by SCITEPRESS – Science and Technology Publications, Lda. Under CC license (CC BY-NC-ND 4.0).
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38.
  • Jakobsson, Hedvig E, et al. (författare)
  • Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.
  • 2016
  • Ingår i: Genome Announcements. - 2169-8287. ; 4:3
  • Tidskriftsartikel (refereegranskat)abstract
    • Moraxella catarrhalis is a Gram-negative commensal and pathogenic bacterium found in the human respiratory tract. It is associated with otitis media and respiratory tract infections. Here, we report the draft genome sequence of M. catarrhalis type strain CCUG 353(T), composed of 18 contigs and a total size of 1.89 Mb.
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39.
  •  
40.
  • Jakobsson, Hedvig E, et al. (författare)
  • Proteotyping of Streptococcus pneumoniae, using tandem mass spectrometry for identification of biomarkers for species and strain differentiation
  • 2016
  • Ingår i: 11th International Meeting on Microbial Epidemiological Markers (IMMEM XI) 9 - 12 March 2016, Estoril, Portugal. - : European Society for Clinical Microbiology and Infectious Diseases.
  • Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
    • Background. Streptococcus pneumoniae (pneumococcus) is the leading cause of community-acquired pneumonia and a major cause of morbidity and mortality worldwide. S. pneumoniae is phenotypically and genotypically similar to commensal species of the upper respiratory tract of the Streptococcus mitis-Group (viridans streptococci), S. mitis, S. oralis, and S. pseudopneumoniae, causing problems of identification in clinical microbiology laboratories. We have applied state-of-the-art proteomics techniques for Streptococcus spp. proteotyping; to detecting and characterizing expressed protein biomarkers for species-level identification, determination of antibiotic resistance and virulence biomarkers and strain typing for epidemiological analyses. Material and methods. The proteins of intact bacteria or cell fractions are bound to a membrane surface, using patented (WO2006068619) Lipid-based Protein Immobilization (LPITM) technology. Peptides are generated from the bound proteins, using enzymatic digestion, separated and analyzed, using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The mass spectra profiles are compared to a database of reference peptide sequences. Subsequently, the identified peptides are compared to a database of reference genome sequences, all complete genomes of the NCBI Reference Sequence (RefSeq) Database. In this study, the type strains of the close-related mitis complex species S. pneumoniae (CCUG 28588T), S. mitis (CCUG 31611T), S. oralis (CCUG 13229T), S. psedopneumoniae (CCUG 49455T) and the more distantly-related S. pyogenes (CCUG 4207T) were analysed individually and in mixtures, to demonstrate proteotyping capability and differentiate closely related species,. Additionally, mixes containing different S. pneumoniae strains were analyzed. Results. Using proteotyping protocols, it was possible to detect and correctly identify S. pneumoniae from the closely related bacterial species, S. mitis, S. oralis S. psedopneumoniae and S. pyogenes, as well as different strains of S. pneumoniae by identification of unique discriminatory peptides. For successful proteotyping,a comprehensive and accurate genomic database is the key to obtaining reliable proteotyping data. Importantly, because of questionable classifications of sequenced genomes in the public databases, before incorporation of reference genomic sequence data for proteotyping, the genome sequences should be verified and confirmed for accurate classifications. Furthermore, it is also essential to include all relevant species with as many as 25 genomes in order to obtain a comprehensive coverage of coding sequences for accurate peptide matching and to be able to discriminate between the most closely related species. In this study, all genomes of the S. mitis-Group in the database were analyzed, using Average Nucleotide Identity Blast (ANIb) and S. mitis-Group strains that cannot be identified to the species level, using standard genotypic and phenotypic approaches, where characterized by proteotyping and whole genome sequencing to describe their taxonomy and to improve the database matching. Conclusions: Proteotyping, using LC-MS/MS, enabled the differentiation and identification of pneumococcus from its closely related species and sub-species-level strain discrimination, all from single MS analyses. The whole method will enhance the identification and characterization of microorganisms, allowing high-resolution discrimination of closely related species through the confident identification of new biomarkers, ultimately for cultivation-independent application to the analyses of clinical samples.
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41.
  • Jonsson, Elise, et al. (författare)
  • An introduction to data-driven modelling of the Water-Energy-Food-Ecosystem nexus
  • 2024
  • Ingår i: Environmental Modelling & Software. - : Elsevier. - 1364-8152 .- 1873-6726. ; 181
  • Tidskriftsartikel (refereegranskat)abstract
    • Attaining resource security in the water, energy, food, and ecosystem (WEFE) sectors, the WEFE nexus, is paramount. This necessitates the use of quantitative modelling, which presents many challenges, as this is a complex system acting at the intersection of the physical- and social sciences. However, as WEFE data is becoming more widely available, data-driven methods of modelling this system are becoming increasingly viable. Here, we discuss two main problems in WEFE nexus modelling: system identification and control. System identification uses Machine Learning algorithms to obtain dynamical models from data and have shown promise in many disciplines with similar characteristics as the nexus. Meanwhile, control algorithms manipulate a system to achieve objectives and are becoming instrumental in shaping nexus policy. Despite the promise of these algorithms, data-driven modelling is a vast and daunting field, and so here we provide an introductory overview of this field, with emphasis on nexus applications.
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42.
  • Karlsson, Roger, 1975, et al. (författare)
  • Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics
  • 2018
  • Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 13:12
  • Tidskriftsartikel (refereegranskat)abstract
    • A range of methodologies may be used for analyzing bacteria, depending on the purpose and the level of resolution needed. The capability for recognition of species distinctions within the complex spectrum of bacterial diversity is necessary for progress in microbiological research. In clinical settings, accurate, rapid and cost-effective methods are essential for early and efficient treatment of infections. Characterization and identification of microorganisms, using, bottom-up proteomics, or "proteotyping", relies on recognition of species-unique or associated peptides, by tandem mass spectrometry analyses, dependent upon an accurate and comprehensive foundation of genome sequence data, allowing for differentiation of species, at amino acid-level resolution. In this study, the high resolution and accuracy of MS/MS-based proteotyping was demonstrated, through analyses of the three phylogenetically and taxonomically most closely-related species of the Mitis Group of the genus Streptococcus: i.e., the pathogenic species, Streptococcus pneumoniae (pneumococcus), and the commensal species, Streptococcus pseudopneumoniae and Streptococcus mitis. To achieve high accuracy, a genome sequence database used for matching peptides was created and carefully curated. Here, MS-based, bottom-up proteotyping was observed and confirmed to attain the level of resolution necessary for differentiating and identifying the most-closely related bacterial species, as demonstrated by analyses of species of the Streptococcus Mitis Group, even when S. pneumoniae were mixed with S. pseudopneumoniae and S. mitis, by matching and identifying more than 200 unique peptides for each species.
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43.
  • Klein, Cristian, 1985-, et al. (författare)
  • Brownout : Building More Robust Cloud Applications
  • 2014
  • Ingår i: 36th International Conference on Software Engineering (ICSE 2014). - New York, NY, USA : ACM Digital Library. ; , s. 700-711
  • Konferensbidrag (refereegranskat)abstract
    • Self-adaptation is a first class concern for cloud applications, which should be able to withstand diverse runtime changes. Variations are simultaneously happening both at the cloud infrastructure level - for example hardware failures - and at the user workload level - flash crowds. However, robustly withstanding extreme variability, requires costly hardware over-provisioning. In this paper, we introduce a self-adaptation programming paradigm called brownout. Using this paradigm, applications can be designed to robustly withstand unpredictable runtime variations, without over-provisioning. The paradigm is based on optional code that can be dynamically deactivated through decisions based on control theory. We modified two popular web application prototypes - RUBiS and RUBBoS - with less than 170 lines of code, to make them brownout-compliant. Experiments show that brownout self-adaptation dramatically improves the ability to withstand flash-crowds and hardware failures.
  •  
44.
  • Klein, Cristian, 1985-, et al. (författare)
  • Improving Cloud Service Resilience using Brownout-Aware Load-Balancing
  • 2014
  • Ingår i: 2014 IEEE 33rd International Symposium On Reliable Distributed Systems (SRDS). - : IEEE Computer Society. - 9781479955848 ; , s. 31-40, s. 31-40
  • Konferensbidrag (refereegranskat)abstract
    • We focus on improving resilience of cloud services (e.g., e-commerce website), when correlated or cascading failures lead to computing capacity shortage. We study how to extend the classical cloud service architecture composed of a load-balancer and replicas with a recently proposed self-adaptive paradigm called brownout. Such services are able to reduce their capacity requirements by degrading user experience (e.g., disabling recommendations).Combining resilience with the brownout paradigm is to date an open practical problem. The issue is to ensure that replica self-adaptivity would not confuse the load-balancing algorithm, overloading replicas that are already struggling with capacity shortage. For example, load-balancing strategies based on response times are not able to decide which replicas should be selected, since the response times are already controlled by the brownout paradigm.In this paper we propose two novel brownout-aware load-balancing algorithms. To test their practical applicability, we extended the popular lighttpd web server and load-balancer, thus obtaining a production-ready implementation. Experimental evaluation shows that the approach enables cloud services to remain responsive despite cascading failures. Moreover, when compared to Shortest Queue First (SQF), believed to be near-optimal in the non-adaptive case, our algorithms improve user experience by 5%, with high statistical significance, while preserving response time predictability.
  •  
45.
  • Klein, Cristian, 1985-, et al. (författare)
  • Introducing Service-level Awareness in the Cloud
  • 2013
  • Ingår i: Proceedings of the 4th annual Symposium on Cloud Computing. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450324281
  • Konferensbidrag (refereegranskat)
  •  
46.
  • Klein, Cristian, 1985-, et al. (författare)
  • Introducing Service-level Awareness in the Cloud
  • 2013
  • Rapport (övrigt vetenskapligt/konstnärligt)abstract
    • Resource allocation in clouds is mostly done assuming hard requirements, applications either receive the requested resources or fail. Given the dynamic nature of workloads, guaranteeing on-demand allocations requires large spare capacity. Hence, one cannot have a system that is both reliable and efficient.To solve this issue, we introduce Service-Level (SL) awareness in clouds, assuming applications contain some optional code that can be dynamically deactivated as needed. First, we design a model for such applications and synthesize a controller to decide when to execute the optional code and when to skip it. Then, we propose a Resource Manager (RM) that allocates resources to multiple SL-aware applications in a fair manner. We theoretically prove properties of the overall system using control and game theory.To show the practical applicability, we implemented SL-aware versions of RUBiS and RUBBoS with less than 170 lines of code. Experiments show that SL-awareness may enable a factor 8 improvement in withstanding flash-crowds or failures. SL-awareness opens up more flexibility in cloud resource management, which is why we encourage further research by publishing all source code.
  •  
47.
  • Klein, Cristian, 1985-, et al. (författare)
  • Resource management for service level aware cloud applications
  • 2013
  • Konferensbidrag (refereegranskat)abstract
    • Resource allocation in clouds is mostly done assuming hard requirements, time-sensitive applications either receive the requested resources or fail. Given the dynamic nature of workloads, guaranteeing on-demand allocations requires large spare capacity. Hence, one cannot have a system that is both reliable and efficient.To mitigate this issue, we introduce service-level awareness in clouds, assuming applications contain some optional code that can be dynamically deactivated as needed. We propose a resource manager that allocates resources to multiple service-level-aware applications in a fair manner. To show the practical applicability, we implemented service-level-aware versions of RUBiS and RUBBoS, two popular cloud benchmarks, together with our resource manager. Experiments show that service-level awareness helps in withstanding flash-crowds or failures, opening up more flexibility in cloud resource management.
  •  
48.
  • Lanzon, Borja, et al. (författare)
  • Lipidomic and Metabolomic Signature of Progression of Chronic Kidney Disease in Patients with Severe Obesity
  • 2021
  • Ingår i: Metabolites. - : MDPI. - 2218-1989. ; 11:12
  • Tidskriftsartikel (refereegranskat)abstract
    • Severe obesity is a major risk for chronic kidney disease (CKD). Early detection and careful monitoring of renal function are critical for the prevention of CKD during obesity, since biopsies are not performed in patients with CKD and diagnosis is dependent on the assessment of clinical parameters. To explore whether distinct lipid and metabolic signatures in obesity may signify early stages of pathogenesis toward CKD, liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-high resolution accurate mass-mass spectrometry (GC-HRAM-MS) analyses were performed in the serum and the urine of severely obese patients with and without CKD. Moreover, the impact of bariatric surgery (BS) in lipid and metabolic signature was also studied, through LC-MS and GC-HRAM-MS analyses in the serum and urine of patients with severe obesity and CKD before and after undergoing BS. Regarding patients with severe obesity and CKD compared to severely obese patients without CKD, serum lipidome analysis revealed significant differences in lipid signature. Furthermore, serum metabolomics profile revealed significant changes in specific amino acids, with isoleucine and tyrosine, increased in CKD patients compared with patients without CKD. LC-MS and GC-HRAM-MS analysis in serum of patients with severe obesity and CKD after BS showed downregulation of levels of triglycerides (TGs) and diglycerides (DGs) as well as a decrease in branched-chain amino acid (BCAA), lysine, threonine, proline, and serine. In addition, BS removed most of the correlations in CKD patients against biochemical parameters related to kidney dysfunction. Concerning urine analysis, hippuric acid, valine and glutamine were significantly decreased in urine from CKD patients after surgery. Interestingly, bariatric surgery did not restore all the lipid species, some of them decreased, hence drawing attention to them as potential targets for early diagnosis or therapeutic intervention. Results obtained in this study would justify the use of comprehensive mass spectrometry-based lipidomics to measure other lipids aside from conventional lipid profiles and to validate possible early markers of risk of CKD in patients with severe obesity.
  •  
49.
  • Lebreton, Sebastien, et al. (författare)
  • A Drosophila female pheromone elicits species-specific long-range attraction via an olfactory channel with dual specificity for sex and food
  • 2017
  • Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 15:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Mate finding and recognition in animals evolves during niche adaptation and involves social signals and habitat cues. Drosophila melanogaster and related species are known to be attracted to fermenting fruit for feeding and egg-laying, which poses the question of whether species-specific fly odours contribute to long-range premating communication. Results: We have discovered an olfactory channel in D. melanogaster with a dual affinity to sex and food odorants. Female flies release a pheromone, (Z)-4-undecenal (Z4-11Al), that elicits flight attraction in both sexes. Its biosynthetic precursor is the cuticular hydrocarbon (Z,Z)-7,11-heptacosadiene (7,11-HD), which is known to afford reproductive isolation between the sibling species D. melanogaster and D. simulans during courtship. Twin olfactory receptors, Or69aB and Or69aA, are tuned to Z4-11Al and food odorants, respectively. They are co-expressed in the same olfactory sensory neurons, and feed into a neural circuit mediating species-specific, long-range communication; however, the close relative D. simulans, which shares food resources with D. melanogaster, does not respond to Z4-11Al. Conclusion: The Or69aA and Or69aB isoforms have adopted dual olfactory traits. The underlying gene yields a collaboration between natural and sexual selection, which has the potential to drive speciation.
  •  
50.
  • Leitao, Jorge, et al. (författare)
  • Prevalence and risk factors of fatty liver in Portuguese adults
  • 2020
  • Ingår i: European Journal of Clinical Investigation. - : WILEY. - 0014-2972 .- 1365-2362. ; 50:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Prevalence of fatty liver (FL) and nonalcoholic fatty liver disease (NAFLD) depends mainly on obesity, diabetes and genetic factors. FL and NAFLD prevalence was evaluated in Portuguese adult population and correlated with several risk factors and related mortality data, within the same period. Materials and methods A cross-sectional, population-based multicenter study, voluntary and randomly selected in 834 Portuguese adults (18-79 years). Participants were evaluated after 12-hour fasting. Anthropometric data, past history including alcohol consumption, and associated diseases were registered. Blood samples were collected for biochemical testing. Dietary intake was evaluated using a semi-quantitative food frequency questionnaire. Presence of FL was evaluated using ultrasound, and NAFLD was diagnosed after exclusion of other causes for liver disease. Results Adjusted prevalence of FL and NAFLD was 37.8% and 17.0%, respectively. FL individuals were older, more frequently males, with increased probability of having obesity, diabetes or harmful alcohol consumption (HAC). NAFLD individuals were also older, but had a similar sex distribution and an increased probability of obesity and diabetes. In both groups, no differences were found regarding dietary pattern or physical activity. During the same time period, nonalcoholic steatohepatitis (NASH) liver-related deaths in Portugal were 0.105/100 000, while alcohol-related liver disease mortality was 6.790/100 000. Conclusion The large spectrum of FL was present in more than one third of the population, although only less than half could be classified as NAFLD. Other significant risk factors, such as HAC, are probably implicated in FL, explaining the low NASH-related mortality compared with the high alcohol-related mortality during the same time period.
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