| 1. |
- Sandås, Kristofer, et al.
(författare)
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Nanometa Live : a user-friendly application for real-time metagenomic data analysis and pathogen identification
- 2024
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Ingår i: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 40:3
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Tidskriftsartikel (refereegranskat)abstract
- Summary: Nanometa Live presents a user-friendly interface designed for real-time metagenomic data analysis and pathogen identification utilizing Oxford Nanopore Technologies’ MinION and Flongle flow cells. It offers an efficient workflow and graphical interface for the visualization and interpretation of metagenomic data as it is being generated. Key features include automated BLAST validation, streamlined handling of custom Kraken2 databases, and a simplified graphical user interface for enhanced user experience. Nanometa Live is particularly notable for its capability to run without constant internet or server access once installed, setting it apart from similar tools. It provides a comprehensive view of taxonomic composition and facilitates the detection of user-defined pathogens or other species of interest, catering to both researchers and clinicians.Availability and implementation: Nanometa Live has been implemented as a local web application using the Dash framework with Snakemake handling the data processing. The source code is freely accessible on the GitHub repository at https://github.com/FOIBioinformatics/nanometa_live and it is easily installable using Bioconda. It includes containerization support via Docker and Singularity, ensuring ease of use, reproducibility, and portability.
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| 2. |
- Ahlstedt, Jonas, et al.
(författare)
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Non-invasive imaging methodologies for assessment of radiation damage to bone marrow and kidneys from peptide receptor radionuclide therapy. : -
- 2019
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Ingår i: Neuroendocrinology. - : S. Karger AG. - 1423-0194 .- 0028-3835. ; 110:1-2, s. 130-138
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Tidskriftsartikel (refereegranskat)abstract
- Background/Aims: Peptide receptor radionuclide therapy (PRRT) is becoming clinical routine for management of neuroendocrine tumours. The number of PRRT cycles is correlated with treatment effect but theoretically limited by off-target radiation damage to kidneys and bone marrow. New imaging biomarkers for assessment of PRRT tissue damage would enable evaluation of novel renal and bone marrow protective agents, as well as personalised PRRT treatment regiments. Methods: Mice treated with [177Lu]Lu-DOTA-TATE PRRT or vehicle were examined at baseline and following treatment with [18F]fluorothymidine (FLT) positron emission tomography (PET) and technetium-99m-mercapto-acetyl-tri-glycine ([99mTc]Tc-Mag3) single-photon emission tomography (SPECT) to assess dynamic changes in bone marrow proliferation and renal function, respectively. Results: Bone marrow proliferation as assessed by [18F]FLT was decreased 2 days after PRRT treatment, but not vehicle, compared to baseline (target-to-background ratio [TBRmax] baseline:1.69 ± 0.29 vs. TBRmax PRRT: 0.91 ± 0.02, p < 0.01). Renal function as assessed by [99mTc]Tc-Mag3 SPECT was similarly decreased 2 days following PRRT compared to vehicle (fractional uptake rate [FUR] vehicle: 0.030 ± 0.014 s–1 vs. FUR PRRT: 0.0051 ± 0.0028 s–1, p < 0.01). Conclusion: [18F]FLT PET and [99mTc]Tc-Mag3 SPECT are promising techniques for assessing bone marrow and renal injury from [177Lu]Lu-DOTA-TATE PRRT and may potentially improve patient management by allowing evaluation of protective interventions as well as enabling personalised PRRT treatments.
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| 3. |
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| 4. |
- Blomberg, Sara, et al.
(författare)
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Bridging the Pressure Gap in CO Oxidation
- 2021
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Ingår i: ACS Catalysis. - : American Chemical Society (ACS). - 2155-5435. ; 11:15, s. 9128-9135
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Tidskriftsartikel (refereegranskat)abstract
- Performing fundamental operando catalysis studies under realistic conditions is a key to further develop and increase the efficiency of industrial catalysts. Operando X-ray photoelectron spectroscopy (XPS) experiments have been limited to pressures, and the relevance for industrial applications has been questioned. Herein, we report on the CO oxidation experiment on Pd(100) performed at a total pressure of 1 bar using XPS. We investigate the light-off regime and the surface chemical composition at the atomistic level in the highly active phase. Furthermore, the observed gas-phase photoemission peaks of CO2, CO, and O2 indicate that the kinetics of the reaction during the light-off regime can be followed operando, and by studying the reaction rate of the reaction, the activation energy is calculated. The reaction was preceded by an in situ oxidation study in 7% O2 in He and a total pressure of 70 mbar to confirm the surface sensitivity and assignment of the oxygen-induced photoemission peaks. However, oxygen-induced photoemission peaks were not observed during the reaction studies, but instead, a metallic Pd phase is present in the highly active regime under the conditions applied. The novel XPS setup utilizes hard X-rays to enable high-pressure studies, combined with a grazing incident angle to increase the surface sensitivity of the measurement. Our findings demonstrate the possibilities of achieving chemical information of the catalyst, operando, on an atomistic level, under industrially relevant conditions.
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| 5. |
- Brindefalk, B., et al.
(författare)
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Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities
- 2022
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Ingår i: Microbiologyopen. - : Wiley. - 2045-8827. ; 11:5
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Tidskriftsartikel (refereegranskat)abstract
- Background Surface raw water used as a source for drinking water production is a critical resource, sensitive to contamination. We conducted a study on Swedish raw water sources, aiming to identify mutually co-occurring metacommunities of bacteria, and environmental factors driving such patterns. Methods The water sources were different regarding nutrient composition, water quality, and climate characteristics, and displayed various degrees of anthropogenic impact. Water inlet samples were collected at six drinking water treatment plants over 3 years, totaling 230 samples. The bacterial communities of DNA sequenced samples (n = 175), obtained by 16S metabarcoding, were analyzed using a joint model for taxa abundance. Results Two major groups of well-defined metacommunities of microorganisms were identified, in addition to a third, less distinct, and taxonomically more diverse group. These three metacommunities showed various associations to the measured environmental data. Predictions for the well-defined metacommunities revealed differing sets of favored metabolic pathways and life strategies. In one community, taxa with methanogenic metabolism were common, while a second community was dominated by taxa with carbohydrate and lipid-focused metabolism. Conclusion The identification of ubiquitous persistent co-occurring bacterial metacommunities in freshwater habitats could potentially facilitate microbial source tracking analysis of contamination issues in freshwater sources.
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| 6. |
- Dick Thelander, Kimberly, et al.
(författare)
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Improving InAs nanotree growth with composition-controlled Au-In nanoparticles
- 2006
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Ingår i: Nanotechnology. - : IOP Publishing. - 0957-4484 .- 1361-6528. ; 17:5, s. 1344-1350
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Tidskriftsartikel (refereegranskat)abstract
- Au nanoparticles are commonly used as seeds for epitaxial growth of III-V semiconductor nanowires. However, the interaction between Au and In-containing III-V materials makes it difficult to control the growth of more complex nanowire structures in materials such as InAs. Here we report the growth of InAs nanowires and branched nanotrees using Au and Au-In nanoparticles. We show that the initial composition of the particle does not affect the morphology of the first-generation nanowires, nor does it affect the final composition of the particle after growth. However, when the Au-In particles were used to seed a second generation of nanowires, producing nanotrees, the branches exhibited a 2-3 times higher growth rate and more regular shape than those seeded by pure Au particles. This result is attributed to the decreased interaction between the seed particle and the trunk nanowires when Au-In particles are used. Thus the incorporation of In into the seed particle during particle production allows for modification of the particle-wire interaction.
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| 7. |
- Dwibedi, Chinmay Kumar, et al.
(författare)
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Long-range dispersal moved Francisella tularensis into Western Europe from the East
- 2016
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Ingår i: Microbial Genomics. - : Microbiology Society. - 2057-5858. ; 2:12
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Tidskriftsartikel (refereegranskat)abstract
- For many infections transmitting to humans from reservoirs in nature, disease dispersal patterns over space and time are largely unknown. Here, a reversed genomics approach helped us understand disease dispersal and yielded insight into evolution and biological properties of Francisella tularensis, the bacterium causing tularemia. We whole-genome sequenced 67 strains and characterized by single-nucleotide polymorphism assays 138 strains, collected from individuals infected 1947-2012 across Western Europe. We used the data for phylogenetic, population genetic and geographical network analyses. All strains (n= 205) belonged to a monophyletic population of recent ancestry not found outside Western Europe. Most strains (n= 195) throughout the study area were assigned to a star-like phylogenetic pattern indicating that colonization of Western Europe occurred via clonal expansion. In the East of the study area, strains were more diverse, consistent with a founder population spreading from east to west. The relationship of genetic and geographic distance within the F. tularensis population was complex and indicated multiple long-distance dispersal events. Mutation rate estimates based on year of isolation indicated null rates; in outbreak hotspots only, there was a rate of 0.4 mutations/genome/year. Patterns of nucleotide substitution showed marked AT mutational bias suggestive of genetic drift. These results demonstrate that tularemia has moved from east to west in Europe and that F. tularensis has a biology characterized by long-range geographical dispersal events and mostly slow, but variable, replication rates. The results indicate that mutation-driven evolution, a resting survival phase, genetic drift and long-distance geographical dispersal events have interacted to generate genetic diversity within this species.
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| 8. |
- Hilner, Emelie, et al.
(författare)
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Direct Atomic Scale Imaging of III-V Nanowire Surfaces.
- 2008
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 8:11, s. 3978-3982
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Tidskriftsartikel (refereegranskat)abstract
- We have succeeded in direct atomic scale imaging of the exterior surfaces of III-V nanowires by scanning tunneling microscopy (STM). By using atomic hydrogen, we expose the crystalline surfaces of InAs nanowires with regular InP segments in vacuum while retaining the wire morphology. We show images with atomic resolution of the two major types of InAs wurtzite nanowire surface facets and scanning tunneling spectroscopy (STS) data. Ab initio calculations of the lowest energy surface structures and simulated STM images, agree very well with experiments.
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| 9. |
- Hägglund, Maria G A, et al.
(författare)
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Transport of L-glutamine, L-alanine, L-arginine and L-histidine by the neuron-specific Slc38a8 (SNAT8) in CNS
- 2015
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 427:6, s. 1495-1512
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Tidskriftsartikel (refereegranskat)abstract
- Glutamine transporters are important for regulating levels of glutamate and GABA in the brain. To date, six members of the SLC38 family (SNATs) have been characterized and functionally subdivided into System A (SNAT1, SNAT2 and SNAT4) and System N (SNAT3, SNAT5 and SNAT7). Here we present a first functional characterization of SLC38A8, one of the previous orphan transporters from the family and we suggest that the encoded protein should be named SNAT8 to adhere with the SNAT nomenclature. We show that SLC38A8 have preference for transporting L-glutamine, L-alanine, L-arginine, L-histidine, and L-aspartate using a Na(+)-dependent transport mechanism and that the functional characteristics of SNAT8 has highest similarity to the known System A transporters. We also provide a comprehensive CNS expression profile in mouse brain for the Slc38a8 gene and the SNAT8 protein. We show that Slc38a8 (SNAT8) is expressed in all neurons, both excitatory and inhibitory, in mouse brain using in situ hybridization and immunohistochemistry. Furthermore, proximity ligation assay show highly similar subcellular expression of SNAT7 and SNAT8. In conclusion, the neuronal SLC38A8 have a broad amino acid transport profile and is the first identified neuronal System A transporter. This suggests a key role of SNAT8 in the glutamine/glutamate(GABA) cycle in the brain.
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