| 1. |
- Menkveld, Albert J., et al.
(författare)
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Nonstandard Errors
- 2024
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Ingår i: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
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Tidskriftsartikel (refereegranskat)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
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| 2. |
- Oksjoki, Riina, et al.
(författare)
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Complement regulation in human atherosclerotic coronary lesions - Immunohistochemical evidence that C4b-binding protein negatively regulates the classical complement pathway, and that C5b-9 is formed via the alternative complement pathway
- 2007
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Ingår i: Atherosclerosis. - : Elsevier BV. - 1879-1484 .- 0021-9150. ; 192:1, s. 40-48
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Tidskriftsartikel (refereegranskat)abstract
- Objective: The complement system is activated in human atherosclerotic lesions and may hence aggravate local inflammation. We studied the presence and localization of C4b-binding protein (C4bp), the major inhibitor of the classical complement pathway, in human atherosclerotic lesions in relation to complement activation products and protein S, which circulates in complex with C4bp. Methods and results: Immunohistochemistry, of human coronary arteries showed C4bp to be virtually absent in normal arteries but present in early and advanced atherosclerotic lesions. In the lesions, C4bp is associated with proteoglycans, and affinity chromatography showed that C4bp interacts with human arterial proteoglycans. Areas containing C4bp also contained IgM and C4 suggesting that C4bp is involved in the regulation of the classical complement pathway. However, C5b-9 was virtually absent in these areas but, instead, colocalized with properdin deeper in the intima, suggesting that C5b-9 is formed by the alternative complement pathway. A fraction of C4bp was associated with protein S and apoptotic cells. Conclusions: The results indicate that C4bp regulates the classical complement pathway in human atherosclerotic lesions. Thus, unlike the alternative pathway, the classical complement pathway does not generate C5b-9, but is likely to be involved in the clean-up of apoptotic cells and cell debris in the arterial intima. (c) 2006 Elsevier Ireland Ltd. All rights reserved.
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| 3. |
- Unneberg, Per, et al.
(författare)
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Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins
- 2024
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Krill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill (Meganyctiphanes norvegica). We assemble and characterize its large genome and compare genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The 19 Gb genome likely evolved through proliferation of retrotransposons, now targeted for inactivation by extensive DNA methylation, and contains many duplicated genes associated with molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect signatures of adaptive divergence across hundreds of genes, implicated in photoreception, circadian regulation, reproduction and thermal tolerance, indicating polygenic adaptation to light and temperature. The top gene candidate for ecological adaptation was nrf-6, a lipid transporter with a Mediterranean variant that may contribute to early spring reproduction. Such variation could become increasingly important for fitness in Atlantic stocks. Our study underscores the widespread but uneven distribution of adaptive variation, necessitating characterization of genetic variation among natural zooplankton populations to understand their adaptive potential, predict risks and support ocean conservation in the face of climate change.
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| 4. |
- Abbadessa, Anna, et al.
(författare)
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Characterization of Two Novel Bio-based Materials from Pulping Process Side Streams : Ecohelix and CleanFlow Black Lignin
- 2018
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Ingår i: BioResources. - : NORTH CAROLINA STATE UNIV DEPT WOOD & PAPER SCI. - 1930-2126. ; 13:4, s. 7606-7627
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Tidskriftsartikel (refereegranskat)abstract
- The characteristics of two novel types of technical lignin, namely Ecohelix (EH) and CleanFlow black lignin (CFBL), isolated from two different pulping process side streams, were analyzed. EH and CFBL were analyzed in terms of general composition, chemical functionalities, molar mass distribution, and thermal stability. For comparison, two relevant types of commercially available lignosulfonate and kraft lignin were used. The results showed that EH contains a large amount of sulfonated lignin, together with carbohydrates and ash. As such, it can be considered a lignin-carbohydrate hybrid molecule. CFBL was found to contain 91.5% Klason lignin and the lowest amount of carbohydrates (0.3%). EH showed the highest content of aliphatic OH groups (5.44 mmol/g) and CFBL a high content of phenols (4.73 mmol/g). EH had a molecular weight of 31.4 kDa and a sufficient thermal stability. CFBL had the lowest molecular weight (M-w = 2.0 kDa) and thermal stability of all kraft lignins analyzed in this study. These properties highlighted that EH is a suitable building block for material development and that CFBL is a promising material for the production of biofuel and biochemicals.
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| 5. |
- Abbadessa, Anna, et al.
(författare)
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Layer-by-layer assembly of sustainable lignin-based coatings for food packaging applications
- 2023
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Ingår i: Progress in organic coatings. - : Elsevier BV. - 0300-9440 .- 1873-331X. ; 182
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Tidskriftsartikel (refereegranskat)abstract
- Packaging plays a critical role in ensuring food safety and shelf life by protecting against e.g., moisture, gases, and light. Polyethylene (PE) is widely used in food packaging, but it is mainly produced from non-renewable resources and it is an inefficient oxygen and light barrier. In this study, the layer-by-layer (LbL) assembly of a sustainably produced lignin-based polymer (EH) with polyethylenimine (PEI) or chitosan (CH) was used to fabricate (partially or fully) bio-based coatings with the aim of improving barrier properties of PE films. The charge density of EH was calculated using a polyelectrolyte titration method and the hydrodynamic diameters of EH, PEI and CH were determined by Dynamic Light Scattering (DLS). LbL assembly was monitored in situ via Quartz Crystal Microbalance with Dissipation (QCM-D) and Stagnation Point Adsorption Reflectometry (SPAR). PE films were coated with a variable number of PEI/EH or CH/EH bilayers (BL) using an immersive LbL assembly method. Coated films were studied in terms of light-blocking ability, wettability, thermal behaviour, surface structure, as well as oxygen and water vapor barrier properties. QCM-D and SPAR data showed a stepwise multilayer formation and strong interactions between the oppositely charged polymers, with PEI/EH coating having a greater amount of deposited polymer compared to CH/EH coating at the same number of BL. Overall, light barrier properties and wettability of the coated films increased with the number of deposited bilayers. Coated PE films maintained the overall thermal behaviour of PE. A number of BL of 20 was found to be the most promising based on the studied properties. Selected samples showed improved oxygen and water vapor barrier properties, with PEI/EH coating performing better than CH/EH coating. Taken altogether, we demonstrated that a novel and sustainable lignin-based polymer can be combined with PEI or CH to fabricate (partially or fully) bio-based coatings for food packaging.
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| 6. |
- Abrego, Nerea, et al.
(författare)
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Airborne DNA reveals predictable spatial and seasonal dynamics of fungi
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 631, s. 835-842
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Tidskriftsartikel (refereegranskat)abstract
- Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions1,2. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores3. The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms4,5.
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| 7. |
- Ahola, Virpi, et al.
(författare)
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The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
- 2014
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 4737-
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n = 31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n = 31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.
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| 8. |
- Andersen, Peter M., 1962-, et al.
(författare)
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Caregivers’ divergent perspectives on patients’ well-being and attitudes towards hastened death in Germany, Poland and Sweden
- 2022
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Ingår i: Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration. - : Taylor & Francis. - 2167-8421 .- 2167-9223. ; 23:3-4, s. 252-262
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Tidskriftsartikel (refereegranskat)abstract
- Background: During the course of amyotrophic lateral sclerosis (ALS), patients and their families are faced with existential decisions concerning life-prolonging and -shortening measures. Correct anticipation of patient’s well-being and preferences is a prerequisite for patient-centered surrogate decision making.Methods: In Germany (N = 84), Poland (N = 77) and Sweden (N = 73) patient-caregiver dyads were interviewed. Standardized questionnaires on well-being (ADI-12 for depressiveness; ACSA for global quality of life) and wish for hastened death (SAHD) were used in ALS patients. Additionally, caregivers were asked to fill out the same questionnaires by anticipating patients’ perspective (surrogate perspective).Results: Caregivers significantly underestimated patients’ well-being in Germany and Poland. For Swedish caregivers, there were just as many who underestimated and overestimated well-being. The same was true for wish for hastened death in all three countries. For Swedish and Polish patients, caregivers’ estimation of well-being was not even associated with patients’ responses and the same was true for estimation of wish for hastened death in all three countries. Older caregivers and those with the most frequent encounter with the patient were the closest in their rating of well-being and wish for hastened death to the patients’ actual state, while caregivers with chronic disease him/herself were more likely to underestimate patient’s well-being.Discussion: Despite distinct cultural differences, there was a clear discrepancy between patients’ and caregivers’ perspective on patients’ well-being and preferences towards life in all three countries. This possible bias in caregivers’ judgment needs to be taken into account in surrogate decision making.
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| 9. |
- Bengtsson, Johan, 1985, et al.
(författare)
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Metaxa: Automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts
- 2011
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Ingår i: SocBiN Bioinformatics Conference, Helsinki, Finland, 2011.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. However, the gene is not only present in the nuclear genome of eukaryotes and the core genome of prokaryotes, but also in the mitochondria and chloroplasts of eukaryotes. The SSU genes in the core genome, mitochondria and chloroplast are conceptually paralogous and should in most situations not be aligned and analyzed jointly, e.g. when estimating species diversity. Identifying the origin of SSU sequences in complex sequence datasets is a time-consuming and largely manual undertaking. To ease this situation, we have created Metaxa, an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacte- rial, nuclear eukaryote, mitochondrial, or chloroplast origin. Metaxa very efficiently detects SSU sequences from fragments as short as 200 base pairs, and correctly classifies 97% of the identified genes at read lengths typically obtained from pyrosequencing. In addition, Metaxa shows a false positive rate of 0.00012% when run on random DNA fragments, showing the robustness of the method. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.
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| 10. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets
- 2011
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Ingår i: Antonie van Leeuwenhoek: international journal of general and molecular microbiology. - : Springer Science and Business Media LLC. - 0003-6072 .- 1572-9699. ; 100:3, s. 471-475
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Tidskriftsartikel (refereegranskat)abstract
- The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.
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