| 1. |
- 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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| 2. |
- Amundin, Mats, et al.
(författare)
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A proposal to use distributional models to analyse dolphin vocalisation
- 2017
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Ingår i: Proceedings of the 1st International Workshop on Vocal Interactivity in-and-between Humans, Animals and Robots, VIHAR 2017. - 9782956202905 ; , s. 31-32
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Konferensbidrag (refereegranskat)abstract
- This paper gives a brief introduction to the starting points of an experimental project to study dolphin communicative behaviour using distributional semantics, with methods implemented for the large scale study of human language.
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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. |
- Schötz, Susanne, et al.
(författare)
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Phonetic Characteristics of Domestic Cat Vocalisations
- 2017
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Ingår i: Proceedings of the 1st International Workshop on Vocal Interactivity in-and-between Humans, Animals and Robots, VIHAR 2017. - 9782956202905 ; , s. 5-6
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Konferensbidrag (refereegranskat)abstract
- The cat (Felis catus, Linneaus 1758) has lived around or with humans for at least 10,000 years, and is now one of the most popular pets of the world with more than 600 millionindividuals. Domestic cats have developed a more extensive, variable and complex vocal repertoire than most other members of the Carnivora, which may be explained by their social organisation, their nocturnal activity and the long period of association between mother and young. Still, we know surprisingly little about the phonetic characteristics of these sounds, and about the interaction between cats and humans.Members of the research project Melody in human–cat communication (Meowsic) investigate the prosodic characteristics of cat vocalisations as well as the communication between human and cat. The first step includes a categorisation of cat vocalisations. In the next step it will be investigated how humans perceive the vocal signals of domestic cats. This paper presents an outline of the project which has only recently started.
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| 5. |
- Chatterjee, Bapi, 1982
(författare)
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Lock-free Concurrent Search
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The contemporary computers typically consist of multiple computing cores with high compute power. Such computers make excellent concurrent asynchronous shared memory system. On the other hand, though many celebrated books on data structure and algorithm provide a comprehensive study of sequential search data structures, unfortunately, we do not have such a luxury if concurrency comes in the setting. The present dissertation aims to address this paucity. We describe novel lock-free algorithms for concurrent data structures that target a variety of search problems. (i) Point search (membership query, predecessor query, nearest neighbour query) for 1-dimensional data: Lock-free linked-list; lock-free internal and external binary search trees (BST). (ii) Range search for 1-dimensional data: A range search method for lock-free ordered set data structures - linked-list, skip-list and BST. (iii) Point search for multi-dimensional data: Lock-free kD-tree, specially, a generic method for nearest neighbour search. We prove that the presented algorithms are linearizable i.e. the concurrent data structure operations intuitively display their sequential behaviour to an observer of the concurrent system. The lock-freedom in the introduced algorithms guarantee overall progress in an asynchronous shared memory system. We present the amortized analysis of lock-free data structures to show their efficiency. Moreover, we provide sample implementations of the algorithms and test them over extensive micro-benchmarks. Our experiments demonstrate that the implementations are scalable and perform well when compared to related existing alternative implementations on common multi-core computers. Our focus is on propounding the generic methodologies for efficient lock-free concurrent search. In this direction, we present the notion of help-optimality, which captures the optimization of amortized step complexity of the operations. In addition to that, we explore the language-portable design of lock-free data structures that aims to simplify an implementation from programmer’s point of view. Finally, our techniques to implement lock-free linearizable range search and nearest neighbour search are independent of the underlying data structures and thus are adaptive to similar data structures.
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| 6. |
- 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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| 7. |
- Homem, Irvin, 1985-
(författare)
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Advancing Automation in Digital Forensic Investigations
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Digital Forensics is used to aid traditional preventive security mechanisms when they fail to curtail sophisticated and stealthy cybercrime events. The Digital Forensic Investigation process is largely manual in nature, or at best quasi-automated, requiring a highly skilled labour force and involving a sizeable time investment. Industry standard tools are evidence-centric, automate only a few precursory tasks (E.g. Parsing and Indexing) and have limited capabilities of integration from multiple evidence sources. Furthermore, these tools are always human-driven.These challenges are exacerbated in the increasingly computerized and highly networked environment of today. Volumes of digital evidence to be collected and analyzed have increased, and so has the diversity of digital evidence sources involved in a typical case. This further handicaps digital forensics practitioners, labs and law enforcement agencies, causing delays in investigations and legal systems due to backlogs of cases. Improved efficiency of the digital investigation process is needed, in terms of increasing the speed and reducing the human effort expended. This study aims at achieving this time and effort reduction, by advancing automation within the digital forensic investigation process.Using a Design Science research approach, artifacts are designed and developed to address these practical problems. Summarily, the requirements, and architecture of a system for automating digital investigations in highly networked environments are designed. The architecture initially focuses on automation of the identification and acquisition of digital evidence, while later versions focus on full automation and self-organization of devices for all phases of the digital investigation process. Part of the remote evidence acquisition capability of this system architecture is implemented as a proof of concept. The speed and reliability of capturing digital evidence from remote mobile devices over a client-server paradigm is evaluated. A method for the uniform representation and integration of multiple diverse evidence sources for enabling automated correlation, simple reasoning and querying is developed and tested. This method is aimed at automating the analysis phase of digital investigations. Machine Learning (ML)-based triage methods are developed and tested to evaluate the feasibility and performance of using such techniques to automate the identification of priority digital evidence fragments. Models from these ML methods are evaluated in identifying network protocols within DNS tunneled network traffic. A large dataset is also created for future research in ML-based triage for identifying suspicious processes for memory forensics.From an ex ante evaluation, the designed system architecture enables individual devices to participate in the entire digital investigation process, contributing their processing power towards alleviating the burden on the human analyst. Experiments show that remote evidence acquisition of mobile devices over networks is feasible, however a single-TCP-connection paradigm scales poorly. A proof of concept experiment demonstrates the viability of the automated integration, correlation and reasoning over multiple diverse evidence sources using semantic web technologies. Experimentation also shows that ML-based triage methods can enable prioritization of certain digital evidence sources, for acquisition or analysis, with up to 95% accuracy.The artifacts developed in this study provide concrete ways to enhance automation in the digital forensic investigation process to increase the investigation speed and reduce the amount of costly human intervention needed.
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| 8. |
- Wilhelmsson, Kenneth, 1976
(författare)
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Huvudansatser för parsningsmetoder. Om programutvecklingens förutsättningar i en svensk kontext
- 2016
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Syftet med denna text var att ge en inblick i området (syntaktisk) parsning. Tanken var att ge en bild av utvecklingen som var 1) fri från alltför tekniska detaljer, då området är programmeringstekniskt, och 2) beskriven ur ett svenskt perspektiv. Bakgrunden till valet av ämne till texten, som var tänkt att finnas med i antologin Text och kontext, var att parsning är relativt okänt för många personer verksamma inom närliggande områden, samtidigt som det är ett absolut nyckelbegrepp för den som ägnar sig åt datorlingvistik eller språkteknologi. Målet var alltså att ge en ganska allmän utifrånblick på några centrala sidor av utvecklingen, samtidigt som det tydligt är så att den som själv arbetat med utveckling kan ha starka åsikter och preferenser rörande metodval, något som i ärlighetens namn kanske inte heller denna text är lösgjord från. Hur ska det göras? Konsten att utveckla automatisk syntaxanalys av naturlig text kan läras ut från ett flertal perspektiv. Det kan t.ex. ske med fokus på användandet av en viss grammatikformalism, med fokus på beräkningssnabbhet, med fokus på entydiggörande av möjliga ambiguiteter. Tolkningsval kan göras med hjälp av antingen handskrivna regler eller inhämtad statistik. En sorts huvudtema i denna text är hur metoder för parsning på senare år uppvisar förändringar som kanske kan förklaras med att programmen har fått andra användningsområden och att metoderna har anpassats därefter (en annan tolkning är att flera senare system inte längre gör parsning i strikt mening). När detta tänkta ”kapitel” var färdigt fick det kommentaren att det inte var anpassat för antologins målgrupp. Det fick skrivas en annan kapiteltext, men det kom samtidigt ett förslag att publicera texten om parsning här som denna rapport.
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| 9. |
- Grünloh, Christiane, 1980-, et al.
(författare)
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"why do they need to check me?" patient participation through ehealth and the doctor-patient relationship : Qualitative study
- 2018
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Ingår i: Journal of Medical Internet Research. - : J M I R Publications, Inc.. - 1438-8871. ; 20:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Roles in the doctor-patient relationship are changing and patient participation in health care is increasingly emphasized. Electronic health (eHealth) services such as patient accessible electronic health records (PAEHRs) have been implemented to support patient participation. Little is known about practical use of PAEHR and its effect on roles of doctors and patients. Objective: This qualitative study aimed to investigate how physicians view the idea of patient participation, in particular in relation to the PAEHR system. Hereby, the paper aims to contribute to a deeper understanding of physicians' constructions of PAEHR, roles in the doctor-patient relationship, and levels and limits of involvement. Methods: A total of 12 semistructured interviews were conducted with physicians in different fields. Interviews were transcribed, translated, and a theoretically informed thematic analysis was performed. Results: Two important aspects were identified that are related to the doctor-patient relationship: roles and involvement. The physicians viewed their role as being the ones to take on the responsibility, determining treatment options, and to be someone who should be trusted. In relation to the patient's role, lack of skills (technical or regarding medical jargon), motives to read, and patients' characteristics were aspects identified in the interviews. Patients were often referred to as static entities disregarding their potential to develop skills and knowledge over time. Involvement captures aspects that support or hinder patients to take an active role in their care. Conclusions: Literature of at least two decades suggests an overall agreement that the paternalistic approach in health care is inappropriate, and a collaborative process with patients should be adopted. Although the physicians in this study stated that they, in principle, were in favor of patient participation, the analysis found little support in their descriptions of their daily practice that participation is actualized. As seen from the results, paternalistic practices are still present, even if professionals might not be aware of this. This can create a conflict between patients who strive to become more informed and their questions being interpreted as signs of critique and mistrust toward the physician. We thus believe that the full potential of PAEHRs is not reached yet and argue that the concept of patient empowerment is problematic as it triggers an interpretation of "power" in health care as a zero-sum, which is not helpful for the maintenance of the relationship between the actors. Patient involvement is often discussed merely in relation to decision making; however, this study emphasizes the need to include also sensemaking and learning activities. This would provide an alternative understanding of patients asking questions, not in terms of "monitoring the doctor" but to make sense of the situation.
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| 10. |
- Petersson, Jesper, 1974
(författare)
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Technospatialities and telehealthcare: Unfolding new spaces of visibility
- 2016
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Ingår i: Information, Communication & Society. - 1369-118X .- 1468-4462. ; 19:6, s. 824-842
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Tidskriftsartikel (refereegranskat)abstract
- The umbrella term ‘telehealthcare’ denotes an array of information and communication technology-based solutions for digitally connecting citizens with healthcare services. Guided by the conviction that bodies can be translated into digital data which may serve as the basis for clinical decisions made elsewhere, these designs are widely assumed to enable a mode of healthcare delivery which is independent of space and time. Addressing the increasing use of telehealthcare for personalized health monitoring targeting the growing populations of elderly and chronic-care patients, this paper suggests that such designs invariably unfold new spaces of visibility. Based on an analysis of articles published in a leading telehealthcare journal, I argue that these new visibilities do not provide a window onto something that is already there. Instead, such visibilities are shaped by the way techno-medical practices and knowledge production processes are intertwined with a specific politico-economic agenda. The paper explores differences with respect to the positioning of older people and chronic-care patients in relation to two versions of health monitoring. While each version represents an attempt to promote individual freedom, improve health outcomes and ensure a functioning healthcare system, contrasting rationales are involved and different types of spaces are being unfolded.
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