| 1. |
- Midtvedt, Benjamin, et al.
(författare)
-
Single-shot self-supervised object detection in microscopy
- 2022
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- Object detection is a fundamental task in digital microscopy, where machine learning has made great strides in overcoming the limitations of classical approaches. The training of state-of-the-art machine-learning methods almost universally relies on vast amounts of labeled experimental data or the ability to numerically simulate realistic datasets. However, experimental data are often challenging to label and cannot be easily reproduced numerically. Here, we propose a deep-learning method, named LodeSTAR (Localization and detection from Symmetries, Translations And Rotations), that learns to detect microscopic objects with sub-pixel accuracy from a single unlabeled experimental image by exploiting the inherent roto-translational symmetries of this task. We demonstrate that LodeSTAR outperforms traditional methods in terms of accuracy, also when analyzing challenging experimental data containing densely packed cells or noisy backgrounds. Furthermore, by exploiting additional symmetries we show that LodeSTAR can measure other properties, e.g., vertical position and polarizability in holographic microscopy.
|
|
| 2. |
- Ahlbäck, Lennart
(författare)
-
Socialdemokratisk kyrkosyn : en studie i Socialdemokraternas kyrkopolitiska riktlinjer 1979-1996
- 2003
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The Social Democratic party of Sweden (SAP) was from its starting point in late 19th century oppositional to the Swedish Church and its position in Swedish society. But soon two different views were formed. The first view was to cut all ties between state and church. The second view was to perform a democratic reformation of the Church. The SAP have since long engaged itself in church politics and governing on different levels.This thesis deals with the ecclesiology of the SAP as presented by the party executive in normative outlines for church-politics. The investigation starts with the first published outlines in 1979 and ends with the outlines published in 1996, the year after the decision of the Swedish parliament to make a juridical separation between state and church by jan 1 2000.These political outlines form a framework for the party´s local, regional och central political activities in the Swedish Church. The starting point is the introduction of the party program and the democratization of the structure of Society. The structure of the Church should therefore also be democratized. Those emplyed by the Church are also to support this democratized structure. The goal of this process is to make the Church available and reachable for everyone in Sweden, also in a new cultural situation when people and church no longer can be looked upon as one unity. The Swedish Church has, says the SAP, therefore no right to set up rules for who can and who can not become a member of the Church.
|
|
| 3. |
- Amato, Alberto, et al.
(författare)
-
Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi
- 2018
-
Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 12, s. 1594-1604
-
Tidskriftsartikel (refereegranskat)abstract
- Diatoms and copepods are main actors in marine food webs. The prey-predator interactions between them affect bloom dynamics, shape marine ecosystems and impact the energy transfer to higher trophic levels. Recently it has been demonstrated that the presence of grazers may affect the diatom prey beyond the direct effect of grazing. Here, we investigated the response of the chain-forming centric diatom Skeletonema marinoi to grazer cues, including changes in morphology, gene expression and metabolic profile. S. marinoi cells were incubated with Calanus finmarchicus or with Centropages typicus and in both cases responded by reducing the chain length, whereas changes in gene expression indicated an activation of stress response, changes in the lipid and nitrogen metabolism, in cell cycle regulation and in frustule formation. Transcripts linked to G protein-coupled receptors and to nitric oxide synthesis were differentially expressed suggesting involvement of these signalling transduction pathways in the response. Downregulation of a lipoxygenase in the transcriptomic data and of its products in the metabolomic data also indicate an involvement of oxylipins. Our data contribute to a better understanding of the gene function in diatoms, providing information on the nature of genes implicated in the interaction with grazers, a crucial process in marine ecosystems.
|
|
| 4. |
- Arias, A., et al.
(författare)
-
Predator Chemical Cue Effects on the Diel Feeding Behaviour of Marine Protists
- 2021
-
Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 82:2, s. 356-364
-
Tidskriftsartikel (refereegranskat)abstract
- We have assessed the effect of copepod chemical cues on the diel feeding rhythms of heterotrophic and mixotrophic marine protists. All phagotrophic protists studied exhibited relatively high diurnal feeding rates. The magnitude of the diel feeding rhythm, expressed as the quotient of day and night ingestion rates, was inversely related to the time that phagotrophic protists were maintained in the laboratory in an environment without predators. In the case of the recently isolated ciliate Strombidium arenicola, the rhythm was lost after a few months. When challenged with chemical alarm signals (copepodamides) from the copepod Calanus finmarchicus at realistic concentrations (0.6-6 pM), S. arenicola partially re-established diurnal feeding. Conversely, the amplitude of the diel feeding rhythm for the ciliate Mesodinium rubrum was not affected by copepodamides, although the 24-h integrated food intake increased by approximately 23%. For the dinoflagellates Gyrodinium dominans and Karlodinium armiger, copepodamides significantly reduced the amplitude of their diel feeding rhythms; significant positive effects on total daily ingestion were only observed in G. dominans. Finally, the dinoflagellate Oxyrrhis marina, isolated >20 years ago, showed inconsistent responses to copepodamides, except for an average 6% increase in its total ingestion over 24 h. Our results demonstrate that the predation risk by copepods affects the diel feeding rhythm of marine protists and suggests a species-specific response to predation threats.
|
|
| 5. |
- Arnoldt, Sina, et al.
(författare)
-
Mass spectroscopy reveals compositional differences in copepodamides from limnic and marine copepods
- 2024
-
Ingår i: Scientific reports. - 2045-2322. ; 14
-
Tidskriftsartikel (refereegranskat)abstract
- Marine copepods, the most abundant animals in the global ocean, imprint their surrounding waters with chemical cues, called copepodamides. Copepodamides induce defensive traits such as toxin production, bioluminescence, and colony size plasticity in a variety of marine phytoplankton. The role of copepodamides in freshwater ecosystems is, however, unknown. Here we report the consistent presence of copepodamides in copepods from six Swedish freshwater lakes. Copepodamide concentrations in freshwater copepods are similar to those of marine copepods, around 0.1ppt of dry mass in millimetre sized individuals. The composition substantially overlaps with marine copepodamides but is also distinctly different. Marine copepods commonly contain both subgroups of copepodamides, the copepodamides (CA) and the dihydro-copepodamides (dhCA), whereas freshwater copepods are dominated by the dhCAs. Taxonomic groups had consistent copepodamide profiles across sampling sites and timepoints, supporting the presence of species-specific copepodamide signatures. We describe 10 new copepodamide structures, four of which were found exclusively in freshwater copepods. The presence of copepodamides in limnic copepods also warrants studies into their potential function as predator alarm cues in freshwater systems.
|
|
| 6. |
- Axner, Torbjörn, 1954-
(författare)
-
Ordo Missæ : Missalen och missaletillägg i Svenska kyrkan 1942-1967
- 2014
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Axner, Torbjörn, Ordo Missæ. Missal supplements in Church of Sweden 1942–1967This work is a study of a certain aspect of the liturgical movement in the Church of Sweden during the years 1942–1967. In 1942 a new Book of Order was published to some extent influenced by the international liturgical movement. However, for some liturgical activists this was not enough. Due to the legal structure of the Church of Sweden they were bound to the Book of Order and could not shape the liturgy according to their liturgical ideas. They chose to work under cover, publishing their own editions of the official Order of Mass supplied with material from the international liturgical movement. In the Swedish Lutheran tradition, missals have very few rubrics and liturgical instructions. These unofficial missals looked like the official and followed the official order of mass, but added complimentary prayers and instructions. The liturgical activists were accused of introducing traditions, that were alien to the tradition of the Church of Sweden. Nevertheless, some of the material introduced in the unofficial missals in the 1940’s and 1950’s, some decades later became parts of the new official Book of Order of 1986. During the period, 1942–1967, the liturgical movement in Sweden was more or less the same as the association “Church Renewal” (Kyrklig förnyelse), a high-church organisation with international inspiration and connections.Towards the end of this period of time new ideas were developing in all areas of society, including mainstream churches. In 1968 an official committee was appointed to conduct a revision of the Book of Order for the Church of Sweden. The committee introduced a period of official liturgical experiments within Church of Sweden. Some of the formerly rejected liturgical ideas were now tried out in the liturgical experiments and became part of the new Book of Order.This study focuses on liturgical elements inspired by the international liturgical movement and how they influenced the liturgical development in the Church of Sweden. The author combines traditional text sources with studies of artwork in the missals and a liturgical database, based on a survey done on liturgical behaviour in 1965.
|
|
| 7. |
- Bachimanchi, Harshith, et al.
(författare)
-
Deep-learning-powered data analysis in plankton ecology
- 2024
-
Ingår i: Limnology And Oceanography Letters. - 2378-2242.
-
Forskningsöversikt (refereegranskat)abstract
- The implementation of deep learning algorithms has brought new perspectives to plankton ecology. Emerging as an alternative approach to established methods, deep learning offers objective schemes to investigate plankton organisms in diverse environments. We provide an overview of deep-learning-based methods including detection and classification of phytoplankton and zooplankton images, foraging and swimming behavior analysis, and finally ecological modeling. Deep learning has the potential to speed up the analysis and reduce the human experimental bias, thus enabling data acquisition at relevant temporal and spatial scales with improved reproducibility. We also discuss shortcomings and show how deep learning architectures have evolved to mitigate imprecise readouts. Finally, we suggest opportunities where deep learning is particularly likely to catalyze plankton research. The examples are accompanied by detailed tutorials and code samples that allow readers to apply the methods described in this review to their own data.
|
|
| 8. |
- Bachimanchi, Harshith, et al.
(författare)
-
Microplankton life histories revealed by holographic microscopy and deep learning
- 2022
-
Ingår i: eLife. - 2050-084X. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- The marine microbial food web plays a central role in the global carbon cycle. However, our mechanistic understanding of the ocean is biased toward its larger constituents, while rates and biomass fluxes in the microbial food web are mainly inferred from indirect measurements and ensemble averages. Yet, resolution at the level of the individual microplankton is required to advance our understanding of the microbial food web. Here, we demonstrate that, by combining holographic microscopy with deep learning, we can follow microplanktons throughout their lifespan, continuously measuring their three-dimensional position and dry mass. The deep-learning algorithms circumvent the computationally intensive processing of holographic data and allow rapid measurements over extended time periods. This permits us to reliably estimate growth rates, both in terms of dry mass increase and cell divisions, as well as to measure trophic interactions between species such as predation events. The individual resolution provides information about selectivity, individual feeding rates, and handling times for individual microplanktons. The method is particularly useful to detail the rates and routes of organic matter transfer in micro-zooplankton, the most important and least known group of primary consumers in the oceans. Studying individual interactions in idealized small systems provides insights that help us understand microbial food webs and ultimately larger-scale processes. We exemplify this by detailed descriptions of micro-zooplankton feeding events, cell divisions, and long-term monitoring of single cells from division to division.
|
|
| 9. |
- Bergkvist, Johanna, 1980, et al.
(författare)
-
Grazer-induced chain length plasticity reduces grazing risk in a marine diatom
- 2012
-
Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590. ; 57:1, s. 318-324
-
Tidskriftsartikel (refereegranskat)abstract
- We show that Skeletonema marinoi suppresses chain formation in response to copepod cues. The presence of three different copepod species (Acartia tonsa, Centropages hamatus, or Temora longicornis) significantly reduced chain length. Furthermore, chain length was significantly reduced when S. marinoi was exposed to chemical cues from caged A. tonsa without physical contact with the responding cells. The reductions in chain length significantly reduced copepod grazing; grazing rates on chains (four cells or more) were several times higher compared to that of single cells. This suggests that chain length plasticity is a means for S. marinoi to reduce copepod grazing. In contrast, chain length was not suppressed in cultures exposed to the microzooplankton grazer Gyrodinium dominans. Size-selective predation may have played a key role in the evolution of chain formation and chain length plasticity in diatoms.
|
|
| 10. |
- Bergkvist, Johanna, 1980, et al.
(författare)
-
Induction of toxin production in dinoflagellates: the grazer makes a difference
- 2008
-
Ingår i: Oecologia. - : Springer Science and Business Media LLC. - 0029-8549 .- 1432-1939. ; 156:1, s. 147-154
-
Tidskriftsartikel (refereegranskat)abstract
- The dinoflagellate Alexandrium minutum has previously been shown to produce paralytic shellfish toxins (PST) in response to waterborne cues from the copepod Acartia tonsa. In order to investigate if grazer-induced toxin production is a general or grazer-specific response of A. minutum to calanoid copepods, we exposed two strains of A. minutum to waterborne cues from three other species of calanoid copepods, Acartia clausi, Centropages typicus and Pseudocalanus sp. Both A. minutum strains responded to waterborne cues from Centropages and Acartia with significantly increased cell-specific toxicity. Waterborne cues from Centropages caused the strongest response in the A. minutum cells, with 5 to > 20 times higher toxin concentrations compared to controls. In contrast, neither of the A. minutum strains responded with significantly increased toxicity to waterborne cues from Pseudocalanus. The absolute increase in PST content was proportional to the intrinsic toxicity of the different A. minutum strains that were used. The results show that grazer-induced PST production is a grazer-specific response in A. minutum, and its potential ecological importance will thus depend on the composition of the zooplankton community, as well as the intrinsic toxin-producing properties of the A. minutum population.
|
|
