| 1. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Strategies to improve usability and preserve accuracy in biological sequence databases
- 2016
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 16:18, s. 2454-2460
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Tidskriftsartikel (refereegranskat)abstract
- Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence of inaccurately annotated or otherwise poorly described sequences introduces noise and bias to biological analyses. Accurate annotations are, for example, pivotal for correct identifications of polypeptide fragments. However, standards for how sequence databases are organized and presented are currently insufficient. Here, we propose five strategies to address fundamental issues in the annotation of sequence databases: (i) to clearly separate experimentally verified and unverified sequence entries; (ii) to enable a system for tracing the origins of annotations; (iii) to separate entries with high-quality, informative annotation from less useful ones; (iv) to integrate automated quality-control software whenever such tools exist; and (v) to facilitate post-submission editing of annotations and metadata associated with sequences. We believe that implementation of these strategies, for example as requirements for publication of database papers, would enable biology to better take advantage of large-scale data.
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| 2. |
- Karlsson, Therese, 1987, et al.
(författare)
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Comparison between manta trawl and in situ pump filtration methods, and guidance for visual identification of microplastics in surface waters
- 2020
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Ingår i: Environmental Science and Pollution Research. - : Springer Science and Business Media LLC. - 0944-1344 .- 1614-7499. ; 27:5, s. 5559-5571
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Tidskriftsartikel (refereegranskat)abstract
- Owing to the development and adoption of a variety of methods for sampling and identifying microplastics, there is now data showing the presence of microplastics in surface waters from all over the world. The difference between the methods, however, hampers comparisons, and to date, most studies are qualitative rather than quantitative. In order to allow for a quantitative comparison of microplastics abundance, it is crucial to understand the differences between sampling methods. Therefore, a manta trawl and an in situ filtering pump were compared during realistic, but controlled, field tests. Identical microplastic analyses of all replicates allowed the differences between the methods with respect to (1) precision, (2) concentrations, and (3) composition to be assessed. The results show that the pump gave higher accuracy with respect to volume than the trawl. The trawl, however, sampled higher concentrations, which appeared to be due to a more efficient sampling of particles on the sea surface microlayer, such as expanded polystyrene and air-filled microspheres. The trawl also sampled a higher volume, which decreased statistical counting uncertainties. A key finding in this study was that, regardless of sampling method, it is critical that a sufficiently high volume is sampled to provide enough particles for statistical evaluation. Due to the patchiness of this type of contaminant, our data indicate that a minimum of 26 particles per sample should be recorded to allow for concentration comparisons and to avoid false null values. The necessary amount of replicates to detect temporal or spatial differences is also discussed. For compositional differences and size distributions, even higher particle counts would be necessary. Quantitative measurements and comparisons would also require an unbiased approach towards both visual and spectroscopic identification. To facilitate the development of such methods, a visual protocol that can be further developed to fit different needs is introduced and discussed. Some of the challenges encountered while using FTIR microspectroscopic particle identification are also critically discussed in relation to specific compositions found.
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| 3. |
- Karlsson, Therese, 1987, et al.
(författare)
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Provtagningsmetoder för mikroplast >300 μm i ytvatten: En jämförelsestudie mellan pump och trål
- 2018
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Sampling and analyzing microplastics (MPs) comes with a unique set of challenges and currently a wide variety of methods are developed and applied. In order to facilitate future environmental monitoring we compared two methods that are often used for sampling MPs >300 μm; a manta trawl and a filtering pump. Six replicates per method were taken during calm weather conditions in the same location on the same day. The volume per replicate was 20 m3 for the pump and approximately 60 m3 for the trawl. Following analysis was done with visual sorting in a stereo microscope. The same person analyzed all samples and the anthropogenic particles were divided into eleven classification categories. In the pump samples zero to eight MPs were found per sample, rendering an arithmetic mean of 0.17 MPs/m3. In the trawl samples the numbers varied between 9 and 33 MPs, which corresponded to a significantly higher concentration per volume than the pump with an arithmetic mean of 0.32 MPs/m3. The results also indicated that in order to reach a statistical power of 60%, ten pump replicates would be needed to measure a difference between the examined area and an uncontaminated area. For the trawl a corresponding number of two replicates would be required. Alternatively a higher sample volume can be applied, which would render a higher certainty as the distribution data would approach a Gaussian distribution. A higher sampling volume would also lower the measurement uncertainty as it would decrease fluctuations in the counting statistics. Variations in measurement uncertainty between the methods was hypothesized to be primarily related to the differences in sample volume and could also be compensated through increasing the volume sampled, which would be somewhat faster than increasing the amount of replicates. The composition of MPs in the study varied between the replicates but mainly consisted of expanded cellular plastics, films, filaments and fragments. Each pump sample had on average 1.3 films and 0.33 expanded cellular plastics whereas each trawl sample had on average 2.5 films and 9.2 expanded cellular plastics. Per unit of volume the majority of the particles in the pump samples (40%) consisted of films, whereas the particles in the trawl predominantly consisted of expanded cellular plastics (46%). Expanded cellular plastics therefore seem to be sampled more efficiently by trawls, which could be because they float on top of the surface, the pump samples a bit lower in the surface water and the results in this study show that the sample compositions were more comparable for particles with more neutral buoyancy. Not enough particles were however obtained to allow for a more in-depth analysis of the compositional differences. The probability of false null-values increase with a lower true value of numbers of particles per sample and this starts to have a significantly negative effect below five particles per sample. Regardless of which method that is used it is therefore crucial to sample a sufficient number of particles (volume times concentration) suitable for comparing spatial, temporal or compositional differences. Background and purpose of the report Even if methods for sampling, extraction and identification of microplastics have developed rapidly during recent years several challenges remain. One of the challenges that remain is how to sample a group of contaminants that is as heterogeneous, both concerning shape and distribution, as microplastics. Additionally it is important to know to what extent results from different types of sampling devices can be compared. Here we compare two methods that are often used to sample microplastics above 300 μm in surface waters; a manta trawl and a pump. During one day (10th of October 2017) six replicates per sampling method was taken in the same spot in Gullmarsfjorden outside Lysekil. Through counting microplastics and other types of microlitter in the samples the aim was to compare differences between replicates and methods. This study was commissioned by the Swedish Environmental Protection Agency and the Swedish Agency for Marine and Water Management, as a step in the work to develop monitoring of microlitter.
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| 4. |
- Schönlau, C., et al.
(författare)
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Microplastics in sea-surface waters surrounding Sweden sampled by manta trawl and in-situ pump
- 2020
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Ingår i: Marine Pollution Bulletin. - : Elsevier. - 0025-326X .- 1879-3363. ; 153
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Tidskriftsartikel (refereegranskat)abstract
- Microplastics were sampled in open surface waters by using a manta trawl and an in-situ filtering pump. A total of 24 trawl samples and 11 pump samples were taken at 12 locations around Sweden. Overall, the concentration of microplastic particles was higher in pump samples compared to trawl samples. The median microplastic particle concentration was 0.04 particles per m−3 for manta trawl samples and 0.10 particles per m−3 in pump samples taken with a mesh size of 0.3 mm. The highest concentrations were recorded on the west coast of Sweden. Fibers were found in all samples and were also more frequent in the pump samples. Even higher concentrations of fibers and particles were found on the 0.05 mm pump filters. Using near-infrared hyperspectral imaging the majority of the particles were identified as polyethylene followed by polypropylene.
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| 5. |
- Terzidis, Emmanouil, 1994, et al.
(författare)
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Assessing the fraction of dose originating from the penumbra region for plans of varied complexity
- 2024
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Ingår i: European Congress of Radiation Oncology (2024.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Purpose: The absorbed dose delivered to the patient that originates from a penumbra region have larger uncertainties compared to the dose delivered from the center of the treatment field. 1,2 The magnitude of these uncertainties could be important input when evaluating absorbed dose to organs at risk (OARs) and target volumes. The aim of this work was to examine the fraction of penumbra dose in three-dimensions (3D) for volumetric modulated arc therapy (VMAT) plans of different complexities. Methods and Materials: A C# software was developed in our department, able to calculate the fraction of penumbra dose in relation to the total dose in each voxel and visualize it as a 3D distribution (penumbra map). Twelve treatment plans of previously treated patients have been selected to represent different types of treatment geometry and different treatment sites (prostate, head & neck, lung and gynecological cancer). The clinical plan used for the actual treatment of the patient was reoptimized in Eclipse TPS (Varian Medical Systems, Palo Alto, CA), to create one plan with reduced complexity (“simple plan”) and one of higher complexity (“complex plan”). These additional plans were generated by altering the monitor unit constraint and the aperture shape controller level, while retaining a similar dose distribution. The fraction of penumbra dose was calculated for both the clinical and the newly generated plans creating in total 36 penumbra maps. Results: The generated penumbra maps were able to highlight anatomical regions with high fraction of penumbra dose (e.g., above 50%). These regions were mostly observed outside the planning target volume (PTV), regardless of treatment site and complexity level. Generally, the fraction of penumbra dose, both inside and outside the PTV, was increased with increased plan complexity. The average fraction of penumbra dose for the body, PTV and an example OAR are shown in Table 1 across all analyzed plans. For certain cases, the absorbed dose in parts of OARs originated from penumbra regions to a considerable degree, even for the least complex version of the plan. Examples are shown in Figure 1 featuring the rectum in a prostate plan and the parotid glands in a head & neck plan. Conclusion: The proposed method functions as a tool for assessing the extent to which the dose to certain voxels is influenced by the penumbra. A link was established between increased complexity and increased mean fraction of penumbra dose. Therefore, this approach could be used to quantify the complexity of the treatment plan in 3D
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| 6. |
- Venkatakrishnan, Vignesh, 1987, et al.
(författare)
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Glycan analysis of human neutrophil granules implicates a maturation-dependent glycosylation machinery
- 2020
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 295:36, s. 12648-12660
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Tidskriftsartikel (refereegranskat)abstract
- Protein glycosylation is essential to trafficking and immune functions of human neutrophils. During granulopoiesis in the bone marrow, distinct neutrophil granules are successively formed. Distinct receptors and effector proteins, many of which are glycosylated, are targeted to each type of granule according to their time of expression, a process called "targeting by timing." Therefore, these granules are time capsules reflecting different times of maturation that can be used to understand the glycosylation process during granulopoiesis. Herein, neutrophil subcellular granules were fractionated by Percoll density gradient centrifugation, andN- andO-glycans present in each compartment were analyzed by LC-MS. We found abundant paucimannosidicN-glycans and lack ofO-glycans in the early-formed azurophil granules, whereas the later-formed specific and gelatinase granules and secretory vesicles contained complexN-andO-glycans with remarkably elongatedN-acetyllactosamine repeats with Lewis epitopes. Immunoblotting and histochemical analysis confirmed the expression of Lewis X and sialyl-Lewis X in the intracellular granules and on the cell surface, respectively. Many glycans identified are unique to neutrophils, and their complexity increased progressively from azurophil granules to specific granules and then to gelatinase granules, suggesting temporal changes in the glycosylation machinery indicative of "glycosylation by timing" during granulopoiesis. In summary, this comprehensive neutrophil granule glycome map, the first of its kind, highlights novel granule-specific glycosylation features and is a crucial first step toward a better understanding of the mechanisms regulating protein glycosylation during neutrophil granulopoiesis and a more detailed understanding of neutrophil biology and function.
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| 7. |
- af Hällström, Anna, 1987, et al.
(författare)
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The role of social ties in collaborative project networks: A tale of two construction cases
- 2021
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Ingår i: Construction Management and Economics. - : Informa UK Limited. - 1466-433X .- 0144-6193. ; 39:9, s. 723-738
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Tidskriftsartikel (refereegranskat)abstract
- Collaborative project delivery models (CPDMs) are increasing in popularity as infrastructure con-struction projects become more complex and grow in scale and scope. CPDMs build on highlevels of trust, information exchange and formal contractual relations, creating complex relation-ships between actors in the project network. The literature emphasizes the procurement phaseand contractual aspects of CPDMs; however, few studies explicitly focus on the role of socialrelationships in CPDM projects. Social network theory has recently been introduced in the archi-tecture, engineering and construction industry industry to study relationships between networkactors, but the role of social ties within CPDM project networks is still unclear. Through twoqualitative case studies, we have analyzed the role of social ties in projects applying a CPDMcontract. The empirical evidence of 41 semi-structured interviews and observations points toaspects that affect the development of social ties in CPDMs, such as initial project setup, projectidentification, perception of actors, resource sharing and shared space, as well as the importanceof formal and informal ties for supporting collaborative project practices. The evidence showshow social ties develop into negative or positive bonds affecting the level of collaboration. Thisstudy contributes by emphasizing the interplay between project networks using CPDMs andsocial ties.
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| 8. |
- Alneberg, Johannes, et al.
(författare)
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Genomes from uncultivated prokaryotes : a comparison of metagenome-assembled and single-amplified genomes
- 2018
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Ingår i: Microbiome. - : BioMed Central. - 2049-2618. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
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| 9. |
- Bang, Charlotte Sahlberg, 1967-, et al.
(författare)
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The antibacterial effect of nitric oxide against ESBL-producing uropathogenic E-coli is improved by combination with miconazole and polymyxin B nonapeptide
- 2014
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Ingår i: BMC Microbiology. - London : BioMed Central. - 1471-2180. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Background: Nitric oxide (NO) is produced as part of the host immune response to bacterial infections, including urinary tract infections. The enzyme flavohemoglobin, coded by the hmp gene, is involved in protecting bacterial cells from the toxic effects of NO and represents a potentially interesting target for development of novel treatment concepts against resistant uropathogenic bacteria. The aim of the present study was to investigate if the in vitro antibacterial effects of NO can be enhanced by pharmacological modulation of the enzyme flavohemoglobin.Results: Four clinical isolates of multidrug-resistant extended-spectrum beta-lactamase (ESBL)-producing uropathogenic E. coli were included in the study. It was shown that the NO-donor substance DETA/NO, but not inactivated DETA/NO, caused an initial growth inhibition with regrowth noted after 8 h of exposure. An hmp-deficient strain showed a prolonged growth inhibition in response to DETA/NO compared to the wild type. The imidazole antibiotic miconazole, that has been shown to inhibit bacterial flavohemoglobin activity, prolonged the DETA/NO-evoked growth inhibition. When miconazole was combined with polymyxin B nonapeptide (PMBN), in order to increase the bacterial wall permeability, DETA/NO caused a prolonged bacteriostatic response that lasted for up to 24 h.Conclusion: An NO-donor in combination with miconazole and PMBN showed enhanced antimicrobial effects and proved effective against multidrug-resistant ESBL-producing uropathogenic E. coli.
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| 10. |
- Bosch-Sijtsema, Petra, 1971, et al.
(författare)
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Tidig Entreprenörmedverkan: Projekteringsprocess i entreprenad med samverkansnivå hög, SBUF 13574
- 2021
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Kontraktsformen tidig entreprenörmedverkan (TEM) är en kontraktsform där entreprenören medverkar i ett tidigt konceptuellt skede. Dessa kontraktsformer stödjer samverkan mellan olika parter för att dra nytta av olika parters kunskap och öka innovation och kvalitet. Med syftet att gebranschen rekommendationer för samverkansprojektering harlicentiatprojektet studeratpå vilka sätt samverkan tillämpats,samt hur detta samarbete påverkat produktivitetgenom frågeställningen”Hur genomförs projektering i samverkansform hög (TEM) mellan beställare, konsult och entreprenör för att bemöta kostnadsdrivande aspekter, kvalitet och innovation?”Projektet har i totalt studerat 3 fallstudier, 1 retrospektiv förstudie, och 2 kontrasterande fallstudier.Totalt genomfördes 41intervjuer, varav 3 intervjuer för förstudien, 20 intervjuer för fallstudie 1 och 21 intervjuer för fallstudie 2.Resultaten tar upp fördelar med TEM. Det krävs en förändring av roller och ansvar för att genomföra TEM ochdet finns vissa nyckelpersoner/rollersom påverkar samverkan. Studien har kommit fram med vikten av informella och sociala relationer för genomförande av TEM projekt. Studien pekar på ett antal aspekter som påverkar utvecklingen av sociala relationer isamverkansprojekt som har positive eller negative konsekvenser för samverkan
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