| 1. |
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| 2. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Mycobiome diversity: high-throughput sequencing and identification of fungi.
- 2019
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Ingår i: Nature reviews. Microbiology. - : Springer Science and Business Media LLC. - 1740-1534 .- 1740-1526. ; 17, s. 95-109
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Forskningsöversikt (refereegranskat)abstract
- Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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| 3. |
- Sanli, Kemal, et al.
(författare)
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Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities
- 2015
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 6:1192
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Tidskriftsartikel (refereegranskat)abstract
- Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.
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| 4. |
- Liu, Yuanhua, 1971, et al.
(författare)
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Considering the importance of user profiles in interface design
- 2009
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Ingår i: User Interfaces. ; , s. 23-
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- User profile is a popular term widely employed during product design processes by industrial companies. Such a profile is normally intended to represent real users of a product. The ultimate purpose of a user profile is actually to help designers to recognize or learn about the real user by presenting them with a description of a real user’s attributes, for instance; the user’s gender, age, educational level, attitude, technical needs and skill level. The aim of this chapter is to provide information on the current knowledge and research about user profile issues, as well as to emphasize the importance of considering these issues in interface design. In this chapter, we mainly focus on how users’ difference in expertise affects their performance or activity in various interaction contexts. Considering the complex interaction situations in practice, novice and expert users’ interactions with medical user interfaces of different technical complexity will be analyzed as examples: one focuses on novice and expert users’ difference when interacting with simple medical interfaces, and the other focuses on differences when interacting with complex medical interfaces. Four issues will be analyzed and discussed: (1) how novice and expert users differ in terms of performance during the interaction; (2) how novice and expert users differ in the perspective of cognitive mental models during the interaction; (3) how novice and expert users should be defined in practice; and (4) what are the main differences between novice and expert users’ implications for interface design. Besides describing the effect of users’ expertise difference during the interface design process, we will also pinpoint some potential problems for the research on interface design, as well as some future challenges that academic researchers and industrial engineers should face in practice.
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| 5. |
- Abarenkov, Kessy, et al.
(författare)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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| 6. |
- Abarenkov, Kessy, et al.
(författare)
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Protax-fungi: A web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences
- 2018
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 220:2, s. 517-525
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Tidskriftsartikel (refereegranskat)abstract
- © 2018 New Phytologist Trust. Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed Protax-fungi, a general tool for taxonomic placement of fungal internal transcribed spacer (ITS) sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. With empirical data on root- and wood-associated fungi, Protax-fungi reliably identified (with at least 90% identification probability) the majority of sequences to the order level but only around one-fifth of them to the species level, reflecting the current limited coverage of the databases. Protax-fungi outperformed the Sintax and Rdb classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. We applied Protax-fungi to examine the internal consistencies of the Index Fungorum and UNITE databases. This revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. Protax-fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships.
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| 7. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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| 8. |
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| 9. |
- Jayasiri, Subashini C., et al.
(författare)
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The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts
- 2015
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Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 74:1, s. 3-18
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Tidskriftsartikel (refereegranskat)abstract
- Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.
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| 10. |
- Buckland, Philip I., 1973-, et al.
(författare)
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BugsCEP, an entomological database twenty-five years on
- 2014
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Ingår i: Antenna (Journal of the Royal Entomological Society). - London : Royal Entomological Society of London. - 0140-1890. ; 38:1, s. 21-28
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Tidskriftsartikel (refereegranskat)
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| 11. |
- Tedersoo, Leho, et al.
(författare)
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Response to Comment on “Global diversity and geography of soil fungi”
- 2015
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 349:6251
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Schadt and Rosling (Technical Comment, 26 June 2015, p. 1438) argue that primer-template mismatches neglected the fungal class Archaeorhizomycetes in a global soil survey. Amplicon-based metabarcoding of nine barcode-primer pair combinations and polymerase chain reaction (PCR)–free shotgun metagenomics revealed that barcode and primer choice and PCR bias drive the diversity and composition of microorganisms in general, but the Archaeorhizomycetes were little affected in the global study. We urge that careful choice of DNA markers and primers is essential for ecological studies using high-throughput sequencing for identification.
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| 12. |
- Wurzbacher, Christian, 1980, et al.
(författare)
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Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.
- 2017
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Ingår i: The ISME journal. - : Springer Science and Business Media LLC. - 1751-7370 .- 1751-7362. ; 11:8, s. 1938-1941
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Tidskriftsartikel (refereegranskat)abstract
- In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.
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| 13. |
- Buckland, Philip I., 1973-, et al.
(författare)
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The Strategic Environmental Archaeology Database : a resource for international, multiproxy and transdisciplinary studies of environmental and climatic change
- 2015
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Konferensbidrag (refereegranskat)abstract
- Climate and environmental change are global challenges which require global data and infrastructure to investigate. These challenges also require a multi-proxy approach, integrating evidence from Quaternary science and archaeology with information from studies on modern ecology and physical processes among other disciplines. The Strategic Environmental Archaeology Database (SEAD http://www.sead.se) is a Swedish based international research e-infrastructure for storing, managing, analysing and disseminating palaeoenvironmental data from an almost unlimited number of analysis methods. The system currently makes available raw data from over 1500 sites (>5300 datasets) and the analysis of Quaternary fossil insects, plant macrofossils, pollen, geochemistry and sediment physical properties, dendrochronology and wood anatomy, ceramic geochemistry and bones, along with numerous dating methods. This capacity will be expanded in the near future to include isotopes, multi-spectral and archaeo-metalurgical data. SEAD also includes expandable climate and environment calibration datasets, a complete bibliography and extensive metadata and services for linking these data to other resources. All data is available as Open Access through http://qsead.sead.se and downloadable software. SEAD is maintained and managed at the Environmental Archaeology Lab and HUMlab at Umea University, Sweden. Development and data ingestion is progressing in cooperation with The Laboratory for Ceramic Research and the National Laboratory for Wood Anatomy and Dendrochronology at Lund University, Sweden, the Archaeological Research Laboratory, Stockholm University, the Geoarchaeological Laboratory, Swedish National Historical Museums Agency and several international partners and research projects. Current plans include expanding its capacity to serve as a data source for any system and integration with the Swedish National Heritage Board's information systems. SEAD is partnered with the Neotoma palaeoecology database (http://www.neotomadb.org) and a new initiative for building cyberinfrastructure for transdisciplinary research and visualization of the long-term human ecodynamics of the North Atlantic funded by the National Science Foundation (NSF).
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| 14. |
- Hartmann, Martin, et al.
(författare)
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Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests
- 2012
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 6:12, s. 2199-2218
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Tidskriftsartikel (refereegranskat)abstract
- Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting.
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| 15. |
- Tedersoo, Leho, et al.
(författare)
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Standardizing metadata and taxonomic identification in metabarcoding studies
- 2015
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Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X .- 2047-217X. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers reanalysis and comparisons among studies. Here we propose an automated workflow covering data submission, compression, storage and public access to allow easy data retrieval and inter-study communication. Such standardized and readily accessible datasets facilitate data management, taxonomic comparisons and compilation of global metastudies.
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| 16. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.
- 2019
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Ingår i: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 47:D1
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Tidskriftsartikel (refereegranskat)abstract
- UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer(ITS) region-and offers all ∼1 000000 public fungal ITS sequences for reference. These are clustered into ∼459000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.
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| 17. |
- Schoch, Conrad L., et al.
(författare)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 18. |
- Mamontov, Eugen, 1955
(författare)
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Ordinary differential equation system for population of individuals and the corresponding probabilistic model
- 2008
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Ingår i: Mathl. Computer Modelling. - : Elsevier BV. - 0895-7177.
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Tidskriftsartikel (refereegranskat)abstract
- The key model for particle populations in statistical mechanics is the Bogolyubov–Born– Green–Kirkwood–Yvon (BBGKY) equation chain. It is derived mainly from the Hamilton ordinary differential equation (ODE) system for the vectors of the particle states in the particle position-momentum phase space. Many problems beyond physics or chemistry, for instance, in the living-matter sciences (biology, medicine, ecology, and scoiology) make it necessary to extend the notion of a particle to an individual, or active particle. This challenge is met by the generalized kinetic theory. It implements the extension by extending the phase space from the space of the position-momentum vectors to more rich spaces formed by the state vectors with the entries which need not be limited to the entries of the position and momentum: they include other scalar variables (e.g., those associated with modelling homeorhesis or other features inherent to the individuals). One can assume that the dynamics of the state vector in the extended space, i.e. the states of the individuals (rather than common particles) is also described by an ODE system. The latter, however, need not be the Hamilton one. The question is how one can derive the analogue of the BBGKY paradigm for the new settings. The present work proposes an answer to this question. It applies a very limited number of carefully selected tools of probability theory and common statistical mechanics. It in particular uses the well-known feature that the maximum number of the individuals which can mutually interact simultaneously is bounded by a fixed value of a few units. The present approach results in the finite system of equations for the reduced many-individual distribution functions thereby eliminating the so-called closure problem inevitable in the BBGKY theory. The thermodynamic-limit assumption is not needed either. The system includes consistently derived terms of all of the basic types known in kinetic theory, in particular, both the “mean-field” and scattering-integral terms, and admits the kinetic equation of the form allowing a direct chemical-reaction reading. The present approach can deal with Hamilton’s equation systems which are nonmonogenic and not treated in statistical mechanics. The proposed modelling suggests the basis of the generalized kinetic theory and may serve as the stochastic mechanics of population of individuals.
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| 19. |
- Checinska, Aleksandra, et al.
(författare)
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Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities
- 2015
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Background - The International Space Station (ISS) is a unique built environment due to the effects of microgravity, space radiation, elevated carbon dioxide levels, and especially continuous human habitation. Understanding the composition of the ISS microbial community will facilitate further development of safety and maintenance practices. The primary goal of this study was to characterize the viable microbiome of the ISS-built environment. A second objective was to determine if the built environments of Earth-based cleanrooms associated with space exploration are an appropriate model of the ISS environment. Results - Samples collected from the ISS and two cleanrooms at the Jet Propulsion Laboratory (JPL, Pasadena, CA) were analyzed by traditional cultivation, adenosine triphosphate (ATP), and propidium monoazide–quantitative polymerase chain reaction (PMA-qPCR) assays to estimate viable microbial populations. The 16S rRNA gene Illumina iTag sequencing was used to elucidate microbial diversity and explore differences between ISS and cleanroom microbiomes. Statistical analyses showed that members of the phyla Actinobacteria, Firmicutes, and Proteobacteria were dominant in the samples examined but varied in abundance. Actinobacteria were predominant in the ISS samples whereas Proteobacteria, least abundant in the ISS, dominated in the cleanroom samples. The viable bacterial populations seen by PMA treatment were greatly decreased. However, the treatment did not appear to have an effect on the bacterial composition (diversity) associated with each sampling site. Conclusions - The results of this study provide strong evidence that specific human skin-associated microorganisms make a substantial contribution to the ISS microbiome, which is not the case in Earth-based cleanrooms. For example, Corynebacterium and Propionibacterium (Actinobacteria) but not Staphylococcus (Firmicutes) species are dominant on the ISS in terms of viable and total bacterial community composition. The results obtained will facilitate future studies to determine how stable the ISS environment is over time. The present results also demonstrate the value of measuring viable cell diversity and population size at any sampling site. This information can be used to identify sites that can be targeted for more stringent cleaning. Finally, the results will allow comparisons with other built sites and facilitate future improvements on the ISS that will ensure astronaut health.
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| 20. |
- Hamon, Thierry, et al.
(författare)
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Combining Compositionality and Pagerank for the Identification of Semantic Relations between Biomedical Words
- 2012
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Ingår i: BioNLP. - 9781937284206 - 1937284204 ; , s. 109-117
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Konferensbidrag (refereegranskat)abstract
- The acquisition of semantic resources and relations is an important task for several applications, such as query expansion, information retrieval and extraction, machine translation. However, their validity should also be computed and indicated, especially for automatic systems and applications. We exploit the compositionality based methods for the acquisition of synonymy relations and of indicators of these synonyms. We then apply pagerank-derived algorithm to the obtained semantic graph in order to filter out the acquired synonyms. Evaluation performed with two independent experts indicates that the quality of synonyms is systematically improved by 10 to 15% after their filtering.
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| 21. |
- Tedersoo, Leho, et al.
(författare)
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Novel soil-inhabiting clades fill gaps in the fungal tree of life
- 2017
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Background - Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. Results - We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH. Conclusions - This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.
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| 22. |
- Kerren, Andreas, 1971-, et al.
(författare)
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Why Integrate InfoVis and SciVis? : An Example from Systems Biology
- 2014
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Ingår i: IEEE Computer Graphics and Applications. - : IEEE. - 0272-1716 .- 1558-1756. ; 34:6, s. 69-73
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The more-or-less artificial barrier between information visualization and scientific visualization hinders knowledge discovery. Having an integrated view of many aspects of the target data, including a seamlessly interwoven visual display of structural abstract data and 3D spatial information, could lead to new discoveries, insights, and scientific questions. Such a view also could reduce the user’s cognitive load—that is, reduce the effort the user expends when comparing views.
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| 23. |
- Hibbett, David, et al.
(författare)
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Sequence-based classification and identification of Fungi
- 2016
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Ingår i: Mycologia. - 0027-5514. ; 108:6, s. 1049-1068
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Forskningsöversikt (refereegranskat)abstract
- Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable valid publication of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.
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| 24. |
- Robinson, Jonathan, 1986, et al.
(författare)
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An atlas of human metabolism
- 2020
-
Ingår i: Science Signaling. - : American Association for the Advancement of Science (AAAS). - 1945-0877 .- 1937-9145. ; 13:624
-
Tidskriftsartikel (refereegranskat)abstract
- Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. Researchers have developed increasingly comprehensive human GEMs, but the disconnect among different model sources and versions impedes further progress. We therefore integrated and extensively curated the most recent human metabolic models to construct a consensus GEM, Human1. We demonstrated the versatility of Human1 through the generation and analysis of cell- and tissue-specific models using transcriptomic, proteomic, and kinetic data. We also present an accompanying web portal, Metabolic Atlas (https://www.metabolicatlas.org/), which facilitates further exploration and visualization of Human1 content. Human1 was created using a version-controlled, open-source model development framework to enable community-driven curation and refinement. This framework allows Human1 to be an evolving shared resource for future studies of human health and disease.
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| 25. |
- Fu, Keren, et al.
(författare)
-
Deepside: A general deep framework for salient object detection
- 2019
-
Ingår i: Neurocomputing. - : Elsevier BV. - 0925-2312 .- 1872-8286. ; 356, s. 69-82
-
Tidskriftsartikel (refereegranskat)abstract
- Deep learning-based salient object detection techniques have shown impressive results compared to con- ventional saliency detection by handcrafted features. Integrating hierarchical features of Convolutional Neural Networks (CNN) to achieve fine-grained saliency detection is a current trend, and various deep architectures are proposed by researchers, including “skip-layer” architecture, “top-down” architecture, “short-connection” architecture and so on. While these architectures have achieved progressive improve- ment on detection accuracy, it is still unclear about the underlying distinctions and connections between these schemes. In this paper, we review and draw underlying connections between these architectures, and show that they actually could be unified into a general framework, which simply just has side struc- tures with different depths. Based on the idea of designing deeper side structures for better detection accuracy, we propose a unified framework called Deepside that can be deeply supervised to incorporate hierarchical CNN features. Additionally, to fuse multiple side outputs from the network, we propose a novel fusion technique based on segmentation-based pooling, which severs as a built-in component in the CNN architecture and guarantees more accurate boundary details of detected salient objects. The effectiveness of the proposed Deepside scheme against state-of-the-art models is validated on 8 benchmark datasets.
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| 26. |
- Strannegård, Claes, 1962, et al.
(författare)
-
Ecosystem Models Based on Artificial Intelligence
- 2022
-
Ingår i: 34th Workshop of the Swedish Artificial Intelligence Society, SAIS 2022. - : IEEE.
-
Konferensbidrag (refereegranskat)abstract
- Ecosystem models can be used for understanding general phenomena of evolution, ecology, and ethology. They can also be used for analyzing and predicting the ecological consequences of human activities on specific ecosystems, e.g., the effects of agriculture, forestry, construction, hunting, and fishing. We argue that powerful ecosystem models need to include reasonable models of the physical environment and of animal behavior. We also argue that several well-known ecosystem models are unsatisfactory in this regard. Then we present the open-source ecosystem simulator Ecotwin, which is built on top of the game engine Unity. To model a specific ecosystem in Ecotwin, we first generate a 3D Unity model of the physical environment, based on topographic or bathymetric data. Then we insert digital 3D models of the organisms of interest into the environment model. Each organism is equipped with a genome and capable of sexual or asexual reproduction. An organism dies if it runs out of some vital resource or reaches its maximum age. The animal models are equipped with behavioral models that include sensors, actions, reward signals, and mechanisms of learning and decision-making. Finally, we illustrate how Ecotwin works by building and running one terrestrial and one marine ecosystem model.
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| 27. |
- Retter, Alice, et al.
(författare)
-
Exploring the taxonomic composition of two fungal communities on the Swedish west coast through metabarcoding
- 2019
-
Ingår i: Biodiversity Data Journal. - 1314-2828 .- 1314-2836. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- Background Fungi are heterotrophic, unicellular or filamentous organisms that exhibit a wide range of different lifestyles as, e.g., symbionts, parasites, and saprotrophs. Mycologists have traditionally considered fungi to be a nearly exclusively terrestrial group of organisms, but it is now known that fungi have a significant presence in aquatic environments as well. We know little about most fungi in limnic and marine systems, including aspects of their taxonomy, ecology, and geographic distribution. The present study seeks to improve our knowledge of fungi in the marine environment. The fungal communities of two coastal marine environments of the Kattegat sea, Sweden, were explored with metabarcoding techniques using the nuclear ribosomal internal transcribed spacer 2 (ITS2) metabarcode. Our data add new information to the current picture of fungal community composition in benthic and coastal habitats in Northern Europe. New information The dataset describes the number of operational taxonomic units (OTUs) and their taxonomic affiliations in two littoral gradients sampled on the Swedish west coast, Gothenburg municipality. Our data include basic diversity indices as well as chemical and edaphic sediment/soil parameters of the sampling sites. From the sites, 3470 and 4315 fungal OTUs, respectively, were recovered. The number of reads were 673,711 and 779,899, respectively, after quality filtering. Within the benthic sites, more than 80% of the sequences could not be classified taxonomically. The phylum composition of the classifiable sequences was dominated in both localities by Dikarya, which made up around 33% of the OTUs. Within Dikarya, Ascomycota was the dominant phylum. Guild assignment failed for more than half of the classifiable OTUs, with undefined saprotrophs being the most common resolved guild. This guild classification was slightly more common in the ocean sediment samples than in the terrestrial ones. Our metadata indicated that ocean sites contain organisms at a lower trophic level and that there are predominantly endophytic, parasitic, and pathogenic fungi in the marine environments. This hints at the presence of interesting and currently poorly understood fungus-driven ecological processes. It is also clear from our results that a very large number of marine fungi are in urgent need of taxonomic study and formal description.
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| 28. |
- Bresin, Roberto, et al.
(författare)
-
Auditory feedback through continuous control of crumpling sound synthesis
- 2008
-
Ingår i: Proceedings of Sonic Interaction Design. - : IUAV University of Venice. - 9788890341304 ; , s. 23-28
-
Konferensbidrag (refereegranskat)abstract
- A realtime model for the synthesis of crumpling sounds ispresented. By capturing the statistics of short sonic transients which give rise to crackling noise, it allows for a consistent description of a broad spectrum of audible physical processes which emerge in several everyday interaction contexts.The model drives a nonlinear impactor that sonifies every transient, and it can be parameterized depending on the physical attributes of the crumpling material. Three different scenarios are described, respectively simulating the foot interaction with aggregate ground materials, augmenting a dining scenario, and affecting the emotional content of a footstep sequence. Taken altogether, they emphasize the potential generalizability of the model to situations in which a precise control of auditory feedback can significantly increase the enactivity and ecological validity of an interface.
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| 29. |
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| 30. |
- Visell, Y., et al.
(författare)
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Sound design and perception in walking interactions
- 2009
-
Ingår i: International journal of human-computer studies. - : Elsevier BV. - 1071-5819 .- 1095-9300. ; 67:11, s. 947-959
-
Tidskriftsartikel (refereegranskat)abstract
- This paper reviews the state of the art in the display and perception of walking generated sounds and tactile vibrations, and their current and potential future uses in interactive systems. As non-visual information sources that are closely linked to human activities in diverse environments, such signals are capable of communicating about the spaces we traverse and activities we encounter in familial and intuitive ways However, in order for them to be effectively employed in human-computer interfaces, significant knowledge is required in areas including the perception of acoustic signatures of walking, and the design, engineering, and evaluation of interfaces that utilize them. Much of this expertise has accumulated in recent years, although many questions remain to be explored We highlight past work and current research directions in this Multidisciplinary area of investigation, and point to potential future trends.
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| 31. |
- Daoud, Adel, 1981, et al.
(författare)
-
Using Satellite Images and Deep Learning to Measure Health and Living Standards in India
- 2023
-
Ingår i: Social Indicators Research. - : SPRINGER. - 0303-8300 .- 1573-0921. ; 167:1-3, s. 475-505
-
Tidskriftsartikel (refereegranskat)abstract
- Using deep learning with satellite images enhances our understanding of human development at a granular spatial and temporal level. Most studies have focused on Africa and on a narrow set of asset-based indicators. This article leverages georeferenced village-level census data from across 40% of the population of India to train deep models that predicts 16 indicators of human well-being from Landsat 7 imagery. Based on the principles of transfer learning, the census-based model is used as a feature extractor to train another model that predicts an even larger set of developmental variables—over 90 variables—included in two rounds of the National Family Health Survey (NFHS). The census-based-feature-extractor model outperforms the current standard in the literature for most of these NFHS variables. Overall, the results show that combining satellite data with Indian Census data unlocks rich information for training deep models that track human development at an unprecedented geographical and temporal resolution.
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| 32. |
- Zanne, Amy E, et al.
(författare)
-
Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.
- 2020
-
Ingår i: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433
-
Tidskriftsartikel (refereegranskat)abstract
- Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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| 33. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
-
A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts
- 2015
-
Ingår i: Microbes and Environments. - 1342-6311 .- 1347-4405. ; 30:2, s. 145-150
-
Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.
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| 34. |
- Kerren, Andreas, 1971-, et al.
(författare)
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Network Visualization for Integrative Bioinformatics
- 2014
-
Ingår i: Approaches in Integrative Bioinformatics. - Berlin Heidelberg : Springer. - 9783642412806 - 9783642412813 ; , s. 173-202
-
Bokkapitel (refereegranskat)abstract
- Approaches to investigate biological processes have been of strong interest in the past few years and are the focus of several research areas like systems biology. Biological networks as representations of such processes are crucial for an extensive understanding of living beings. Due to their size and complexity, their growth and continuous change, as well as their compilation from databases on demand, researchers very often request novel network visualization, interaction and exploration techniques. In this chapter, we first provide background information that is needed for the interactive visual analysis of various biological networks. Fields such as (information) visualization, visual analytics and automatic layout of networks are highlighted and illustrated by a number of examples. Then, the state of the art in network visualization for the life sciences is presented together with a discussion of standards for the graphical representation of cellular networks and biological processes.
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| 35. |
- Gerken, Jan, 1991, et al.
(författare)
-
Equivariance versus augmentation for spherical images
- 2022
-
Ingår i: Proceedings of Machine Learning Resaerch. ; , s. 7404-7421
-
Konferensbidrag (refereegranskat)abstract
- We analyze the role of rotational equivariance in convolutional neural networks (CNNs) applied to spherical images. We compare the performance of the group equivariant networks known as S2CNNs and standard non-equivariant CNNs trained with an increasing amount of data augmentation. The chosen architectures can be considered baseline references for the respective design paradigms. Our models are trained and evaluated on single or multiple items from the MNIST- or FashionMNIST dataset projected onto the sphere. For the task of image classification, which is inherently rotationally invariant, we find that by considerably increasing the amount of data augmentation and the size of the networks, it is possible for the standard CNNs to reach at least the same performance as the equivariant network. In contrast, for the inherently equivariant task of semantic segmentation, the non-equivariant networks are consistently outperformed by the equivariant networks with significantly fewer parameters. We also analyze and compare the inference latency and training times of the different networks, enabling detailed tradeoff considerations between equivariant architectures and data augmentation for practical problems.
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| 36. |
- Nilsson, R. Henrik, 1976
(författare)
-
Unifying fungi
- 2015
-
Ingår i: Science & Technology. - 2049-2391 .- 2049-2405. ; :14, s. 204-206
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 37. |
- Uhen, Mark D., et al.
(författare)
-
The EarthLife Consortium API: an extensible, open-source service foraccessing fossil data and taxonomies from multiple communitypaleodata resources
- 2021
-
Ingår i: Frontiers of Biogeography. - : International Biogeography Society. ; 13:2
-
Tidskriftsartikel (refereegranskat)abstract
- Paleobiologists and paleoecologists interested in studying biodiversity dynamics over broadspatial and temporal scales have built multiple community-curated data resources, eachemphasizing a particular spatial domain, timescale, or taxonomic group(s). This multiplicity ofdata resources is understandable, given the enormous diversity of life across Earth's history,but creates a barrier to achieving a truly global understanding of the diversity and distributionof life across time. Here we present the Earth Life Consortium Application ProgrammingInterface (ELC API), a lightweight data service designed to search and retrieve fossil occurrenceand taxonomic information from across multiple paleobiological resources. Key endpointsinclude Occurrences (returns spatiotemporal locations of fossils for selected taxa), Locales(returns information about sites with fossil data), References (returns bibliographicinformation), and Taxonomy (returns names of subtaxa associated with selected taxa). Dataobjects are returned as JSON or CSV format. The ELC API supports tectonic-driven shifts ingeographic position back to 580 Ma using services from Macrostrat and GPlates. The ELC APIhas been implemented first for the Paleobiology Database and Neotoma PaleoecologyDatabase, with a test extension to the Strategic Environmental Archaeology Database. The ELCAPI is designed to be readily extensible to other paleobiological data resources, with allendpoints fully documented and following open-source standards (e.g., Swagger, OGC). Thebroader goal is to help build an interlinked and federated ecosystem of paleobiological andpaleoenvironmental data resources, which together provide paleobiologists, macroecologists,biogeographers, and other interested scientists with full coverage of the diversity anddistribution of life across time.
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| 38. |
- Klingström, Tomas, et al.
(författare)
-
Supporting the Development of Biobanks in Low and Medium Income Countries
- 2016
-
Ingår i: 2016 IST-AFRICA WEEK CONFERENCE. - 9781905824557
-
Konferensbidrag (refereegranskat)abstract
- Biobanks are an organized collection of biological material and associated data. They are a fundamental resource for life science research and contribute to the development of pharmaceutical drugs, diagnostic markers and to a deeper understanding of the genetics that regulate the development of all life on earth. Biobanks are well established in High Income Countries (HIC) and are rapidly emerging in Low and Middle Income Countries (LMIC). Surveys among biobanks operating in a LMIC setting indicate that limited resources and short term funding tied to specific projects threaten the sustainability of the biobanks. Fit-for-purpose biobanks targeting major societal challenges such as HIV and Malaria provide an excellent basis for integrating biobanks with the available research communities in LMIC regions. But to become sustainable for the future it is important that biobanks become an integrated part of local research communities. To achieve this, the cost of operating biobanks must be lowered, templates must be developed to support local ethics committees and researchers must be given the opportunity to build experience in successfully operating biobank based research projects. The B3Africa consortium is based on these conclusions and set up to support biobank based research by creating a cost efficient Laboratory Information Management System (LIMS) for developing biobanks and also contribute to the training and capacity building in the local research community. The technical platform called the eB3Kit is open source and consists of a LIMS and a bioinformatics module based on the eBiokit that allow researchers to take control over the analysis of their own data. Along with the technical platform the consortium will also contribute training and support for the associated infrastructures necessary to regulate the ethical and legal implications of biobank based research.
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| 39. |
-
- 2019
-
Tidskriftsartikel (refereegranskat)
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| 40. |
- Younes, Sara
(författare)
-
Uncovering biomarkers and molecular heterogeneity of complex diseases : Utilizing the power of Data Science
- 2021
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Uncovering causal drivers of complex diseases is yet a difficult challenge. Unlike single-gene disorders complex diseases are heterogeneous and are caused by a combination of genetic, environmental, and lifestyle factors which complicates the identification of patient subgroups and the disease causal drivers. In order to study the dimensions of complex diseases analyzing different omics data is a necessity.The main goal of this thesis is to provide computational approaches for analyzing omics data of two complex diseases; mainly, Acute Myeloid Leukaemia (AML) and Systemic Lupus Erythematosus (SLE). Additionally, we aim at providing a method that would deal with integration issues that usually arise when combining complex diseases omics (specifically metabolomics) data from multiple data sources. AML is a cancer of the myeloid blood cells that is known for its heterogeneity. Patients usually respond to treatment and achieve a complete remission state. However, a majority of patients relapse or develop treatment resistance. In paper I, we focus on investigating recurrent genomic alterations in adult and pediatric relapsed and primary resistant AML that may explain disease progression. In paper II, we characterize changes in the transcriptome of AML over the course of the disease, incorporating machine learning analysis.SLE is a heterogeneous autoimmune disease characterized by unpredictable periods of flares. The flares are presented as different SLE disease activities (DA). Studies on the combinatorial effects of genes towards the manifestation of SLE DAs in patients’ subgroups have been limited. In paper III, we analyze gene expression data of pediatric SLE using interpretable machine learning. The aim was to study the co-predictive transcriptomic factors driving disease progression, discover the disease subtypes, and explore the relationship between transcriptomics factors and the phenotypes associated with the discovered subtypes.Recently, Metabolomics has been a crucial dimension in major multi-omics complex disease studies. Small-compound databases contain a large amount of information for metabolites. However, the existing redundancy of information in the databases leads to major standardization issues. In paper IV, we aim at resolving the inconsistencies that exist when linking and combining metabolomics data from several databases by introducing the new R package MetaFetcheR.
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| 41. |
- Munappy, Aiswarya Raj, 1990, et al.
(författare)
-
On the Trade-off Between Robustness and Complexity in Data Pipelines
- 2021
-
Ingår i: Quality of Information and Communications Technology. - Cham : Springer. - 9783030853464 - 9783030853471 ; 1439 CCIS, s. 401-415
-
Konferensbidrag (refereegranskat)abstract
- Data pipelines play an important role throughout the data management process whether these are used for data analytics or machine learning. Data-driven organizations can make use of data pipelines for producing good quality data applications. Moreover, data pipelines ensure end-to-end velocity by automating the processes involved in extracting, transforming, combining, validating, and loading data for further analysis and visualization. However, the robustness of data pipelines is equally important since unhealthy data pipelines can add more noise to the input data. This paper identifies the essential elements for a robust data pipeline and analyses the trade-off between data pipeline robustness and complexity.
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| 42. |
- de Dios, Eddie, et al.
(författare)
-
Introduction to Deep Learning in Clinical Neuroscience
- 2022
-
Ingår i: Acta Neurochirurgica, Supplement. - Cham : Springer International Publishing. - 2197-8395 .- 0065-1419. ; 134, s. 79-89
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- The use of deep learning (DL) is rapidly increasing in clinical neuroscience. The term denotes models with multiple sequential layers of learning algorithms, architecturally similar to neural networks of the brain. We provide examples of DL in analyzing MRI data and discuss potential applications and methodological caveats. Important aspects are data pre-processing, volumetric segmentation, and specific task-performing DL methods, such as CNNs and AEs. Additionally, GAN-expansion and domain mapping are useful DL techniques for generating artificial data and combining several smaller datasets. We present results of DL-based segmentation and accuracy in predicting glioma subtypes based on MRI features. Dice scores range from 0.77 to 0.89. In mixed glioma cohorts, IDH mutation can be predicted with a sensitivity of 0.98 and specificity of 0.97. Results in test cohorts have shown improvements of 5–7% in accuracy, following GAN-expansion of data and domain mapping of smaller datasets. The provided DL examples are promising, although not yet in clinical practice. DL has demonstrated usefulness in data augmentation and for overcoming data variability. DL methods should be further studied, developed, and validated for broader clinical use. Ultimately, DL models can serve as effective decision support systems, and are especially well-suited for time-consuming, detail-focused, and data-ample tasks.
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| 43. |
- Lidstrom, D, et al.
(författare)
-
Agent based match racing simulations : Starting practice
- 2022
-
Ingår i: SNAME 24th Chesapeake Sailing Yacht Symposium, CSYS 2022. - : Society of Naval Architects and Marine Engineers.
-
Konferensbidrag (refereegranskat)abstract
- Match racing starts in sailing are strategically complex and of great importance for the outcome of a race. With the return of the America's Cup to upwind starts and the World Match Racing Tour attracting young and development sailors, the tactical skills necessary to master the starts could be trained and learned by means of computer simulations to assess a large range of approaches to the starting box. This project used game theory to model the start of a match race, intending to develop and study strategies using Monte-Carlo tree search to estimate the utility of a player's potential moves throughout a race. Strategies that utilised the utility estimated in different ways were defined and tested against each other through means of simulation and with an expert advice on match racing start strategy from a sailor's perspective. The results show that the strategies that put greater emphasis on what the opponent might do, perform better than those that did not. It is concluded that Monte-Carlo tree search can provide a basis for decision making in match races and that it has potential for further use.
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| 44. |
- Lindgren, Erik, 1980, et al.
(författare)
-
Analysis of industrial X-ray computed tomography data with deep neural networks
- 2021
-
Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. - 0277-786X .- 1996-756X. ; 11840
-
Konferensbidrag (refereegranskat)abstract
- X-ray computed tomography (XCT) is increasingly utilized industrially at material- and process development as well as in non-destructive quality control; XCT is important to many emerging manufacturing technologies, for example metal additive manufacturing. These trends lead to increased needs of safe automatic or semi-automatic data interpretation, considered an open research question for many critical high value industrial products such as within the aerospace industry. By safe, we mean that the interpretation is not allowed to unawarely or unexpectedly fail; specifically the algorithms must react sensibly to inputs dissimilar to the training data, so called out-of-distribution (OOD) inputs. In this work we explore data interpretation with deep neural networks to address: robust safe data interpretation which includes a confidence estimate with respect to OOD data, an OOD detector; generation of realistic synthetic material aw indications for the material science and nondestructive evaluation community. We have focused on industrial XCT related challenges, addressing difficulties with spatially correlated X-ray quantum noise. Results are reported on training auto-encoders (AE) and generative adversarial networks (GAN), on a publicly available XCT dataset of additively manufactured metal. We demonstrate that adding modeled X-ray noise during training reduces artefacts in the generated imperfection indications as well as improves the OOD detector performance. In addition, we show that the OOD detector can detect real and synthetic OOD data and still model the accepted in-distribution data down to the X-ray noise levels.
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| 45. |
- Hyde, Kevin D., et al.
(författare)
-
Incorporating molecular data in fungal systematics: a guide for aspiring researchers
- 2013
-
Ingår i: Current Research in Environmental and Applied Mycology. - : Mushroom Research Foundation. - 2229-2225. ; 3:1
-
Tidskriftsartikel (refereegranskat)abstract
- The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that draws from molecular data involves a long series of steps, ranging from taxon sampling through the various laboratory procedures and data analysis to the publication process. All steps are important and influence the results and the way they are perceived by the scientific community. The present paper provides a reflective overview of all major steps in such a project with the purpose to assist research students about to begin their first study using DNA-based methods. We also take the opportunity to discuss the role of taxonomy in biology and the life sciences in general in the light of molecular data. While the best way to learn molecular methods is to work side by side with someone experienced, we hope that the present paper will serve to lower the learning threshold for the reader.
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| 46. |
- Lindén, Joakim, et al.
(författare)
-
Evaluating the Robustness of ML Models to Out-of-Distribution Data Through Similarity Analysis
- 2023
-
Ingår i: Commun. Comput. Info. Sci.. - : Springer Science and Business Media Deutschland GmbH. - 9783031429408 ; , s. 348-359, s. 348-359
-
Konferensbidrag (refereegranskat)abstract
- In Machine Learning systems, several factors impact the performance of a trained model. The most important ones include model architecture, the amount of training time, the dataset size and diversity. We present a method for analyzing datasets from a use-case scenario perspective, detecting and quantifying out-of-distribution (OOD) data on dataset level. Our main contribution is the novel use of similarity metrics for the evaluation of the robustness of a model by introducing relative Fréchet Inception Distance (FID) and relative Kernel Inception Distance (KID) measures. These relative measures are relative to a baseline in-distribution dataset and are used to estimate how the model will perform on OOD data (i.e. estimate the model accuracy drop). We find a correlation between our proposed relative FID/relative KID measure and the drop in Average Precision (AP) accuracy on unseen data.
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| 47. |
- Baltzer, Nicholas, 1983-, et al.
(författare)
-
||-ROSETTA
-
Annan publikation (övrigt vetenskapligt/konstnärligt)
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| 48. |
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| 49. |
- Isaksson, Martin, et al.
(författare)
-
Adaptive Expert Models for Federated Learning
- 2023
-
Ingår i: <em>Lecture Notes in Computer Science </em>Volume 13448 Pages 1 - 16 2023. - Cham : Springer Science and Business Media Deutschland GmbH. - 9783031289958 ; 13448 LNAI, s. 1-16
-
Konferensbidrag (refereegranskat)abstract
- Federated Learning (FL) is a promising framework for distributed learning when data is private and sensitive. However, the state-of-the-art solutions in this framework are not optimal when data is heterogeneous and non-IID. We propose a practical and robust approach to personalization in FL that adjusts to heterogeneous and non-IID data by balancing exploration and exploitation of several global models. To achieve our aim of personalization, we use a Mixture of Experts (MoE) that learns to group clients that are similar to each other, while using the global models more efficiently. We show that our approach achieves an accuracy up to 29.78% better than the state-of-the-art and up to 4.38% better compared to a local model in a pathological non-IID setting, even though we tune our approach in the IID setting. © 2023, The Author(s)
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| 50. |
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