| 1. |
- Andersson, Robin, 1990, et al.
(författare)
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EMBRACE: The emotion sharing bracelet
- 2015
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Ingår i: Proceedings of SIDeR’15 – student interaction design research conference.
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Konferensbidrag (refereegranskat)abstract
- In this study we present Embrace; a wearable device that explores the potential of wearable technology harnessing the affordance of human form and deformable displays. We research new ways of communicating with loved ones in order to improve the experience of connectedness when they are apart. Embrace is a wearable device in the form of a bracelet that shares emotion between peers by providing both visual and haptic feedback. Other devices like smartphones and tablets have a rigid form and material. In contrast, the deformable display used in Embrace enables the user to wear the technology seamlessly on the body. The haptic feedback for sharing emotions is believed to provide a different experience since the physical sensation is more close to feeling heartbeats, hugs, and skin contact, compared to only visual information of today’s mobile devices.
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| 2. |
- Berglund, Andreas, et al.
(författare)
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15 koncept för bättre ergonomi : Inom äldreomsorg, fysioterapi, däckmontering och varuhantering
- 2015
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Rapport (populärvet., debatt m.m.)abstract
- Den här boken är resultatet av en kurs i ergonomi vid Teknisk design, Luleå tekniska universitet, våren 2015. 15 kursdeltagare har under 10 veckor använt designmetodik och ergonomiska teorier och metoder för att utveckla 15 konceptuella förbättringsförslag baserade på de 4 undersökta kontexterna äldreomsorg, fysioterapi, däckmontering och varuhantering. Fokus för ergonomi inom området teknisk design är att se till att all design, oavsett vilket system det avser, kompletterar människans styrkor och förmågor. Vi ska kort och gott se till att arbetsuppgifter, utrustning, apparater, processer, miljöer och organisationer utformas med människan som utgångspunkt, istället för att tvinga människan att anpassa sig med olika former av överbelastning som möjlig påföljd. För att uppnå detta behöver vi förstå och designa för den variabilitet som är representerad bland oss människor: vi är olika, har olika åldrar, storlek, styrka, kognitiv förmåga, erfarenheter, förväntningar och mål. Att tillämpa ergonomi betyder att studera hur människor interagerar med produkter, processer, miljöer och system för att förbättra dem, dvs. göra dem enklare, säkrare, bekvämare och effektivare att använda. För att kunna göra det behöver vi kunskap om människans förutsättningar och behov. Teknisk design med utgångspunkt och mål i god ergonomi innebär att exempelvis: Att designa produkter och utrustning som är enkla och tillförlitliga att använda med utgångspunkt i kunskap om kognitiv ergonomi, antropometri och belastningsergonomiska och biomekaniska analyserAtt designa säkra och effektiva tillverkningsprocesser med utgångspunkt i kunskap om kognitiv ergonomi och belastningsergonomiska analyserAtt designa organisationer utifrån kunskap om arbetslivsfysiologi och organisationsergonomiAtt designa arbetsuppgifter utifrån kunskap om kognitiv ergonomi, biomekanik och belastningsergonomiska analyserAtt designa enkla och användarvänliga gränssnitt med utgångspunkt i kognitiv ergonomiErgonomisk anpassning av en produkt eller en arbetsmiljö kan exempelvis handla om att se till att människan inte använder kroppen felaktigt. Det kan handla om fysisk belastning när en uppgift utförs, såväl som sensorisk input från olika system eller psykosocial belastning i form av stress. Det handlar om att utveckla kunskaper om människans begränsningar och förmågor, vilket ger bättre förutsättningar att bidra till användarvänliga lösningar. Det i sin tur bidrar till säkerhet och användarvänlighet och i slutändan att alla produkter, system och miljöer i vår omvärld fungerar väl för människan – det är hållbar utveckling om något. I kursen Ergonomi 2 vid civilingenjörsutbildningen Teknisk design, Luleå tekniska universitet, ingår en projektuppgift. Den syftar till att få fördjupad förståelse inom ergonomi genom att tillämpa kunskap och metoder i ett designprojekt för en verklig situation. Våren 2015 omfattade projektuppgiften att enanalys av valfri kontext, med syfte att förstå problem och utmaningar i den miljö, det sammanhang, den situation och för de personer som var berörda. Inledningsvis arbetade kursdeltagarna i grupper bestående av 3-4 personer, för att sedan gå in i en konceptutvecklingsfas individuellt. Det innebar att kursdeltagarna kunde genomföra ergonomiska analyser gemensamt och sedan utveckla konceptuella lösningar på egen hand. Det resulterade i att kursdeltagarna utvecklade tämligen olika lösningar, även om de haft en gemensam utgångspunkt. Bokens kapitel omfattar en beskrivning av respektive kontext följt av de konceptförslag som kursdeltagarna utvecklade. Som lärare är det alltid extra roligt när kursdeltagare är motiverade och engagerade inför projektuppgifter. Vår förhoppning är att det engagemanget ska framgå på följande sidor och att koncepten ska ge inspiration till att förbättra ergonomin i våra vardagsliv. Åsa Wikberg Nilsson, Therese Öhrling, Lars Sundström, Agneta Larsson och Ulrik RöijezonTeknisk design Luleå tekniska universitet, Augusti 2015
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| 3. |
- Berglund, Fanny, et al.
(författare)
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An updated phylogeny of the metallo-β-lactamases.
- 2021
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Ingår i: The Journal of antimicrobial chemotherapy. - : Oxford University Press (OUP). - 1460-2091 .- 0305-7453. ; 76:1, s. 117-123
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Tidskriftsartikel (refereegranskat)abstract
- Metallo-β-lactamases (MBLs) are enzymes that use zinc-dependent hydrolysis to confer resistance to almost all available β-lactam antibiotics. They are hypothesized to originate from commensal and environmental bacteria, from where some have mobilized and transferred horizontally to pathogens. The current phylogeny of MBLs, however, is biased as it is founded largely on genes encountered in pathogenic bacteria. This incompleteness is emphasized by recent findings of environmental MBLs with new forms of zinc binding sites and atypical functional profiles.To expand the phylogeny of MBLs to provide a more accurate view of their evolutionary history.We searched more than 16 terabases of genomic and metagenomic data for MBLs of the three subclasses B1, B2 and B3 using the validated fARGene method. Predicted genes, together with the previously known ones, were used to infer phylogenetic trees.We identified 2290 unique MBL genes forming 817 gene families, of which 741 were previously uncharacterized. MBLs from subclasses B1 and B3 separated into distinct monophyletic groups, in agreement with their taxonomic and functional properties. We present evidence that clinically associated MBLs were mobilized from Proteobacteria. Additionally, we identified three new variants of the zinc binding sites, indicating that the functional repertoire is broader than previously reported.Based on our results, we recommend that the nomenclature of MBLs is refined into the phylogenetic groups B1.1-B1.5 and B3.1-B3.4 that more accurately describe their molecular and functional characteristics. Our results will also facilitate the annotation of novel MBLs, reflecting their taxonomic organization and evolutionary origin.
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| 4. |
- Berglund, Fanny, et al.
(författare)
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Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes
- 2020
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Ingår i: Microbial genomics. - : Microbiology Society. - 2057-5858. ; 6:11
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Tidskriftsartikel (refereegranskat)abstract
- Tetracyclines are broad-spectrum antibiotics used to prevent or treat a variety of bacterial infections. Resistance is often mediated through mobile resistance genes, which encode one of the three main mechanisms: active efflux, ribosomal target protection or enzymatic degradation. In the last few decades, a large number of new tetracycline-resistance genes have been discovered in clinical settings. These genes are hypothesized to originate from environmental and commensal bacteria, but the diversity of tetracycline-resistance determinants that have not yet been mobilized into pathogens is unknown. In this study, we aimed to characterize the potential tetracycline resistome by screening genomic and metagenomic data for novel resistance genes. By using probabilistic models, we predicted 1254 unique putative tetracycline resistance genes, representing 195 gene families (<70% amino acid sequence identity), whereof 164 families had not been described previously. Out of 17 predicted genes selected for experimental verification, 7 induced a resistance phenotype in an Escherichia coli host. Several of the predicted genes were located on mobile genetic elements or in regions that indicated mobility, suggesting that they easily can be shared between bacteria. Furthermore, phylogenetic analysis indicated several events of horizontal gene transfer between bacterial phyla. Our results also suggested that acquired efflux pumps originate from proteobacterial species, while ribosomal protection genes have been mobilized from Firmicutes and Actinobacteria. This study significantly expands the knowledge of known and putatively novel tetracycline resistance genes, their mobility and evolutionary history. The study also provides insights into the unknown resistome and genes that may be encountered in clinical settings in the future.
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| 5. |
- Berglund, Fanny, et al.
(författare)
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Dietary habits among snus users : a population-based cross-sectional study
- 2023
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Ingår i: Food & Nutrition Research. - : SNF Swedish Nutrition Foundation. - 1654-6628 .- 1654-661X. ; 67
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Tidskriftsartikel (refereegranskat)abstract
- Background: The dietary habits among snus users are largely unknown and have not been accounted for in observational studies on the health effects of snus use.Aim: To examine whether snus users eat unhealthier than never tobacco users.Methods: A total of 3,397 male participants, examined between 1994 and 2014 in the Northern Sweden Monitoring of Trends and Determinants in Cardiovascular Disease (MONICA) study, were included. Snus use and dietary habits were self-reported using questionnaires, from which intakes of different food groups, macronutrients, and a healthy diet score (HDS) were calculated (the latter as a proxy for overall diet quality). The association between snus use and dietary habits was examined by quantile regression models.Results: In the multivariable-adjusted model, current snus users had a lower HDS (median difference: -0.86 [95% confidence interval: -1.32, -0.40]) than never tobacco users. Snus users also consumed fewer weekly servings of fruits and berries (median difference: -1.03 [-1.65, -0.40]), and their estimated percentage of energy intake con -sisted of less carbohydrates (median difference: -1.43 [-2.12, -0.74]) and of more total fat (median difference: 0.99 [0.30, 1.67]), saturated fat (median difference: 0.67 [0.29, 1.05]), monounsaturated fat (median difference: 0.44 [0.20, 0.68]), trans fat (median difference: 0.03 [0.01, 0.06]), and alcohol (median difference: 0.21 [0.02, 0.40]).Conclusion: We observed that snus users had an unhealthier diet than never tobacco users. Future studies on the association between snus use and health outcomes should, therefore, consider diet as a potential confounder.
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| 6. |
- Berglund, Fanny, et al.
(författare)
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Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge
- 2023
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- The emergence and spread of mobile antibiotic resistance genes (ARGs) in pathogens have become a serious threat to global health. Still little is known about where ARGs gain mobility in the first place. Here, we aimed to collect evidence indicating where suchinitial mobilizationevents of clinically relevant ARGs may have occurred. We found that the majority of previously identified origin species did not carry the mobilizing elements that likely enabled intracellular mobility of the ARGs, suggesting a necessary interplay between different bacteria. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements. Most origin species were only occasionally detected in other environments. Co-occurrence of origin species and corresponding mobilizing elements were rare in human microbiota. Our results identify wastewaters and wastewater-impacted environments as plausible arenas for the initial mobilization of resistance genes.
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| 7. |
- Berglund, Fanny, 1988, et al.
(författare)
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Identification and reconstruction of novel antibiotic resistance genes from metagenomes
- 2019
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundEnvironmental and commensal bacteria maintain a diverse and largely unknown collection of antibiotic resistance genes (ARGs) that, over time, may be mobilized and transferred to pathogens. Metagenomics enables cultivation-independent characterization of bacterial communities but the resulting data is noisy and highly fragmented, severely hampering the identification of previously undescribed ARGs. We have therefore developed fARGene, a method for identification and reconstruction of ARGs directly from shotgun metagenomic data.ResultsfARGene uses optimized gene models and can therefore with high accuracy identify previously uncharacterized resistance genes, even if their sequence similarity to known ARGs is low. By performing the analysis directly on the metagenomic fragments, fARGene also circumvents the need for a high-quality assembly. To demonstrate the applicability of fARGene, we reconstructed -lactamases from five billion metagenomic reads, resulting in 221 ARGs, of which 58 were previously not reported. Based on 38 ARGs reconstructed by fARGene, experimental verification showed that 81% provided a resistance phenotype in Escherichia coli. Compared to other methods for detecting ARGs in metagenomic data, fARGene has superior sensitivity and the ability to reconstruct previously unknown genes directly from the sequence reads.ConclusionsWe conclude that fARGene provides an efficient and reliable way to explore the unknown resistome in bacterial communities. The method is applicable to any type of ARGs and is freely available via GitHub under the MIT license.
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| 8. |
- Berglund, Fanny, 1988, et al.
(författare)
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Identification of 76 novel B1 metallo-beta-lactamases through large-scale screening of genomic and metagenomic data
- 2017
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5:1, s. 134-134
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Tidskriftsartikel (refereegranskat)abstract
- Background: Metallo-beta-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with their broad substrate spectrum and lack of clinically useful inhibitors, make them a particularly problematic class of antibiotic resistance determinants. We hypothesized that there is a large and unexplored reservoir of unknown metallo-beta-lactamases, some of which may spread to pathogens, thereby threatening public health. The aim of this study was to identify novel metallo-beta-lactamases of class B1, the most clinically important subclass of these enzymes. Results: Based on a new computational method using an optimized hidden Markov model, we analyzed over 10,000 bacterial genomes and plasmids together with more than 5 terabases of metagenomic data to identify novel metallo-beta-lactamase genes. In total, 76 novel genes were predicted, forming 59 previously undescribed metallo-beta-lactamase gene families. The ability to hydrolyze imipenem in an Escherichia coli host was experimentally confirmed for 18 of the 21 tested genes. Two of the novel B1 metallo-beta-lactamase genes contained atypical zinc-binding motifs in their active sites, which were previously undescribed for metallo-beta-lactamases. Phylogenetic analysis showed that B1 metallo-beta-lactamases could be divided into five major groups based on their evolutionary origin. Our results also show that, except for one, all of the previously characterized mobile B1 beta-lactamases are likely to have originated from chromosomal genes present in Shewanella spp. and other Proteobacterial species. Conclusions: This study more than doubles the number of known B1 metallo-beta-lactamases. The findings have further elucidated the diversity and evolutionary history of this important class of antibiotic resistance genes and prepare us for some of the challenges that may be faced in clinics in the future.
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| 9. |
- Berglund, Fanny
(författare)
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Identification of novel antibiotic resistance genes through large-scale data analysis
- 2017
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Antibiotic resistance is increasing worldwide, and is considered a serious threat to public health by e.g. the World Health Organization. Antibiotic resistance genes are hypothesized to originate from harmless bacteria in and around us, from where they are horizontally transfered into human pathogens. It is therefore of great importance to explore human-associated and environmental bacterial communities to identify novel antibiotic resistance genes before they reach clinical settings. The three papers presented in this thesis aim to identify novel antibiotic resistance genes in large genomic and metagenomic datasets. In paper I, the aim was to identify novel genes of the clinically important subclass B1 metallo-β-lactamases. By analyzing whole bacterial genomes as well as metagenomes from environmental and human-associated bacterial communities, 76 novel putative B1 genes were predicted. Twenty-one of these were selected for experimental validation, whereof 18 expressed the predicted phenotype in E. coli. Phylogentic analysis revealed that the novel genes formed 59 previously undescribed gene families. In paper II, a large volume of genomic and metagenomic data was searched for novel plasmid-mediated quinolone resistance (qnr ) genes. In total, 611 qnr genes were predicted, of which 20 were putative novel. Nine of these were experimentally tested in E. coli, whereof eight expressed the predicted phenotype. In paper III, a new method for identification and reconstruction of novel antibiotic resistance genes from fragmented metagenomic data was presented. The method is based on gene specific models, which are optimized for a high sensitivity and specificity. The method is furthermore computationally efficient and can be applied to any class of resistance genes. The results of this thesis provides a deeper insight to the diversity and evolutionary history of two types of clinically relevant antibiotic resistance genes. It also provides new methods for efficient and reliable identification of novel resistance genes in fragmented metagenomic data.
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| 10. |
- Berglund, Fanny, 1988
(författare)
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New antibiotic resistance genes and their diversity
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Antibiotic resistance is increasing worldwide and is considered a severe threat to public health. Often, antibiotic resistance is caused by antibiotic resistance genes, of which many are hypothesized to have been transferred into human pathogens from environmental bacteria. It is, therefore, of great importance to explore bacterial communities to identify new antibiotic resistance genes before they reach clinical settings. The six papers presented in this thesis aim to identify new antibiotic resistance genes in large genomic and metagenomic datasets and to place them in an evolutionary context. In Paper I, a new method for the identification and reconstruction of new antibiotic resistance genes directly from fragmented metagenomic data was developed and was shown to outperform other methods significantly. In Papers II and III, novel genes of the clinically important class metallo-β-lactamases were identified. By analyzing metagenomes and bacterial genomes, 96 novel putative metallo-β-lactamase genes were predicted. In Paper IV, the diversity and phylogeny of the metallo-β-lactamases were further investigated. The results showed that the genes mainly clustered based on the taxonomy of the host species and that many of the mobile metallo-β-lactamases potentially were mobilized from species of the phylum Proteobacteria. In Paper V, the aim was to identify new genes providing resistance to the antibiotic class tetracyclines. A total of 195 gene families were predicted, of which 164 were new putative tetracycline resistance genes. Finally, in Paper VI, we searched for and predicted 20 novel putative quinolone resistance (qnr) genes from a large amount of metagenomic data. Throughout the thesis, a total of 54 novel genes have been functionally verified in Escherichia coli, of which 37 expressed the predicted phenotype. The results of this thesis provide deeper insights into the diversity and evolutionary history of three major classes of antibiotic resistance genes. It also provides new methodologies for efficient and reliable identification of new resistance genes in genomic and metagenomic data.
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