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1.	Klionsky, Daniel J, et al. (författare) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). 2016 Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 12:1, s. 1-222 Tidskriftsartikel (refereegranskat)
2.	Kattge, Jens, et al. (författare) TRY plant trait database - enhanced coverage and open access 2020 Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188 Tidskriftsartikel (refereegranskat)abstract Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
3.	Klionsky, Daniel J., et al. (författare) Guidelines for the use and interpretation of assays for monitoring autophagy 2012 Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544 Forskningsöversikt (refereegranskat)abstract In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
4.	Bazarian, Jeffrey J., et al. (författare) Serum GFAP and UCH-L1 for prediction of absence of intracranial injuries on head CT (ALERT-TBI) : a multicentre observational study 2018 Ingår i: Lancet Neurology. - : Lancet Publishing Group. - 1474-4422 .- 1474-4465. ; 17:9, s. 782-789 Tidskriftsartikel (refereegranskat)abstract Background: More than 50 million people worldwide sustain a traumatic brain injury (TBI) annually. Detection of intracranial injuries relies on head CT, which is overused and resource intensive. Blood-based brain biomarkers hold the potential to predict absence of intracranial injury and thus reduce unnecessary head CT scanning. We sought to validate a test combining ubiquitin C-terminal hydrolase-L1 (UCH-L1) and glial fibrillary acidic protein (GFAP), at predetermined cutoff values, to predict traumatic intracranial injuries on head CT scan acutely after TBI.Methods: This prospective, multicentre observational trial included adults (≥18 years) presenting to participating emergency departments with suspected, non-penetrating TBI and a Glasgow Coma Scale score of 9-15. Patients were eligible if they had undergone head CT as part of standard emergency care and blood collection within 12 h of injury. UCH-L1 and GFAP were measured in serum and analysed using prespecified cutoff values of 327 pg/mL and 22 pg/mL, respectively. UCH-L1 and GFAP assay results were combined into a single test result that was compared with head CT results. The primary study outcomes were the sensitivity and the negative predictive value (NPV) of the test result for the detection of traumatic intracranial injury on head CT.Findings: Between Dec 6, 2012, and March 20, 2014, 1977 patients were recruited, of whom 1959 had analysable data. 125 (6%) patients had CT-detected intracranial injuries and eight (<1%) had neurosurgically manageable injuries. 1288 (66%) patients had a positive UCH-L1 and GFAP test result and 671 (34%) had a negative test result. For detection of intracranial injury, the test had a sensitivity of 0·976 (95% CI 0·931-0·995) and an NPV of 0·996 (0·987-0·999). In three (<1%) of 1959 patients, the CT scan was positive when the test was negative.Interpretation: These results show the high sensitivity and NPV of the UCH-L1 and GFAP test. This supports its potential clinical role for ruling out the need for a CT scan among patients with TBI presenting at emergency departments in whom a head CT is felt to be clinically indicated. Future studies to determine the value added by this biomarker test to head CT clinical decision rules could be warranted.Funding: Banyan Biomarkers and US Army Medical Research and Materiel Command.
5.	Bentham, James, et al. (författare) A century of trends in adult human height 2016 Ingår i: eLIFE. - 2050-084X. ; 5 Tidskriftsartikel (refereegranskat)abstract Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.522.7) and 16.5 cm (13.319.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
6.	Bentham, James, et al. (författare) A century of trends in adult human height 2016 Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 5 Tidskriftsartikel (refereegranskat)abstract Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3– 19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8– 144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
7.	Di Cesare, Mariachiara, et al. (författare) Trends in adult body-mass index in 200 countries from 1975 to 2014: A pooled analysis of 1698 population-based measurement studies with 19.2 million participants 2016 Ingår i: The Lancet. - : Lancet Publishing Group. - 0140-6736 .- 1474-547X. ; 387:10026, s. 1377-1396 Tidskriftsartikel (refereegranskat)
8.	Jacobs, Kevin B, et al. (författare) Detectable clonal mosaicism and its relationship to aging and cancer. 2012 Ingår i: Nature Genetics. - New York : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 44:6, s. 651-658 Tidskriftsartikel (refereegranskat)abstract In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.
9.	Patkowski, Jonasz B., et al. (författare) The F-pilus biomechanical adaptability accelerates conjugative dissemination of antimicrobial resistance and biofilm formation 2023 Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14 Tidskriftsartikel (refereegranskat)abstract Conjugation is used by bacteria to propagate antimicrobial resistance (AMR) in the environment. Central to this process are widespread conjugative F-pili that establish the connection between donor and recipient cells, thereby facilitating the spread of IncF plasmids among enteropathogenic bacteria. Here, we show that the F-pilus is highly flexible but robust at the same time, properties that increase its resistance to thermochemical and mechanical stresses. By a combination of biophysical and molecular dynamics methods, we establish that the presence of phosphatidylglycerol molecules in the F-pilus contributes to the structural stability of the polymer. Moreover, this structural stability is important for successful delivery of DNA during conjugation and facilitates rapid formation of biofilms in harsh environmental conditions. Thus, our work highlights the importance of F-pilus structural adaptations for the efficient spread of AMR genes in a bacterial population and for the formation of biofilms that protect against the action of antibiotics.
10.	The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data 2022 Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2 Tidskriftsartikel (refereegranskat)abstract This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
11.	Wayman, Joseph P., et al. (författare) Assessing taxonomic and functional change in British breeding bird assemblages over time 2022 Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 31:5, s. 925-939 Tidskriftsartikel (refereegranskat)abstract Aim: The aim was to identify the primary drivers of compositional change in breeding bird assemblages over a 40-year period. Location: Britain. Time period: From 1970 to 2010. Major taxa studied: Birds. Methods: Using morphological trait measurements and a dataset of presence–absence data for British breeding birds surveyed in 10 km × 10 km hectads during two time periods, we calculated temporal taxonomic and functional beta diversity for each hectad alongside the change in species richness, mean nearest taxon distance (MNTD) and mean pairwise distance (MPD). We also estimated potential drivers of beta diversity, including climatic and land-use and land-cover (LULC) change variables, elevation and assemblage species richness in 1970 (1970rich). We used random forest regressions to test which variables best explained compositional change in the assemblages. We also assessed spatial taxonomic and functional change by analysing multiple-site beta diversity and pairwise dissimilarities between time periods. Results: Initial (1970) species richness was the most important predictor (highest importance score) across all models, with areas characterized by higher initial richness experiencing less assemblage change overall. The coordinates included to capture spatial autocorrelation in the data were also important predictors of change. Most climate and LULC variables had relatively low explanatory power; elevation and average temperature were the most influential. All metrics increased slightly with increasing elevation, except for species richness change and MPD, which decreased. Main conclusions: The composition of British breeding bird assemblages changed substantially between 1970 and 2010. Spatial heterogeneity increased, both taxonomically and functionally. We show evidence that hectads with larger assemblages have been buffered from temporal diversity change and that those at higher elevations changed more in composition than those at lower elevations. Overall, coarse-resolution climate and LULC explained only small to moderate amounts of variation, suggesting that stochastic assembly change or finer-scale drivers might be drivers of temporal changes in assemblage composition.
12.	Wayman, Joseph P., et al. (författare) Identifying the Drivers of Spatial Taxonomic and Functional Beta-Diversity of British Breeding Birds 2021 Ingår i: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 9 Tidskriftsartikel (refereegranskat)abstract Spatial variation in community composition may be driven by a variety of processes, including environmental filtering and dispersal limitation. While work has been conducted on the relative importance of these processes on various taxa and at varying resolutions, tests using high-resolution empirical data across large spatial extents are sparse. Here, we use a dataset on the presence/absence of breeding bird species collected at the 10 km × 10 km scale across the whole of Britain. Pairwise spatial taxonomic and functional beta diversity, and the constituent components of each (turnover and nestedness/richness loss or gain), were calculated alongside two other measures of functional change (mean nearest taxon distance and mean pairwise distance). Predictor variables included climate and land use measures, as well as a measure of elevation, human influence, and habitat diversity. Generalized dissimilarity modeling was used to analyze the contribution of each predictor variable to variation in the different beta diversity metrics. Overall, we found that there was a moderate and unique proportion of the variance explained by geographical distance per se, which could highlight the role of dispersal limitation in community dissimilarity. Climate, land use, and human influence all also contributed to the observed patterns, but a large proportion of the explained variance in beta diversity was shared between these variables and geographical distance. However, both taxonomic nestedness and functional nestedness were uniquely predicted by a combination of land use, human influence, elevation, and climate variables, indicating a key role for environmental filtering. These findings may have important conservation implications in the face of a warming climate and future land use change.
13.	Abelev, Betty, et al. (författare) Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV 2013 Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41 Tidskriftsartikel (refereegranskat)abstract Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
14.	Abelev, Betty, et al. (författare) Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV 2012 Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11 Tidskriftsartikel (refereegranskat)abstract The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
15.	Abelev, Betty, et al. (författare) Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC 2012 Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7 Tidskriftsartikel (refereegranskat)abstract We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
16.	Anchang-Kimbi, Judith K., et al. (författare) Antenatal care visit attendance, intermittent preventive treatment during pregnancy (IPTp) and malaria parasitaemia at delivery 2014 Ingår i: Malaria Journal. - : Springer Science and Business Media LLC. - 1475-2875. ; 13, s. 162- Tidskriftsartikel (refereegranskat)abstract Background: The determinants and barriers for delivery and uptake of IPTp vary with different regions in sub-Saharan Africa. This study evaluated the determinants of ANC clinic attendance and IPTp-SP uptake among parturient women from Mount Cameroon Area and hypothesized that time of first ANC clinic attendance could influence uptake of IPTp-SP/dosage and consequently malaria parasite infection status at delivery. Methods: Two cross sectional surveys were carried out at the Government Medical Centre in the Mutengene Health Area, Mt Cameroon Area from March to October 2007 and June 2008 to April 2009. Consented parturient women were consecutively enrolled in both surveys. In 2007, socio-demographic data, ANC clinic attendance, gestational age, fever history and reported use/dosage of IPTp-SP were documented using a structured questionnaire. In the second survey only IPT-SP usage/dosage was recorded. Malaria parasitaemia at delivery was determined by blood smear microscopy and placental histology. Results and discussion: In 2007, among the 287 women interviewed, 2.2%, 59.7%, and 38.1% enrolled in the first, second and third trimester respectively. About 90% of women received at least one dose SP but only 53% received the two doses in 2007 and by 2009 IPTp-two doses coverage increased to 64%. Early clinic attendance was associated (P = 0.016) with fever history while being unmarried (OR = 2.2; 95% CI: 1.3-3.8) was significantly associated with fewer clinic visits (<4visits). Women who received one SP dose (OR = 3.7; 95% CI: 2.0-6.8) were more likely not to have attended >= 4visits. A higher proportion (P < 0.001) of women with first visit during the third trimester received only one dose, meanwhile, those who had an early first ANC attendance were more likely (OR = 0.4; 95% CI = 0.2 - 0.7) to receive two or more doses. Microscopic parasitaemia at delivery was frequent (P = 0.007) among women who enrolled in the third trimester and had received only one SP dose than in those with two doses. Conclusion: In the study area, late first ANC clinic enrolment and fewer clinic visits may prevent the uptake of two SP doses and education on early and regular ANC clinic visits can increase IPTp coverage.
17.	Baker, Joseph, et al. (författare) Impact of an alpha helix and a cysteine-cysteine disulfide bond on the resistance of bacterial adhesion pili to stress 2021 Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:21 Tidskriftsartikel (refereegranskat)abstract Escherichia coli express adhesion pili that mediate attachment to host cell surfaces and are exposed to body fluids in the urinary and gastrointestinal tracts. Pilin subunits are organized into helical polymers, with a tip adhesin for specific host binding. Pili can elastically unwind when exposed to fluid flow forces, reducing the adhesin load, thereby facilitating sustained attachment. Here we investigate biophysical and structural differences of pili commonly expressed on bacteria that inhabit the urinary and intestinal tracts. Optical tweezers measurements reveal that Class 1a pili of uropathogenic E. coli (UPEC), as well as Class 1b of enterotoxigenic E. coli (ETEC), undergo an additional conformational change beyond pilus unwinding, providing significantly more elasticity to their structure than ETEC Class 5 pili. Examining structural and steered molecular dynamics simulation data, we find this difference in Class 1 pili subunit behavior originates from an alpha-helical motif that can unfold when exposed to force. A disulfide bond cross-linking beta-strands in Class 1 pili stabilizes subunits, allowing them to tolerate higher forces than Class 5 pili that lack this covalent bond. We suggest that these extra contributions to pilus resiliency are relevant for the UPEC niche since resident bacteria are exposed to stronger, more transient drag forces compared to those experienced by ETEC bacteria in the mucosa of the intestinal tract. Interestingly, Class 1b ETEC pili include the same structural features seen in UPEC pili, while requiring lower unwinding forces that are more similar to those of Class 5 ETEC pili.
18.	Baker, Joseph, et al. (författare) Unveiling the Contributions of Secondary Structure and Disulfide Bonds for Bacterial Adhesion Pili Extension using a Multiscale Approach 2021 Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495. Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract Bacterial adhesion pili are essential virulence factors for many pathogenic Escherichia coli, including bacteria that cause urinary tract infections (UPEC) and diarrheal diseases (ETEC). To sustain adhesion under forces similar to those in the fluid environments of the urinary tract and gastrointestinal tract, these pili (also called fimbriae) can extend to over seven times their original length. Both UPEC and ETEC can uncoil their quaternary structure under pulling force and re-coil to their helical form when the force is reduced, as observed using optical tweezers. However, after extension to a linear polymer UPEC undergo an additional reversible conformational change, that is not seen in ETEC. The mechanism for this conformational change in UPEC is not known. Therefore, to obtain a comprehensive picture of pilus extension we have taken a synergistic approach that combines optical tweezer experiments, structural data from cryo-EM, and steered molecular dynamics simulations to investigate the response of pilin subunits to force.Our multi-faceted approach provides novel molecular-scale insights into the structural changes that occur in UPEC and ETEC pili under pulling forces. We find that the conformational change observed in UPEC pili in optical tweezer experiments is correlated with the presence of an alpha helix. In addition, structural analysis and steered molecular dynamics simulations show that there is a disulfide bond that provides additional stability of UPEC pilin subunits that is not observed in ETEC pilins, which lack cysteine residues. Together, these results suggest that the mechanism of extension of bacterial adhesion pili is related to their environmental niche, and the magnitude of fluid forces in the urinary tract versus the GI tract.
19.	Benselfelt, Tobias, 1989- (författare) Design of Cellulose-based Materials by Supramolecular Assemblies 2019 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Due to climate change and plastic pollution, there is an increasing demand for bio-based materials with similar properties to those of common plastics yet biodegradable. In this respect, cellulose is a strong candidate that is already being refined on a large industrial scale, but the properties differ significantly from those of common plastics in terms of shapeability and water-resilience.This thesis investigates how supramolecular interactions can be used to tailor the properties of cellulose-based materials by modifying cellulose surfaces or control the assembly of cellulose nanofibrils (CNFs). Most of the work is a fundamental study on interactions in aqueous environments, but some material concepts are presented and potential applications are discussed.The first part deals with the modification of cellulose by the spontaneous adsorption of xyloglucan or polyelectrolytes. The results indicate that xyloglucan adsorbs to cellulose due to the increased entropy of water released from the surfaces, which is similar to the increased entropy of released counter-ions that drives polyelectrolyte adsorption. The polyelectrolyte adsorption depends on the charge of the cellulose up to a limit after which the charge density affects only the first adsorbed layer in a multilayer formation.Latex nanoparticles with polyelectrolyte coronas can be adsorbed onto cellulose in order to prepare hydrophobic cellulose surfaces with strong and ductile wet adhesion, provided the glass transition of the core is below the ambient temperature.The second part of the thesis seeks to explain the interactions between different types of cellulose nanofibrils in the presence of different ions, using a model consisting of ion-ion correlation and specific ion effects, which can be employed to rationally design water-resilient and transparent nanocellulose films. The addition of small amounts of alginate also creates interpenetrating double networks, and these networks lead to a synergy which improves both the stiffness and the ductility of the films in water.A network model has been developed to understand these materials, with the aim to explain the properties of fibril networks, based on parameters such as the aspect ratio of the fibrils, the solidity of the network, and the ion-induced interactions that increase the friction between fibrils. With the help of this network model and the model for ion-induced interactions, we have created films with wet-strengths surpassing those of common plastics, or a ductility suitable for hygroplastic forming into water-resilient and biodegradable packages. Due to their transparency, water content, and the biocompatibility of cellulose, these materials are also suitable for biomaterial or bioelectronics applications.
20.	Beryani, Ali, et al. (författare) Occurrence, Concentration, and Distribution of 35 PFASs and Their Precursors Retained in 20 Stormwater Biofilters 2024 Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 58:32, s. 14518-14529 Tidskriftsartikel (refereegranskat)abstract Current knowledge about the fate and transport behaviors of per- and polyfluoroalkyl substances (PFASs) in urban stormwater biofilter facilities is very limited. C5–14,16 perfluoroalkyl carboxylic acids [perfluorinated carboxylic acids (PFCAs)], C4,8,10 perfluoroalkanesulfonic acids (PFSAs), methyl-perfluorooctane sulfonamide acetic acid (MeFOSAA, a PFSA precursor), and unknown C6–8 PFCA and perfluorooctanesulfonic acid precursors were frequently found in bioretention media and forebay sediments at Σ35PFAS concentrations of <0.03–19 and 0.064–16 μg/kg-DW, respectively. Unknown C6–8 PFCA precursor concentrations were up to ten times higher than the corresponding PFCAs, especially at forebays and biofilters’ top layer. No significant trend could be attributed to PFAS and precursor concentrations versus depth of filter media, though PFAS concentrations were 2–3 times higher in the upper layers on average (significant difference between the upper (0–5 cm) and deepest (35–50 cm) layer). PFASs had a similar spatial concentration distribution in each filter media (no clear difference between short- and long-chain PFASs). Commercial land use and organic matter were important factors explaining the concentration variations among the biofilters and between the sampling depths, respectively. Given the comparable PFAS accumulations in deeper and superficial layers and possible increased mobility after precursor biotransformation, designing shallow-depth, nonamended sand biofilters or maintaining only the top layer may be insufficient for stormwater PFAS management.
21.	Cagnoli, Patricia C, et al. (författare) Changes in Regional Brain Morphology in Neuropsychiatric Systemic Lupus Erythematosus. 2012 Ingår i: Journal of Rheumatology. - : The Journal of Rheumatology. - 0315-162X .- 1499-2752. ; 39:5, s. 959-967 Tidskriftsartikel (refereegranskat)abstract OBJECTIVE: Neuropsychiatric lupus (NPSLE) is a severe and potentially life-threatening condition, reported to occur in 25%-70% of patients with systemic lupus erythematosus (SLE). Brain imaging, especially magnetic resonance imaging, is frequently used to diagnose or exclude overt cerebral pathologies such as edema, hemorrhage, and central thrombosis. More advanced imaging techniques have been applied to demonstrate subtle changes in regional cerebral blood flow and brain structure. We investigated changes in regional gray-matter (GM) volume in SLE patients without neurological manifestations and NPSLE patients at an acute stage of the disease. METHODS: Using high-resolution structural images and voxel-based morphometry (VBM), we investigated regional GM volume in 20 NPSLE patients (within 2 weeks of the acute manifestation), 18 SLE patients without neurologic and/or psychiatric manifestations, and 18 healthy controls. RESULTS: VBM analyses revealed several regions of GM atrophy in various parts of the brain in NPSLE and SLE patients. GM atrophy was seen in both groups in the temporal and parietal lobes and was most pronounced in the posterior thalamus bilaterally. Both groups showed an increase in regional GM volume in the posterior parahippocampal gyrus. CONCLUSION: Our data suggest that changes in regional brain morphology are present in acute NPSLE, but also in SLE (as compared to controls), which might be indicative of a subclinical neurodegenerative process. Further research is needed to investigate whether specific neuropsychiatric symptoms are related to these changes.
22.	Chambers, Josephine M., et al. (författare) Co-productive agility and four collaborative pathways to sustainability transformations 2022 Ingår i: Global Environmental Change. - : Elsevier BV. - 0959-3780 .- 1872-9495. ; 72 Tidskriftsartikel (refereegranskat)abstract Co-production, the collaborative weaving of research and practice by diverse societal actors, is argued to play an important role in sustainability transformations. Yet, there is still poor understanding of how to navigate the tensions that emerge in these processes. Through analyzing 32 initiatives worldwide that co-produced knowledge and action to foster sustainable social-ecological relations, we conceptualize 'co-productive agility' as an emergent feature vital for turning tensions into transformations. Co-productive agility refers to the willingness and ability of diverse actors to iteratively engage in reflexive dialogues to grow shared ideas and actions that would not have been possible from the outset. It relies on embedding knowledge production within processes of change to constantly recognize, reposition, and navigate tensions and opportunities. Co-productive agility opens up multiple pathways to transformation through: (1) elevating marginalized agendas in ways that maintain their integrity and broaden struggles for justice; (2) questioning dominant agendas by engaging with power in ways that challenge assumptions, (3) navigating conflicting agendas to actively transform interlinked paradigms, practices, and structures; (4) exploring diverse agendas to foster learning and mutual respect for a plurality of perspectives. We explore six process considerations that vary by these four pathways and provide a framework to enable agility in sustainability transformations. We argue that research and practice spend too much time closing down debate over different agendas for change - thereby avoiding, suppressing, or polarizing tensions, and call for more efforts to facilitate better interactions among different agendas.
23.	Chambers, Josephine M., et al. (författare) Six modes of co-production for sustainability 2021 Ingår i: Nature Sustainability. - : Springer Science and Business Media LLC. - 2398-9629. ; 4, s. 983-996 Tidskriftsartikel (refereegranskat)abstract Co-production includes diverse aims, terminologies and practices. This study explores such diversity by mapping differences in how 32 initiatives from 6 continents co-produce diverse outcomes for the sustainable development of ecosystems at local to global scales. The promise of co-production to address complex sustainability challenges is compelling. Yet, co-production, the collaborative weaving of research and practice, encompasses diverse aims, terminologies and practices, with poor clarity over their implications. To explore this diversity, we systematically mapped differences in how 32 initiatives from 6 continents co-produce diverse outcomes for the sustainable development of ecosystems at local to global scales. We found variation in their purpose for utilizing co-production, understanding of power, approach to politics and pathways to impact. A cluster analysis identified six modes of co-production: (1) researching solutions; (2) empowering voices; (3) brokering power; (4) reframing power; (5) navigating differences and (6) reframing agency. No mode is ideal; each holds unique potential to achieve particular outcomes, but also poses unique challenges and risks. Our analysis provides a heuristic tool for researchers and societal actors to critically explore this diversity and effectively navigate trade-offs when co-producing sustainability.
24.	Dahlberg, Tobias, 1990-, et al. (författare) Unveiling molecular interactions that stabilize bacterial adhesion pili 2022 Ingår i: Biophysical Journal. - : Biophysical Society. - 0006-3495 .- 1542-0086. ; 121:11, s. 2096-2106 Tidskriftsartikel (refereegranskat)abstract Adhesion pili assembled by the chaperone-usher pathway are superelastic helical filaments on the surface of bacteria, optimized for attachment to target cells. Here, we investigate the biophysical function and structural interactions that stabilize P pili from uropathogenic bacteria. Using optical tweezers, we measure P pilus subunit-subunit interaction dynamics and show that pilus compliance is contour-length dependent. Atomic details of subunit-subunit interactions of pili under tension are shown using steered molecular dynamics (sMD) simulations. sMD results also indicate that the N-terminal “staple” region of P pili, which provides interactions with pilins that are four and five subunits away, significantly stabilizes the helical filament structure. These data are consistent with previous structural data, and suggest that more layer-to-layer interactions could compensate for the lack of a staple in type 1 pili. This study informs our understanding of essential structural and dynamic features of adhesion pili, supporting the hypothesis that the function of pili is critically dependent on their structure and biophysical properties.
25.	Dahlberg, Tobias, et al. (författare) Unveiling molecular interactions that stabilize the chaperone-usher pili rod and their role for mechanical and kinetic properties Annan publikation (övrigt vetenskapligt/konstnärligt)
26.	Doran, Matthew, et al. (författare) CS20 bridge the gap between class 1 and class 5 bacterial adhesion pili 2022 Ingår i: Biophysical Journal. - : Cell press. - 0006-3495 .- 1542-0086. ; 121:3, suppl. 1, s. 168a-168a Tidskriftsartikel (refereegranskat)abstract Enterotoxigenic Escherichia coli (ETEC) are pathogenic bacteria that cause diarrheal disease that disrupts the nutrition and the growth of children under the age of 5 and causes illness in travelers to countries where these bacteria are endemic. ETEC express long thin helical filaments on their surface, ∼1 micron long and 8 nm in diameter, called pili or fimbriae. Often essential virulence factors, these filaments, including ETEC CS20 pili, are composed of approximately 1,000 copies of the major pilin protein and one copy of a tip protein that provides binding specificity. While the structures of ETEC pili from different strains are similar, there are critical differences that alter their biophysical properties.ETEC express Class 1 and/or Class 5 pilins. The Class 1 CS20 pilin, CsbA, is genetically similar to FimA from Type 1 pili that are expressed on many strains of Escherichia coli, including bacteria that infect the urinary tract or the gastrointestinal tract, and also to PapA pilins expressed on bacteria that infect the kidneys. Thus, despite CS20 being expressed on ETEC, its pilin is genetically distant from the Class 5 CFA/I pilin, CfaB, the most commonly expressed ETEC pilin.We show here the three-dimensional structure and surface coulombic charge of CS20 pili, determined at 3.4 Å resolution by electron cryomicroscopy (cryo-EM). Our force spectroscopy data show that CS20 pili have a helix unwinding force that is twice that of CFA/I pili, and half that of Type 1 pili. Molecular dynamics simulations are further used to unveil features along the unwinding pathway at an atomistic scale. We see that CS20 pili bridge the genetic and environmental gap between Class 1 and Class 5 adhesion pili that are expressed on pathogenic bacteria.
27.	Doran, Matthew H., et al. (författare) Three structural solutions for bacterial adhesion pilus stability and superelasticity 2023 Ingår i: Structure. - : Elsevier. - 0969-2126 .- 1878-4186. Tidskriftsartikel (refereegranskat)abstract Bacterial adhesion pili are key virulence factors that mediate host-pathogen interactions in diverse epithelial environments. Deploying a multimodal approach, we probed the structural basis underpinning the biophysical properties of pili originating from enterotoxigenic (ETEC) and uropathogenic bacteria. Using cryo-electron microscopy we solved the structures of three vaccine target pili from ETEC bacteria, CFA/I, CS17, and CS20. Pairing these and previous pilus structures with force spectroscopy and steered molecular dynamics simulations, we find a strong correlation between subunit-subunit interaction energies and the force required for pilus unwinding, irrespective of genetic similarity. Pili integrate three structural solutions for stabilizing their assemblies: layer-to-layer interactions, N-terminal interactions to distant subunits, and extended loop interactions from adjacent subunits. Tuning of these structural solutions alters the biophysical properties of pili and promotes the superelastic behavior that is essential for sustained bacterial attachment.
28.	Ekanem, Emmanuel, et al. (författare) Safety of pulsed field ablation in more than 17,000 patients with atrial fibrillation in the MANIFEST-17K study 2024 Ingår i: Nature Medicine. - : NATURE PORTFOLIO. - 1078-8956 .- 1546-170X. Tidskriftsartikel (refereegranskat)abstract Pulsed field ablation (PFA) is an emerging technology for the treatment of atrial fibrillation (AF), for which pre-clinical and early-stage clinical data are suggestive of some degree of preferentiality to myocardial tissue ablation without damage to adjacent structures. Here in the MANIFEST-17K study we assessed the safety of PFA by studying the post-approval use of this treatment modality. Of the 116 centers performing post-approval PFA with a pentaspline catheter, data were received from 106 centers (91.4% participation) regarding 17,642 patients undergoing PFA (mean age 64, 34.7% female, 57.8% paroxysmal AF and 35.2% persistent AF). No esophageal complications, pulmonary vein stenosis or persistent phrenic palsy was reported (transient palsy was reported in 0.06% of patients; 11 of 17,642). Major complications, reported for similar to 1% of patients (173 of 17,642), were pericardial tamponade (0.36%; 63 of 17,642) and vascular events (0.30%; 53 of 17,642). Stroke was rare (0.12%; 22 of 17,642) and death was even rarer (0.03%; 5 of 17,642). Unexpected complications of PFA were coronary arterial spasm in 0.14% of patients (25 of 17,642) and hemolysis-related acute renal failure necessitating hemodialysis in 0.03% of patients (5 of 17,642). Taken together, these data indicate that PFA demonstrates a favorable safety profile by avoiding much of the collateral damage seen with conventional thermal ablation. PFA has the potential to be transformative for the management of patients with AF.
29.	Fazey, Ioan, et al. (författare) Transforming knowledge systems for life on Earth : Visions of future systems and how to get there 2020 Ingår i: Energy Research & Social Science. - : Elsevier. - 2214-6296 .- 2214-6326. ; 70 Tidskriftsartikel (refereegranskat)abstract Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
30.	Furén, Robert, Industridoktorand, et al. (författare) Concentration, distribution, and fractionation of metals in the filter material of 29 bioretention facilities: a field study 2023 Ingår i: Environmental Science. - : Royal Society of Chemistry. - 2053-1400 .- 2053-1419. ; 9:12, s. 3158-3173 Tidskriftsartikel (refereegranskat)abstract Pollutant loads stemming from anthropogenic activities conveyed in urban stormwater runoff contribute to the impairment of downstream water bodies. Cities and municipalities are increasingly turning toward green infrastructure stormwater control measures to treat pollutants at the source of runoff. One example of these technologies is bioretention, which is commonly applied for stormwater treatment in urban areas due to its demonstrated effectiveness in removing various pollutants from water, including sediment, nutrients (e.g., N and P), and metals. As metals are mainly removed by filtration or adsorption to soil particles, the filter media is important for metal removal in bioretention. However, the capacity to remove metals through adsorption by bioretention media is finite; thus, the media may need to be replaced and disposed of after maintenance or at the end of its operational lifespan. Pollutant accumulation in bioretention media has the potential to approach toxicity thresholds, which may introduce complexities for safe handling and disposal. To fully capture the potential challenges associated with metals accumulation in media over time, it is important to understand the accumulation processes and mobility of metals in bioretention facilities as they age. Although several studies have investigated metal accumulation and distribution in bioretention media, few have assessed metal mobility by fractionation using sequential extraction methods in older (i.e., >7 years) facilities. In November 2019, we conducted a comprehensive field study of older facilities in Ohio, Michigan, and Kentucky (USA) to improve the understanding of the accumulation processes and metal mobility in bioretention. In this study, concentrations of several metals (i.e., Cr, Cu, Ni, Pb, and Zn) were analyzed in samples of filter material from 29 bioretention sites in operation for 7–16 years. Except for Cd, all metals were found in all samples. Metals accumulation was clear with highest concentrations found in the top (0–5 cm) layer of the filter material, attributable to the filtration of particles percolating through the media profile. Lower concentrations were observed in deeper (i.e., >10 cm) layers of the bioretention media. The fractionation showed that the metals of interest were present at high levels with a risk of leaching over time, among which Cd, Zn, and Pb were suggested to be mobile from the filter material during precipitation. Thus, there is a potential risk of leakage from filter material or sediment removed from biofilters, e.g., during maintenance and disposal. The results of principal component analysis indicated specifically correlations between metal concentrations and the filter material soil texture including the organic matter content. These results contribute to improved design and operation and suggest regular maintenance to reduce long-term risks associated with the accumulation of metals in bioretention and similar urban stormwater treatment facilities. Since most metals are trapped in the top layer of the filter it may be enough to remove only the top layer. However, metal fractionation should be considered when handling the material.
31.	Furén, Robert, Industridoktorand, et al. (författare) Stormwater bioretention: Occurrence and accumulation of metals, PAHs, PCBs, alkylphenols, phthalates, PFASs and microplastics 2024 Konferensbidrag (övrigt vetenskapligt/konstnärligt)
32.	Gao, Hong, et al. (författare) The landscape of tolerated genetic variation in humans and primates 2023 Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6648 Tidskriftsartikel (refereegranskat)abstract Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
33.	Global hälsa : en praktisk guide 2023. - 2 Rapport (övrigt vetenskapligt/konstnärligt)abstract Introduktion: Behovet av ett globalt perspektiv på hälsa.Det har gått fem år sedan Global Hälsa – En praktisk guide släpptes. Sedan dess har världen förändrats. Covid-19-pandemin har i grunden påverkat förutsättningarna för den global hälsan och visar på hur svårt det är att isolera sig från globala hälsohot. Hälsokonsekvenserna av klimatförändringarna, liksom hälso- och sjukvårdens klimatpåverkan har tydliggjorts. Fler väpnade konflikter, inklusive kriget i Ukraina, riskerar många år av folkhälsoarbete. I kriser drabbas de fattigaste hårdast. Detta gäller globalt såväl som i Sverige.I årets halvtidsgenomgång av världens utvecklingsagenda, Agenda 2030 och de globala målen, konstateras att många viktiga framsteg har gjorts, men att dessa hotas av det förändrade världsläget. Ett förnyat fokus på globala hälsofrågor krävs och här är svensk kunskap viktig. Många av de utmaningar som Sverige står inför delar vi dessutom med andra länder, såsom till exempel personalbrist, som leder till stängda vårdplatser och för låg täckning i primärvården. Här kan vi lära av varandra.Svenska Läkaresällskapet har sedan 2013 aktivt arbetat med globala hälsofrågor, med övertygelsen om att större medvetenhet om global hälsa kan minska konsekvenserna från världens gemensamma utmaningar. Sedan den förra guiden kom ut har läkaresällskapet bidragit till mobilisering och kunskapsspridning om Covid-19 under pandemin, en hybridkonferens om planetär hälsa har hållits med världsledande forskare, och svensk hälso- och sjukvårds möjligheter att stötta den ukrainska befolkningen under pågående krig har lyfts i en webinarie-serie.Liksom förra gången är guiden framtagen av läkarstudenter och läkare tidigt i karriären under handledning av kommittén för global hälsa. Den är tänkt som ett handfast stöd för de som vill engagera sig för global hälsa – genom klinik, forskning eller folkhälsoarbete och berör bland annat hälso- och sjukvårdens utmaningar i omställningen till ett klimatneutralt samhälle.Fältets ambition om att skapa alltmer jämlika samarbeten, genom att ifrågasätta äldre beslutsstrukturer, berörs också som en röd tråd genom guiden.Därför vill vi rikta ett stort tack till de studenter och yngre läkare som med vägledning av projektledarna har möjliggjort denna nya och förbättrade upplaga av guiden!Tillsammans kan vi verka för förbättrad hälsa, här hemma och utomlands!
34.	Grüning, Björn, et al. (författare) Bioconda: A sustainable and comprehensive software distribution for the life sciences 2017 Annan publikation (övrigt vetenskapligt/konstnärligt)abstract We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
35.	Helbig, Manuel, et al. (författare) Integrating continuous atmospheric boundary layer and tower-based flux measurements to advance understanding of land-atmosphere interactions 2021 Ingår i: Agricultural and Forest Meteorology. - : Elsevier BV. - 0168-1923. ; 307 Forskningsöversikt (refereegranskat)abstract The atmospheric boundary layer mediates the exchange of energy, matter, and momentum between the land surface and the free troposphere, integrating a range of physical, chemical, and biological processes and is defined as the lowest layer of the atmosphere (ranging from a few meters to 3 km). In this review, we investigate how continuous, automated observations of the atmospheric boundary layer can enhance the scientific value of co-located eddy covariance measurements of land-atmosphere fluxes of carbon, water, and energy, as are being made at FLUXNET sites worldwide. We highlight four key opportunities to integrate tower-based flux measurements with continuous, long-term atmospheric boundary layer measurements: (1) to interpret surface flux and atmospheric boundary layer exchange dynamics and feedbacks at flux tower sites, (2) to support flux footprint modelling, the interpretation of surface fluxes in heterogeneous and mountainous terrain, and quality control of eddy covariance flux measurements, (3) to support regional-scale modeling and upscaling of surface fluxes to continental scales, and (4) to quantify land-atmosphere coupling and validate its representation in Earth system models. Adding a suite of atmospheric boundary layer measurements to eddy covariance flux tower sites, and supporting the sharing of these data to tower networks, would allow the Earth science community to address new emerging research questions, better interpret ongoing flux tower measurements, and would present novel opportunities for collaborations between FLUXNET scientists and atmospheric and remote sensing scientists.
36.	Hoffmann, Thomas J., et al. (författare) Genome-wide association study of prostate-specific antigen levels identifies novel loci independent of prostate cancer 2017 Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8 Tidskriftsartikel (refereegranskat)abstract Prostate-specific antigen (PSA) levels have been used for detection and surveillance of prostate cancer (PCa). However, factors other than PCa - such as genetics - can impact PSA. Here we present findings from a genome-wide association study (GWAS) of PSA in 28,503 Kaiser Permanente whites and 17,428 men from replication cohorts. We detect 40 genome-wide significant (P<5 × 10-8) single-nucleotide polymorphisms (SNPs): 19 novel, 15 previously identified for PSA (14 of which were also PCa-associated), and 6 previously identified for PCa only. Further analysis incorporating PCa cases suggests that at least half of the 40 SNPs are PSA-associated independent of PCa. The 40 SNPs explain 9.5% of PSA variation in non-Hispanic whites, and the remaining GWAS SNPs explain an additional 31.7%; this percentage is higher in younger men, supporting the genetic basis of PSA levels. These findings provide important information about genetic markers for PSA that may improve PCa screening, thereby reducing over-diagnosis and over-treatment.
37.	Huser, Brian, et al. (författare) Spatial and temporal variation in Arctic freshwater chemistry : Reflecting climate-induced landscape alterations and a changing template for biodiversity 2022 Ingår i: Freshwater Biology. - : John Wiley & Sons. - 0046-5070 .- 1365-2427. ; 67:1, s. 14-29 Tidskriftsartikel (refereegranskat)abstract 1. Freshwater chemistry across the circumpolar region was characterised using a pan-Arctic data set from 1,032 lake and 482 river stations. Temporal trends were estimated for Early (1970-1985), Middle (1986-2000), and Late (2001-2015) periods. Spatial patterns were assessed using data collected since 2001.2. Alkalinity, pH, conductivity, sulfate, chloride, sodium, calcium, and magnesium (major ions) were generally higher in the northern-most Arctic regions than in the Near Arctic (southern-most) region. In particular, spatial patterns in pH, alkalinity, calcium, and magnesium appeared to reflect underlying geology, with more alkaline waters in the High Arctic and Sub Arctic, where sedimentary bedrock dominated.3. Carbon and nutrients displayed latitudinal trends, with lower levels of dissolved organic carbon (DOC), total nitrogen, and (to a lesser extent) total phosphorus (TP) in the High and Low Arctic than at lower latitudes. Significantly higher nutrient levels were observed in systems impacted by permafrost thaw slumps.4. Bulk temporal trends indicated that TP was higher during the Late period in the High Arctic, whereas it was lower in the Near Arctic. In contrast, DOC and total nitrogen were both lower during the Late period in the High Arctic sites. Major ion concentrations were higher in the Near, Sub, and Low Arctic during the Late period, but the opposite bulk trend was found in the High Arctic.5. Significant pan-Arctic temporal trends were detected for all variables, with the most prevalent being negative TP trends in the Near and Sub Arctic, and positive trends in the High and Low Arctic (mean trends ranged from +0.57%/year in the High/Low Arctic to -2.2%/year in the Near Arctic), indicating widespread nutrient enrichment at higher latitudes and oligotrophication at lower latitudes.6. The divergent P trends across regions may be explained by changes in deposition and climate, causing decreased catchment transport of P in the south (e.g. increased soil binding and trapping in terrestrial vegetation) and increased P availability in the north (deepening of the active layer of the permafrost and soil/sediment sloughing). Other changes in concentrations of major ions and DOC were consistent with projected effects of ongoing climate change. Given the ongoing warming across the Arctic, these region-specific changes are likely to have even greater effects on Arctic water quality, biota, ecosystem function and services, and human well-being in the future.
38.	Kehoe, Laura, et al. (författare) Inclusion, Transparency, and Enforcement: How the EU-Mercosur Trade Agreement Fails the Sustainability Test Comment 2020 Ingår i: One Earth. - : Elsevier BV. - 2590-3322 .- 2590-3330. ; 3:3, s. 268-272 Tidskriftsartikel (refereegranskat)abstract Trade agreements could help to protect human rights, critical ecosystems, and the climate-but only if sustainability becomes a cornerstone of international trade. The EU-Mercosur trade agreement fails to meet our three tenets of sustainable trade agreements: (1) inclusion of local communities, (2) transparency mechanisms to trace commodities and provide open-access information, and (3) enforcement to legally uphold sustainability commitments.
39.	Kjær, Kasper S., et al. (författare) Ligand manipulation of charge transfer excited state relaxation and spin crossover in [Fe(2,2'-bipyridine)2(CN)2] 2017 Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 4:4 Tidskriftsartikel (refereegranskat)abstract We have used femtosecond resolution UV-visible and Kβ x-ray emission spectroscopy to characterize the electronic excited state dynamics of [Fe(bpy)2(CN)2], where bpy=2,20-bipyridine, initiated by metal-to-ligand charge transfer (MLCT) excitation. The excited-state absorption in the transient UV-visible spectra, associated with the 2,20-bipyridine radical anion, provides a robust marker for the MLCT excited state, while the transient Kβ x-ray emission spectra provide a clear measure of intermediate and high spin metal-centered excited states. From these measurements, we conclude that the MLCT state of [Fe(bpy)2(CN)2] undergoes ultrafast spin crossover to a metalcentered quintet excited state through a short lived metal-centered triplet transient species. These measurements of [Fe(bpy)2(CN)2] complement prior measurement performed on [Fe(bpy)3]2+ and [Fe(bpy)(CN)4]2- in dimethylsulfoxide solution and help complete the chemical series [Fe(bpy)N(CN)6-2N]2N-4, whereN=1-3. The measurements confirm that simple ligand modifications can significantly change the relaxation pathways and excited state lifetimes and support the further investigation of light harvesting and photocatalytic applications of 3d transition metal complexes.
40.	Klein, Alison P., et al. (författare) Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer 2018 Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 9 Tidskriftsartikel (refereegranskat)abstract In 2020, 146,063 deaths due to pancreatic cancer are estimated to occur in Europe and the United States combined. To identify common susceptibility alleles, we performed the largest pancreatic cancer GWAS to date, including 9040 patients and 12,496 controls of European ancestry from the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4). Here, we find significant evidence of a novel association at rs78417682 (7p12/TNS3, P = 4.35 x 10(-8)). Replication of 10 promising signals in up to 2737 patients and 4752 controls from the PANcreatic Disease ReseArch (PAN-DoRA) consortium yields new genome-wide significant loci: rs13303010 at 1p36.33 (NOC2L, P = 8.36 x 10(-14)), rs2941471 at 8q21.11 (HNF4G, P = 6.60 x 10(-10)), rs4795218 at 17q12 (HNF1B, P = 1.32 x 10(-8)), and rs1517037 at 18q21.32 (GRP, P = 3.28 x 10(-8)). rs78417682 is not statistically significantly associated with pancreatic cancer in PANDoRA. Expression quantitative trait locus analysis in three independent pancreatic data sets provides molecular support of NOC2L as a pancreatic cancer susceptibility gene.
41.	Lange, Katharina, et al. (författare) Abundance, distribution, and composition of microplastics in the filter media of nine aged stormwater bioretention systems 2023 Ingår i: Chemosphere. - : Elsevier Ltd. - 0045-6535 .- 1879-1298. ; 320 Tidskriftsartikel (refereegranskat)abstract Bioretention systems are designed for quality treatment of stormwater. Particulate contaminants are commonly treated efficiently and accumulate mainly in the surface layer of the bioretention filter material. However, concerns exist that microplastic particles may not show equal accumulation behavior as other sediment particles. So far only two field and two laboratory studies are available on the fate of microplastics in few relatively newly built bioretention systems. Therefore, this study investigated the abundance and distribution of microplastics in nine 7–12 years old stormwater bioretention systems. It was found that microplastics generally accumulate on the surface of bioretention systems. Microplastic median particle concentrations decreased significantly from the surface layer (0–5 cm) of the filter material to the 10–15 cm depth layer from 448 to 136 particles/100 g, respectively. The distance to the inlet did not significantly affect the surface accumulation of microplastic particles, suggesting modest spatial variability in microplastics accumulation in older bioretention systems. Further, this study investigated the polymer composition in bioretention systems. It was shown that PP, EVA, PS and EPDM rubber are the most abundant polymer types in bioretention systems. Also, it was found that large percentages of microplastic particles are black particles (median percentage of black particles: 39%) which were found in 28 of the 33 investigated samples. This underlines the importance of including black particles in microplastic studies on stormwater, which has been overlooked in most previous studies.
42.	Machiela, Mitchell J., et al. (författare) Characterization of Large Structural Genetic Mosaicism in Human Autosomes 2015 Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 96:3, s. 487-497 Tidskriftsartikel (refereegranskat)abstract Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 x 3 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.
43.	Machiela, Mitchell J, et al. (författare) Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome 2016 Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 7 Tidskriftsartikel (refereegranskat)abstract To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.
44.	Maehrlein, Sebastian F., et al. (författare) Dissecting spin-phonon equilibration in ferrimagnetic insulators by ultrafast lattice excitation 2018 Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 4:7 Tidskriftsartikel (refereegranskat)abstract To gain control over magnetic order on ultrafast time scales, a fundamental understanding of the way electron spins interact with the surrounding crystal lattice is required. However, measurement and analysis even of basic collective processes such as spin-phonon equilibration have remained challenging. Here, we directly probe the flow of energy and angular momentum in the model insulating ferrimagnet yttrium iron garnet. After ultrafast resonant lattice excitation, we observe that magnetic order reduces on distinct time scales of 1 ps and 100 ns. Temperature-dependent measurements, a spin-coupling analysis, and simulations show that the two dynamics directly reflect two stages of spin lattice equilibration. On the 1-ps scale, spins and phonons reach quasi-equilibrium in terms of energy through phonon-induced modulation of the exchange interaction. This mechanism leads to identical demagnetization of the ferrimagnet's two spin sublattices and to a previously inaccessible ferrimagnetic state of increased temperature yet unchanged total magnetization. Finally, on the much slower, 100-ns scale, the excess of spin angular momentum is released to the crystal lattice, resulting in full equilibrium. Our findings are relevant for all insulating ferrimagnets and indicate that spin manipulation by phonons, including the spin Seebeck effect, can be extended to antiferromagnets and into the terahertz frequency range.
45.	Nyström, Anna-Greta, et al. (författare) Current issues of sustainability in esports 2022 Ingår i: International Journal of Esports. - : International Journal of Esports. - 2634-1069. ; 1:1 Tidskriftsartikel (refereegranskat)abstract Aims: The aim of the paper is to explore emerging themes, which support the development of a sustainable esports industry.Methods and results: This study is based on a workshop methodology, which aims to identify and explore topics perceived as most pertinent by individuals with an intimate understanding of the dynamics of the esports context. Two workshops were held with a total of 64 participants, representing both academia and industry stakeholders. Interpretations of the sustainability of esports were thus recorded, developed, critiqued, and refined through social interaction with experts. The results indicate three critical themes to address regarding the development of sustainability of esports, namely a) health and inclusiveness, b) the incomplete industry structure, and c) the immature business logic.Conclusions: Sustainability refers to the ability of esports to survive or persist. We argue that sustainability is dependent on how well industry stakeholders can address the identified themes. Currently, social sustainability is the primary concern of both practitioners and researchers of esports. Economic sustainability mostly deals with securing business growth, while environmental sustainability is not yet perceived as a relevant topic (e.g., using sustainable technologies and energy-saving related to gaming and competitive events). Structures and processes within esports presently constitute the focus of sustainability in esports.
46.	Olofsson, Tobias, et al. (författare) A scientific note on the lactic acid bacterial flora within the honeybee subspecies Apis mellifera (Buckfast), A. m. scutellata, A. m. mellifera, and A. m. monticola 2011 Ingår i: Apidologie. - : Springer Science and Business Media LLC. - 0044-8435 .- 1297-9678. ; 42:6, s. 696-699 Tidskriftsartikel (refereegranskat)
47.	Persson, Jonas, et al. (författare) Food quantity and quality regulation of trophic transfer between primary producers and a keystone grazer (Daphnia) in pelagic freshwater food webs 2007 Ingår i: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 116:7, s. 1152-1163 Tidskriftsartikel (refereegranskat)abstract The transfer of energy and nutrients from plants to animals is a key process in all ecosystems. In lakes, inefficient transfer of primary producer derived energy can result in low animal growth rates, accumulation of nuisance phytoplankton blooms and dissipation of energy from the ecosystem. Most research on carbon transfer efficiency in pelagic food webs has focused on either food quantity or food quality, with the latter considered separately as either elemental stoichiometry or biochemical composition. The natural occurrence and magnitude of these types of growth limitations and their combined effects on Daphnia, a keystone grazer in pelagic freshwater ecosystems, are largely unknown. Our empirical models predict that the strength and nature of food quantity and quality limitation varies greatly with lake trophic state (total phosphorus, TP) and that Daphnia growth rates and thus energy and nutrient transfer efficiency are highest in lakes with intermediate trophic status (TP 10-25 μg l−1). We predict that food availability place the greatest constraint on Daphnia growth in nutrient poor lakes (TP≤4 μg l−1). Phosphorus limitation of Daphnia growth increased with decreasing TP, but the overall effect was never predicted to be the dominant constraining factor. Eicosapentaenoic acid (EPA, 20:5ω3) limitation was predicted to occur in both nutrient poor and nutrient rich lakes and placed the primary constraint on food quality in the most productive lakes. Two contrasting EPA-models gave different results on the magnitude of EPA-limitation, implying that additional food quality factors decrease Daphnia growth at high TP. In conclusion, the model predicts that Daphnia growth should peak in mesotrophic lakes, food quantity will place the greatest constraint on growth in oligotrophic lakes and EPA will primarily limit growth in eutrophic lakes.
48.	Petersen, Gloria M, et al. (författare) A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33 2010 Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:3, s. 224-228 Tidskriftsartikel (refereegranskat)abstract We conducted a genome-wide association study of pancreatic cancer in 3,851 affected individuals (cases) and 3,934 unaffected controls drawn from 12 prospective cohort studies and 8 case-control studies. Based on a logistic regression model for genotype trend effect that was adjusted for study, age, sex, self-described ancestry and five principal components, we identified eight SNPs that map to three loci on chromosomes 13q22.1, 1q32.1 and 5p15.33. Two correlated SNPs, rs9543325 (P = 3.27 x 10(-11), per-allele odds ratio (OR) 1.26, 95% CI 1.18-1.35) and rs9564966 (P = 5.86 x 10(-8), per-allele OR 1.21, 95% CI 1.13-1.30), map to a nongenic region on chromosome 13q22.1. Five SNPs on 1q32.1 map to NR5A2, and the strongest signal was at rs3790844 (P = 2.45 x 10(-10), per-allele OR 0.77, 95% CI 0.71-0.84). A single SNP, rs401681 (P = 3.66 x 10(-7), per-allele OR 1.19, 95% CI 1.11-1.27), maps to the CLPTM1L-TERT locus on 5p15.33, which is associated with multiple cancers. Our study has identified common susceptibility loci for pancreatic cancer that warrant follow-up studies.
49.	Pham, Thu Thi, et al. (författare) Pre-diagnostic circulating resistin concentrations and mortality among individuals with colorectal cancer : results from the european prospective investigation into cancer and nutrition study 2024 Ingår i: International Journal of Cancer. - : John Wiley & Sons. - 0020-7136 .- 1097-0215. ; 154:9, s. 1596-1606 Tidskriftsartikel (refereegranskat)abstract Resistin is a protein involved in inflammation and angiogenesis processes and may play a role in the progression of colorectal cancer (CRC). However, it remains unclear whether resistin is associated with increased mortality after CRC diagnosis. We examined pre-diagnostic serum resistin concentrations in relation to CRC-specific and all-cause mortality among 1343 incident CRC cases from the European Prospective Investigation into Cancer and Nutrition cohort. For CRC-specific mortality as the primary outcome, hazard ratios (HRs) and 95% confidence intervals (95% CI) were estimated from competing risk analyses based on cause-specific Cox proportional hazards models and further in sensitivity analyses using Fine–Gray proportional subdistribution hazards models. For all-cause mortality as the secondary outcome, Cox proportional hazards models were used. Subgroup analyses were performed by sex, tumor subsite, tumor stage, body mass index and time to CRC diagnosis. Resistin was measured on a median of 4.8 years before CRC diagnosis. During a median follow-up of 8.2 years, 474 deaths from CRC and 147 deaths from other causes were observed. Resistin concentrations were not associated with CRC-specific mortality (HRQ4vsQ1 = 0.95, 95% CI: 0.73–1.23; Ptrend =.97; and HRper doubling of resistin concentration = 1.00; 95% CI: 0.84–1.19; P =.98) or all-cause mortality. Results from competing risk (sensitivity) analysis were similar. No associations were found in any subgroup analyses. These findings suggest no association between pre-diagnostic circulating resistin concentrations and CRC-specific or all-cause mortality among persons with CRC, and the potential insignificance of resistin in CRC progression.
50.	Quentin, Audrey G, et al. (författare) Non-structural carbohydrates in woody plants compared among laboratories. 2015 Ingår i: Tree physiology. - : Oxford University Press (OUP). - 1758-4469 .- 0829-318X. ; 35:11, s. 1146-1165 Tidskriftsartikel (refereegranskat)abstract Non-structural carbohydrates (NSC) in plant tissue are frequently quantified to make inferences about plant responses to environmental conditions. Laboratories publishing estimates of NSC of woody plants use many different methods to evaluate NSC. We asked whether NSC estimates in the recent literature could be quantitatively compared among studies. We also asked whether any differences among laboratories were related to the extraction and quantification methods used to determine starch and sugar concentrations. These questions were addressed by sending sub-samples collected from five woody plant tissues, which varied in NSC content and chemical composition, to 29 laboratories. Each laboratory analyzed the samples with their laboratory-specific protocols, based on recent publications, to determine concentrations of soluble sugars, starch and their sum, total NSC. Laboratory estimates differed substantially for all samples. For example, estimates for Eucalyptus globulus leaves (EGL) varied from 23 to 116 (mean = 56) mg g(-1) for soluble sugars, 6-533 (mean = 94) mg g(-1) for starch and 53-649 (mean = 153) mg g(-1) for total NSC. Mixed model analysis of variance showed that much of the variability among laboratories was unrelated to the categories we used for extraction and quantification methods (method category R(2) = 0.05-0.12 for soluble sugars, 0.10-0.33 for starch and 0.01-0.09 for total NSC). For EGL, the difference between the highest and lowest least squares means for categories in the mixed model analysis was 33 mg g(-1) for total NSC, compared with the range of laboratory estimates of 596 mg g(-1). Laboratories were reasonably consistent in their ranks of estimates among tissues for starch (r = 0.41-0.91), but less so for total NSC (r = 0.45-0.84) and soluble sugars (r = 0.11-0.83). Our results show that NSC estimates for woody plant tissues cannot be compared among laboratories. The relative changes in NSC between treatments measured within a laboratory may be comparable within and between laboratories, especially for starch. To obtain comparable NSC estimates, we suggest that users can either adopt the reference method given in this publication, or report estimates for a portion of samples using the reference method, and report estimates for a standard reference material. Researchers interested in NSC estimates should work to identify and adopt standard methods.

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