SwePub
Sök i SwePub databas

  Extended search

Träfflista för sökning "WFRF:(Schramm Andreas) "

Search: WFRF:(Schramm Andreas)

  • Result 1-50 of 60
Sort/group result
   
EnumerationReferenceCoverFind
1.
  • 2019
  • Journal article (peer-reviewed)
  •  
2.
  • Eme, Laura, et al. (author)
  • Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
  • 2023
  • In: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 618:7967, s. 992-
  • Journal article (peer-reviewed)abstract
    • In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes(1). However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved(2-4). Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.
  •  
3.
  • Stief, Peter, et al. (author)
  • Intracellular nitrate storage by diatoms can be an important nitrogen pool in freshwater and marine ecosystems
  • 2022
  • In: Communications Earth and Environment. - : Springer Science and Business Media LLC. - 2662-4435. ; 3:1
  • Journal article (peer-reviewed)abstract
    • Identifying and quantifying nitrogen pools is essential for understanding the nitrogen cycle in aquatic ecosystems. The ubiquitous diatoms represent an overlooked nitrate pool as they can accumulate nitrate intracellularly and utilize it for nitrogen assimilation, dissipation of excess photosynthetic energy, and Dissimilatory Nitrate Reduction to Ammonium (DNRA). Here, we document the global co-occurrence of diatoms and intracellular nitrate in phototrophic microbial communities in freshwater (n = 69), coastal (n = 44), and open marine (n = 4) habitats. Diatom abundance and total intracellular nitrate contents in water columns, sediments, microbial mats, and epilithic biofilms were highly significantly correlated. In contrast, diatom community composition had only a marginal influence on total intracellular nitrate contents. Nitrate concentrations inside diatom cells exceeded ambient nitrate concentrations ∼100–4000-fold. The collective intracellular nitrate pool of the diatom community accounted for <1% of total nitrate in pelagic habitats and 65–95% in benthic habitats. Accordingly, nitrate-storing diatoms are emerging as significant contributors to benthic nitrogen cycling, in particular through Dissimilatory Nitrate Reduction to Ammonium activity under anoxic conditions.
  •  
4.
  •  
5.
  •  
6.
  •  
7.
  •  
8.
  •  
9.
  •  
10.
  •  
11.
  •  
12.
  •  
13.
  •  
14.
  •  
15.
  •  
16.
  •  
17.
  •  
18.
  •  
19.
  •  
20.
  •  
21.
  • Abbasi, Maisam, et al. (author)
  • Themes and Challenges in Making Supply Chains Socially Sustainable
  • 2014
  • In: [Host publication title missing]. - 9788799743308 ; , s. 182-200
  • Conference paper (peer-reviewed)abstract
    • Purpose Purpose of this paper is to explore and classify pattern of the currently discussed themes and challenges in making supply chains socially sustainable. Design/methodology/approach The methodology was based on a systematic review of the existing literature in order to explore what major themes and challenges have been discussed as well as the significant gaps where opportunities for further research can be found. Findings In total five categories of themes were identified, namely goods/service-centric, humancentric, organization-centric, corporate-centric, and management/governance-centric. Challenges were classified into eight categories namely, inadequate and asymmetric knowledge, shifting the values, operationalization, subjectivity in evaluation, difficulties of SMEs, governance complexity,sustainability leakage, and sustainability washing. Research limitations/implications Focus of the paper is on social pillar of sustainable development in context of supply chains. A more holistic investigation of all the three pillars/ bottom lines of sustainable development (economic, environmental, and social) can be an opportunity for further research. Practical implications Taking a more holistic view of the pattern of currently discussed themes and challenges may be beneficial in increasing the absorptive capacity of industrial and business practitioners when they design and operationalize innovative strategies in developing sustainable supply chains. Originality/value This paper may increase awareness about the social responsibilities of supply chains actors and stakeholders. It may also guide managers, decision makers, and practitioners to better understand the difficulties, obstacles, or dilemmas that can hinder sustainable development of supply chains. The discussion section provides suggestions for tackling the challenges and a section that elaborates on opportunities for further research.
  •  
22.
  • Abbasi, Maisam, et al. (author)
  • Who controls logistics emissions? Challenges in making fragmented supply chains environmentally sustainable from a logistics service provider's perspective
  • 2014
  • In: Proceedings of the 26th Conference of the Nordic Logistics Research Network: NOFOMA 2014. - 9788799743308 ; , s. 201-218
  • Conference paper (peer-reviewed)abstract
    • Purpose The purpose of this article is to explore the environmental impact of Logistics Service Provider (LSP) activities in the light of increased customer attention and fragmentation of the industry. We try to answer the question, to what extent the LSPs can actually monitor the environmental impact of logistics activities in the supply chain? Design/methodology/approach The methodology of this paper is a literature review, a qualitative interview survey, and three case studies. A framework on sustainability challenges in supply chains derived from the literature is used to structure and analyze the findings. Findings Our findings reveal that despite ambitious environmental schemes communicated by several LSPs, LSPs exert very little control over the actual emissions created from their transport operations. Furthermore, it is clear from this study that any real interest in environmental solutions that impact the cost and time requirements from customers of logistics services are not yet a reality. Research limitations/implications This paper implies that LSP sustainability cannot be investigated in isolation if a company does not manage proprietary resources. Practical implications Our findings imply that environmental policies between different LSPs appear similar, but in practice differs, which stresses the importance of follow-up control by environmentally aware logistics service buyers. Originality/value This paper represents a novel approach as to how LSP environmental policies should be viewed.
  •  
23.
  • Abercrombie, Daniel, et al. (author)
  • Dark Matter benchmark models for early LHC Run-2 Searches : Report of the ATLAS/CMS Dark Matter Forum
  • 2020
  • In: Physics of the Dark Universe. - : Elsevier BV. - 2212-6864. ; 27
  • Journal article (peer-reviewed)abstract
    • This document is the final report of the ATLAS-CMS Dark Matter Forum, a forum organized by the ATLAS and CMS collaborations with the participation of experts on theories of Dark Matter, to select a minimal basis set of dark matter simplified models that should support the design of the early LHC Run-2 searches. A prioritized, compact set of benchmark models is proposed, accompanied by studies of the parameter space of these models and a repository of generator implementations. This report also addresses how to apply the Effective Field Theory formalism for collider searches and present the results of such interpretations.
  •  
24.
  • Adjuik, Martin A., et al. (author)
  • The effect of dosing strategies on the therapeutic efficacy of artesunate-amodiaquine for uncomplicated malaria : a meta-analysis of individual patient data
  • 2015
  • In: BMC Medicine. - : Springer Science and Business Media LLC. - 1741-7015. ; 13
  • Journal article (peer-reviewed)abstract
    • Background: Artesunate-amodiaquine (AS-AQ) is one of the most widely used artemisinin-based combination therapies (ACTs) to treat uncomplicated Plasmodium falciparum malaria in Africa. We investigated the impact of different dosing strategies on the efficacy of this combination for the treatment of falciparum malaria. Methods: Individual patient data from AS-AQ clinical trials were pooled using the WorldWide Antimalarial Resistance Network (WWARN) standardised methodology. Risk factors for treatment failure were identified using a Cox regression model with shared frailty across study sites. Results: Forty-three studies representing 9,106 treatments from 1999-2012 were included in the analysis; 4,138 (45.4%) treatments were with a fixed dose combination with an AQ target dose of 30 mg/kg (FDC), 1,293 (14.2%) with a non-fixed dose combination with an AQ target dose of 25 mg/kg (loose NFDC-25), 2,418 (26.6%) with a non-fixed dose combination with an AQ target dose of 30 mg/kg (loose NFDC-30), and the remaining 1,257 (13.8%) with a co-blistered non-fixed dose combination with an AQ target dose of 30 mg/kg (co-blistered NFDC). The median dose of AQ administered was 32.1 mg/kg [IQR: 25.9-38.2], the highest dose being administered to patients treated with co-blistered NFDC (median = 35.3 mg/kg [IQR: 30.6-43.7]) and the lowest to those treated with loose NFDC-25 (median = 25.0 mg/kg [IQR: 22.7-25.0]). Patients treated with FDC received a median dose of 32.4 mg/kg [IQR: 27-39.0]. After adjusting for reinfections, the corrected antimalarial efficacy on day 28 after treatment was similar for co-blistered NFDC (97.9% [95% confidence interval (CI): 97.0-98.8%]) and FDC (98.1% [95% CI: 97.6%-98.5%]; P = 0.799), but significantly lower for the loose NFDC-25 (93.4% [95% CI: 91.9%-94.9%]), and loose NFDC-30 (95.0% [95% CI: 94.1%-95.9%]) (P < 0.001 for all comparisons). After controlling for age, AQ dose, baseline parasitemia and region; treatment with loose NFDC-25 was associated with a 3.5-fold greater risk of recrudescence by day 28 (adjusted hazard ratio, AHR = 3.51 [95% CI: 2.02-6.12], P < 0.001) compared to FDC, and treatment with loose NFDC-30 was associated with a higher risk of recrudescence at only three sites. Conclusions: There was substantial variation in the total dose of amodiaquine administered in different AS-AQ combination regimens. Fixed dose AS-AQ combinations ensure optimal dosing and provide higher antimalarial treatment efficacy than the loose individual tablets in all age categories.
  •  
25.
  • Bergquist, Annika, et al. (author)
  • Impact on follow-up strategies in patients with primary sclerosing cholangitis
  • 2023
  • In: Liver international (Print). - Chichester, United Kingdom : Wiley-Blackwell Publishing Inc.. - 1478-3223 .- 1478-3231. ; 43:1, s. 127-138
  • Journal article (peer-reviewed)abstract
    • BACKGROUND & AIMS: Evidence for the benefit of scheduled imaging for early detection of hepatobiliary malignancies in primary sclerosing cholangitis (PSC) is limited. We aimed to compare different follow-up strategies in PSC with the hypothesis that regular imaging improves survival.METHODS: We collected retrospective data from 2,975 PSC patients from 27 centers. Patients were followed from the start of scheduled imaging or in case of clinical follow-up from January 1, 2000, until death or last clinical follow-up alive. The primary endpoint was all-cause mortality.RESULTS: A broad variety of different follow-up strategies were reported. All except one center used regular imaging, ultrasound (US) and/or magnetic resonance imaging (MRI). Two centers used scheduled ERCP in addition to imaging for surveillance purposes. The overall HR (CI95%) for death, adjusted for sex, age and start year of follow-up, were 0.61 (0.47-0.80) for scheduled imaging with and without ERCP; 0.64 (0.48-0.86) for US/MRI and 0.53 (0.37-0.75) for follow-up strategies including scheduled ERCP. The lower risk of death remained for scheduled imaging with and without ERCP after adjustment for cholangiocarcinoma (CCA) or high-grade dysplasia as a time-dependent covariate, HR 0.57 (0.44-0.75). Hepatobiliary malignancy was diagnosed in 175 (5.9%) of the patients at 7.9 years follow-up. Asymptomatic patients (25%) with CCA had better survival if scheduled imaging had been performed.CONCLUSIONS: Follow-up strategies vary considerably across centers. Scheduled imaging was associated with improved survival. Multiple factors may contribute to this result including early tumor detection and increased endoscopic treatment of asymptomatic benign biliary strictures.
  •  
26.
  •  
27.
  • Dahal, Prabin, et al. (author)
  • Competing risk events in antimalarial drug trials in uncomplicated Plasmodium falciparum malaria : a WorldWide Antimalarial Resistance Network individual participant data meta-analysis
  • 2019
  • In: Malaria Journal. - : BMC. - 1475-2875. ; 18
  • Journal article (peer-reviewed)abstract
    • Background: Therapeutic efficacy studies in uncomplicated Plasmodium falciparum malaria are confounded by new infections, which constitute competing risk events since they can potentially preclude/pre-empt the detection of subsequent recrudescence of persistent, sub-microscopic primary infections.Methods: Antimalarial studies typically report the risk of recrudescence derived using the Kaplan-Meier (K-M) method, which considers new infections acquired during the follow-up period as censored. Cumulative Incidence Function (CIF) provides an alternative approach for handling new infections, which accounts for them as a competing risk event. The complement of the estimate derived using the K-M method (1 minus K-M), and the CIF were used to derive the risk of recrudescence at the end of the follow-up period using data from studies collated in the WorldWide Antimalarial Resistance Network data repository. Absolute differences in the failure estimates derived using these two methods were quantified. In comparative studies, the equality of two K-M curves was assessed using the log-rank test, and the equality of CIFs using Gray's k-sample test (both at 5% level of significance). Two different regression modelling strategies for recrudescence were considered: cause-specific Cox model and Fine and Gray's sub-distributional hazard model.Results: Data were available from 92 studies (233 treatment arms, 31,379 patients) conducted between 1996 and 2014. At the end of follow-up, the median absolute overestimation in the estimated risk of cumulative recrudescence by using 1 minus K-M approach was 0.04% (interquartile range (IQR): 0.00-0.27%, Range: 0.00-3.60%). The overestimation was correlated positively with the proportion of patients with recrudescence [Pearson's correlation coefficient (rho): 0.38, 95% Confidence Interval (CI) 0.30-0.46] or new infection [rho: 0.43; 95% CI 0.35-0.54]. In three study arms, the point estimates of failure were greater than 10% (the WHO threshold for withdrawing antimalarials) when the K-M method was used, but remained below 10% when using the CIF approach, but the 95% confidence interval included this threshold.Conclusions: The 1 minus K-M method resulted in a marginal overestimation of recrudescence that became increasingly pronounced as antimalarial efficacy declined, particularly when the observed proportion of new infection was high. The CIF approach provides an alternative approach for derivation of failure estimates in antimalarial trials, particularly in high transmission settings.
  •  
28.
  • Davies, Lucy Rebecca, et al. (author)
  • The importance of environmental microbes for Drosophila melanogaster during seasonal macronutrient variability
  • 2021
  • In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
  • Journal article (peer-reviewed)abstract
    • Experiments manipulating the nutritional environment and the associated microbiome of animals have demonstrated their importance for key fitness components. However, there is little information on how macronutrient composition and bacterial communities in natural food sources vary across seasons in nature and on how these factors affect the fitness components of insects. In this study, diet samples from an orchard compost heap, which is a natural habitat for many Drosophila species and other arthropods, were collected over 9 months covering all seasons in a temperate climate. We developed D. melanogaster on diet samples and investigated stress resistance and life-history traits as well as the microbial community of flies and compost. Nutrient and microbial community analysis of the diet samples showed marked differences in macronutrient composition and microbial community across seasons. However, except for the duration of development on these diet samples and Critical Thermal maximum, fly stress resistance and life-history traits were unaffected. The resulting differences in the fly microbial community were also more stable and less diverse than the microbial community of the diet samples. Our study suggests that when D. melanogaster are exposed to a vastly varying nutritional environment with a rich, diverse microbial community, the detrimental consequences of an unfavourable macronutrient composition are offset by the complex interactions between microbes and nutrients.
  •  
29.
  •  
30.
  • Jeske, Jan Torsten, 1983- (author)
  • Microbial adaptations and controlling mechanisms of surface-associated microhabitat heterogeneity in aquatic systems
  • 2015
  • Doctoral thesis (other academic/artistic)abstract
    • Habitat heterogeneity is a driving factor for speciation and ecosystem functioning and is well studied in macro-ecology. Yet our understanding of microbial adaptations, and governing processes is incomplete. The here presented thesis aims at giving us a better understanding of patterns in micro-heterogeneity, and microbial adaptations to such heterogeneity with particular focus on surface-dominated, aquatic habitats. The most prominent microbial adaptation to surface associated mode of life is biofilm formation. Biofilms rely heavily on type IV pili. These pili systems are well studied in Bacteria, but largely unknown in Archaea. Therefore, the first part of this thesis focuses on resolving genetic and structural feature of the type IV like aap-pilus of the thermo-acidophilic Sulfolobus acidocaldarius. We found the aap-pilus to be indispensible for biofilm formation, and to be unparalleled in variability of its quaternary structure and cross regulation with other filaments. The second part of this thesis investigates particle colonization in the water column, focusing on diatoms as a model system, allowing an in situ assessment of different stages of particle colonization, and potential particle-specificity of the associated bacterial community. Opposing reports from marine systems, we did not observe diatom-specificity in the associated bacterial community. Instead we found bacterial community subsets, one likely originating from sediment resuspension, and the other being controlled by biofilm-forming populations (e.g. Flexibacter), able to attach to newly formed particle surfaces and subsequently facilitate secondary colonization by other bacteria. Finally, the habitat heterogeneity in top-layers of lake sediments were investigated in experimental microcosms. Cell-specific oxygen consumption rates were determined, to assess microbial activity across different scales. Individual activity rates differed strongly across all investigated scales, likely due to spatially heterogeneous distribution of nutrients with differing quality. Vice versa, the influence of microbial activity on micro-habitat-heterogeneity was investigated. We correlated sediment redox-state with bacterial community composition and populations. Our results indicate that habitat heterogeneity is generally beneficial for microorganism, and greater heterogeneity results in greater bacterial diversity. However, this heterogeneity-diversity relationship is limited and microorganisms actively stabilize their immediate redox environment to a preferred, community-specific, stable state, if cell abundances exceed a minimum threshold.
  •  
31.
  • Keck, Michaela Kristina, et al. (author)
  • Amplification of the PLAG-family genes—PLAGL1 and PLAGL2—is a key feature of the novel tumor type CNS embryonal tumor with PLAGL amplification
  • 2023
  • In: Acta Neuropathologica. - : Springer Science and Business Media LLC. - 0001-6322 .- 1432-0533. ; 145:1, s. 49-69
  • Journal article (peer-reviewed)abstract
    • Pediatric central nervous system (CNS) tumors represent the most common cause of cancer-related death in children aged 0–14 years. They differ from their adult counterparts, showing extensive clinical and molecular heterogeneity as well as a challenging histopathological spectrum that often impairs accurate diagnosis. Here, we use DNA methylation-based CNS tumor classification in combination with copy number, RNA-seq, and ChIP-seq analysis to characterize a newly identified CNS tumor type. In addition, we report histology, patient characteristics, and survival data in this tumor type. We describe a biologically distinct pediatric CNS tumor type (n = 31 cases) that is characterized by focal high-level amplification and resultant overexpression of either PLAGL1 or PLAGL2, and an absence of recurrent genetic alterations characteristic of other pediatric CNS tumor types. Both genes act as transcription factors for a regulatory subset of imprinted genes (IGs), components of the Wnt/β-Catenin pathway, and the potential drug targets RET and CYP2W1, which are also specifically overexpressed in this tumor type. A derived PLAGL-specific gene expression signature indicates dysregulation of imprinting control and differentiation/development. These tumors occurred throughout the neuroaxis including the cerebral hemispheres, cerebellum, and brainstem, and were predominantly composed of primitive embryonal-like cells lacking robust expression of markers of glial or neuronal differentiation (e.g., GFAP, OLIG2, and synaptophysin). Tumors with PLAGL1 amplification were typically diagnosed during adolescence (median age 10.5 years), whereas those with PLAGL2 amplification were diagnosed during early childhood (median age 2 years). The 10-year overall survival was 66% for PLAGL1-amplified tumors, 25% for PLAGL2-amplified tumors, 18% for male patients, and 82% for female patients. In summary, we describe a new type of biologically distinct CNS tumor characterized by PLAGL1/2 amplification that occurs predominantly in infants and toddlers (PLAGL2) or adolescents (PLAGL1) which we consider best classified as a CNS embryonal tumor and which is associated with intermediate survival. The cell of origin and optimal treatment strategies remain to be defined.
  •  
32.
  • Kjeldsen, Kasper Urup, et al. (author)
  • Two types of endosymbiotic bacteria in the enigmatic marine worm Xenoturbella.
  • 2010
  • In: Applied and Environmental Microbiology. - 1098-5336. ; 76:8, s. 2657-2662
  • Journal article (peer-reviewed)abstract
    • Two types of endosymbiotic bacteria were identified in the gastrodermis of the marine invertebrate Xenoturbella bocki (Xenoturbellida, Bilateria). While previously described Chlamydia-like endosymbionts were rare, Gammaproteobacteria distantly related to other endosymbionts and pathogens were abundant. The endosymbionts should be considered when interpreting the poorly understood ecology and evolution of Xenoturbella.
  •  
33.
  • Kuliński, Karol, et al. (author)
  • Biogeochemical functioning of the Baltic Sea
  • 2022
  • In: Earth System Dynamics. - : Copernicus GmbH. - 2190-4979 .- 2190-4987. ; 13, s. 633-685
  • Research review (peer-reviewed)abstract
    • Location, specific topography, and hydrographic setting together with climate change and strong anthropogenic pressure are the main factors shaping the biogeochemical functioning and thus also the ecological status of the Baltic Sea. The recent decades have brought significant changes in the Baltic Sea. First, the rising nutrient loads from land in the second half of the 20th century led to eutrophication and spreading of hypoxic and anoxic areas, for which permanent stratification of the water column and limited ventilation of deep-water layers made favourable conditions. Since the 1980s the nutrient loads to the Baltic Sea have been continuously decreasing. This, however, has so far not resulted in significant improvements in oxygen availability in the deep regions, which has revealed a slow response time of the system to the reduction of the land-derived nutrient loads. Responsible for that is the low burial efficiency of phosphorus at anoxic conditions and its remobilization from sediments when conditions change from oxic to anoxic. This results in a stoichiometric excess of phosphorus available for organic-matter production, which promotes the growth of N2-fixing cyanobacteria and in turn supports eutrophication. This assessment reviews the available and published knowledge on the biogeochemical functioning of the Baltic Sea. In its content, the paper covers the aspects related to changes in carbon, nitrogen, and phosphorus (C, N, and P) external loads, their transformations in the coastal zone, changes in organic-matter production (eutrophication) and remineralization (oxygen availability), and the role of sediments in burial and turnover of C, N, and P. In addition to that, this paper focuses also on changes in the marine CO2 system, the structure and functioning of the microbial community, and the role of contaminants for biogeochemical processes. This comprehensive assessment allowed also for identifying knowledge gaps and future research needs in the field of marine biogeochemistry in the Baltic Sea. Copyright:
  •  
34.
  • Li, Miao, et al. (author)
  • 0.7-GHz Solution-Processed Indium Oxide Rectifying Diodes
  • 2020
  • In: IEEE Transactions on Electron Devices. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 0018-9383 .- 1557-9646. ; 67:1, s. 360-364
  • Journal article (peer-reviewed)abstract
    • Solution-based deposition, with its simplicity and possibility for upscaling through printing, is a promising process for low-cost electronics. Metal oxide semiconductor devices, especially indium oxide with its excellent electrical properties, offer high performance compared to amorphous Si-based rivals, and with a form factor conducive to flexible and wearable electronics. Here, rectifying diodes based on an amorphous spin-coated indium oxide are fabricated for high-speed applications. We report a solution-processed diode approaching the UHF range, based on indium oxide, with aluminum and gold as the electrodes. The device was spin-coated from a precursor material and configured into a half-wave rectifier. The J-V and frequency behavior of the diodes were studied, and the material composition of the diode was investigated by X-ray photoemission spectroscopy (XPS). The 3-dB point was found to be over 700 MHz. The results are promising for the development of autonomously powered wireless Internet-of-Things systems based on scalable, low-cost processes.
  •  
35.
  • Liu, Jimmy Z, et al. (author)
  • Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis.
  • 2013
  • In: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:6, s. 670-5
  • Journal article (peer-reviewed)abstract
    • Primary sclerosing cholangitis (PSC) is a severe liver disease of unknown etiology leading to fibrotic destruction of the bile ducts and ultimately to the need for liver transplantation. We compared 3,789 PSC cases of European ancestry to 25,079 population controls across 130,422 SNPs genotyped using the Immunochip. We identified 12 genome-wide significant associations outside the human leukocyte antigen (HLA) complex, 9 of which were new, increasing the number of known PSC risk loci to 16. Despite comorbidity with inflammatory bowel disease (IBD) in 72% of the cases, 6 of the 12 loci showed significantly stronger association with PSC than with IBD, suggesting overlapping yet distinct genetic architectures for these two diseases. We incorporated association statistics from 7 diseases clinically occurring with PSC in the analysis and found suggestive evidence for 33 additional pleiotropic PSC risk loci. Together with network analyses, these findings add to the genetic risk map of PSC and expand on the relationship between PSC and other immune-mediated diseases.
  •  
36.
  • Lynch, Kate D, et al. (author)
  • Effects of Vedolizumab in Patients with Primary Sclerosing Cholangitis and Inflammatory Bowel Diseases.
  • 2020
  • In: Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. - : Elsevier BV. - 1542-7714. ; 18:1
  • Journal article (peer-reviewed)abstract
    • Gut-homing lymphocytes that express the integrin α4β7 and CCR9 might contribute to development of primary sclerosing cholangitis (PSC). Vedolizumab, which blocks the integrin α4β7, is used to treat patients with inflammatory bowel diseases (IBD), but there are few data on its efficacy in patients with PSC. We investigated the effects of vedolizumab in a large international cohort of patients with PSC and IBD.We collected data from European and North American centers participating in the International PSC Study Group from patients with PSC and IBD who received at least 3 doses of vedolizumab (n= 102; median vedolizumab treatment duration, 412 days). Demographic and clinical data were collected from baseline and during the follow-up period (until liver transplantation, death, or 56 days after the final vedolizumab infusion). We analyzed overall changes in biochemical features of liver and proportions of patients with reductions in serum levels of alkaline phosphatase (ALP) of 20% or more, from baseline through last follow-up evaluation. Other endpoints included response of IBD to treatment (improved, unchanged, or worsened, judged by the treating clinician, as well as endoscopic score) and liver-related outcomes.In the entire cohort, the median serum level of ALP increased from 1.54-fold the upper limit of normal at baseline to 1.64-fold the upper limit of normal at the last follow-up examination (P= .018); serum levels of transaminases and bilirubin also increased by a small amount between baseline and the last follow-up examination. Serum levels of ALP decreased by 20% or more in 21 patients (20.6%); only the presence of cirrhosis (odds ratio, 4.48; P= .019) was independently associated with this outcome. Of patients with available endoscopic data, 56.8% had a response of IBD to treatment. Liver-related events occurred in 21 patients (20.6%), including bacterial cholangitis, cirrhosis decompensation, or transplantation.In an analysis of patients with PSC and IBD in an international study group, we found no evidence for a biochemical response to vedolizumab, although serum level of ALP decreased by 20% or more in a subset of patients. Vedolizumab appears to be well tolerated and the overall response of IBD was the same as expected for patients without PSC.
  •  
37.
  • Marshall, Ian P. G., et al. (author)
  • The novel bacterial phylum Calditrichaeota is diverse, widespread and abundant in marine sediments and has the capacity to degrade detrital proteins
  • 2017
  • In: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 9:4, s. 397-403
  • Journal article (peer-reviewed)abstract
    • Calditrichaeota is a recently recognized bacterial phylum with three cultured representatives, isolated from hydrothermal vents. Here we expand the phylogeny and ecology of this novel phylum with metagenome-derived and single-cell genomes from six uncultivated bacteria previously not recognized as members of Calditrichaeota. Using 16S rRNA gene sequences from these genomes, we then identified 322 16S rRNA gene sequences from cultivation-independent studies that can now be classified as Calditrichaeota for the first time. This dataset was used to re-analyse a collection of 16S rRNA gene amplicon datasets from marine sediments showing that the Calditrichaeota are globally distributed in the seabed at high abundance, making up to 6.7% of the total bacterial community. This wide distribution and high abundance of Calditrichaeota in cold marine sediment has gone unrecognized until now. All Calditrichaeota genomes show indications of a chemoorganoheterotrophic metabolism with the potential to degrade detrital proteins through the use of extracellular peptidases. Most of the genomes contain genes encoding proteins that confer O-2 tolerance, consistent with the relatively high abundance of Calditrichaeota in surficial bioturbated part of the seabed and, together with the genes encoding extracellular peptidases, suggestive of a general ecophysiological niche for this newly recognized phylum in marine sediment.
  •  
38.
  • Marzocchi, Ugo, et al. (author)
  • Transient bottom water oxygenation creates a niche for cable bacteria in long‐term anoxic sediments of the Eastern Gotland Basin
  • 2018
  • In: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 20:8, s. 3031-3041
  • Journal article (peer-reviewed)abstract
    • Cable bacteria have been reported in sediments from marine and freshwater locations, but the environmental factors that regulate their growth in natural settings are not well understood. Most prominently, the physiological limit of cable bacteria in terms of oxygen availability remains poorly constrained. In this study, we investigated the presence, activity and diversity of cable bacteria in relation to a natural gradient in bottom water oxygenation in a depth transect of the Eastern Gotland Basin (Baltic Sea). Cable bacteria were identified by FISH at the oxic and transiently oxic sites, but not at the permanently anoxic site. Three species of the candidate genus Electrothrix, i.e. marina, aarhusiensis and communis were found coexisting within one site. The highest filament density (33 m cm−2) was associated with a 6.3 mm wide zone depleted in both oxygen and free sulphide, and the presence of an electric field resulting from the electrogenic sulphur oxidizing metabolism of cable bacteria. However, the measured filament densities and metabolic activities remained low overall, suggesting a limited impact of cable bacteria at the basin level. The observed bottom water oxygen levels (< 5 μM) are the lowest so far reported for cable bacteria, thus expanding their known environmental distribution.
  •  
39.
  • Schramm, Christoph, et al. (author)
  • Primary liver transplantation for autoimmune hepatitis: a comparative analysis of the European Liver Transplant Registry.
  • 2010
  • In: Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society. - : Ovid Technologies (Wolters Kluwer Health). - 1527-6473. ; 16:4, s. 461-9
  • Journal article (peer-reviewed)abstract
    • The principal aim of this study was to compare the probability of and potential risk factors for death and graft loss after primary adult and pediatric liver transplantation in patients undergoing transplantation for autoimmune hepatitis (AIH) to those in patients undergoing transplantation for primary biliary cirrhosis (PBC; used as the reference group) or alcoholic cirrhosis (used as an example of a nonautoimmune liver disease). The 5-year survival of patients undergoing transplantation for AIH (n = 827) was 0.73 [95% confidence interval (CI) = 0.67-0.77]. This was similar to that of patients undergoing transplantation for alcoholic cirrhosis (0.74, 95% CI = 0.72-0.76, n = 6424) but significantly worse than that of patients undergoing transplantation for PBC (0.83, 95% CI = 0.80-0.85, n = 1588). Fatal infectious complications occurred at an increased rate in patients with AIH (hazard ratio = 1.8, P = 0.002 with PBC as the reference). The outcome of pediatric AIH patients was similar to that of adult patients undergoing transplantation up to the age of 50 years. However, the survival of AIH patients undergoing transplantation beyond the age of 50 years (0.61 at 5 years, 95% CI = 0.51-0.70) was significantly reduced in comparison with the survival of young adult AIH patients (0.78 at 18-34 years, 95% CI = 0.70-0.86) and in comparison with the survival of patients of the same age group with PBC or alcoholic cirrhosis. In conclusion, age significantly affects patient survival after liver transplantation for AIH. The increased risk of dying of infectious complications in the early postoperative period, especially above the age of 50 years, should be acknowledged in the management of AIH patients with advanced-stage liver disease who are listed for liver transplantation. It should be noted that not all risk factors relevant to patient and graft survival could be analyzed with the European Liver Transplant Registry database.
  •  
40.
  • Schreiber, Lars, et al. (author)
  • Description of Endozoicomonas ascidiicola sp nov., isolated from Scandinavian ascidians
  • 2016
  • In: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020 .- 1618-0984. ; 39:5, s. 313-318
  • Journal article (peer-reviewed)abstract
    • Two gram-negative, facultative anaerobic, chemoorganoheterotrophic, motile and rod-shaped bacteria, strains AVMARTO5(T) and KASP37, were isolated from ascidians (Tunicata, Ascidiaceae) of the genus Ascidiella collected at Gullmarsfjord, Sweden. The strains are the first cultured representatives of an ascidian-specific lineage within the genus Endozoicomonas (Gammaproteobacteria, Oceanospirillales, Hahellaceae). Both strains feature three distinct 16S rRNA gene paralogs, with identities of 98.9-99.1% (AVMARTO5(T)) and 97.7-98.8% (KASP37) between paralogs. The strains are closely related to Endozoicomonas atrinae and Endozoicomonas elysicola, with which they share 97.3-98.0% 16S rRNA gene sequence identity. Digital DNA-DNA hybridization, average nucleotide identity, and tetra-nucleotide correlation analysis indicate that both strains belong to a single species distinct from their closest relatives. Both strains feature similar DNA G + C contents of 46.70 mol%(AVMARTO5T) and 44.64 mol%(KASP37).The fatty acid patterns of AVMARTO5(T) and KASP37 are most similar to those of Endozoicomonas euniceicola and Endozoicomonas gorgoniicola. Based on the polyphasic approach, we propose the species Endozoicomonas ascidiicola sp. nov. to accommodate the newly isolated strains. E. ascidiicola sp. nov. is represented by the type strain AVMARTO5(T) (=DSM 100913(T) = LMG 29095(T)) and strain KASP37 (=DSM 100914= LMG 29096).
  •  
41.
  • Simon, Matthias, et al. (author)
  • TERT promoter mutations: a novel independent prognostic factor in primary glioblastomas.
  • 2015
  • In: Neuro-Oncology. - : Oxford University Press (OUP). - 1523-5866 .- 1522-8517. ; 17:1, s. 45-52
  • Journal article (peer-reviewed)abstract
    • Activating somatic mutations in the promoter region of the telomerase reverse transcriptase gene (TERT) have been detected in several cancers. In this study we investigated the TERT promoter mutations and their impact on patient survival in World Health Organization grade IV glioblastoma multiforme (GBM).
  •  
42.
  • Starnawski, Piotr, et al. (author)
  • Microbial community assembly and evolution in subseafloor sediment
  • 2017
  • In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:11, s. 2940-2945
  • Journal article (peer-reviewed)abstract
    • Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface. We followed patterns of genome diversity with depth in four dominant lineages of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes. Nucleotide sequence diversity was uniformly low and did not change with age and depth of the sediment. Likewise, there was no detectable change inmutation rates and efficacy of selection. Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation.
  •  
43.
  • Venkatesan, Meera, et al. (author)
  • Polymorphisms in Plasmodium falciparum chloroquine resistance transporter and multidrug resistance 1 genes : parasite risk factors that affect treatment outcomes for P. falciparum malaria after artemether-lumefantrine and artesunate-amodiaquine.
  • 2014
  • In: The American journal of tropical medicine and hygiene. - : American Society of Tropical Medicine and Hygiene. - 1476-1645 .- 0002-9637. ; 91:4, s. 833-43
  • Journal article (peer-reviewed)abstract
    • Adequate clinical and parasitologic cure by artemisinin combination therapies relies on the artemisinin component and the partner drug. Polymorphisms in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and P. falciparum multidrug resistance 1 (pfmdr1) genes are associated with decreased sensitivity to amodiaquine and lumefantrine, but effects of these polymorphisms on therapeutic responses to artesunate-amodiaquine (ASAQ) and artemether-lumefantrine (AL) have not been clearly defined. Individual patient data from 31 clinical trials were harmonized and pooled by using standardized methods from the WorldWide Antimalarial Resistance Network. Data for more than 7,000 patients were analyzed to assess relationships between parasite polymorphisms in pfcrt and pfmdr1 and clinically relevant outcomes after treatment with AL or ASAQ. Presence of the pfmdr1 gene N86 (adjusted hazards ratio = 4.74, 95% confidence interval = 2.29 - 9.78, P < 0.001) and increased pfmdr1 copy number (adjusted hazards ratio = 6.52, 95% confidence interval = 2.36-17.97, P < 0.001 : were significant independent risk factors for recrudescence in patients treated with AL. AL and ASAQ exerted opposing selective effects on single-nucleotide polymorphisms in pfcrt and pfmdr1. Monitoring selection and responding to emerging signs of drug resistance are critical tools for preserving efficacy of artemisinin combination therapies; determination of the prevalence of at least pfcrt K76T and pfmdr1 N86Y should now be routine.
  •  
44.
  • Wynberg, Elke, et al. (author)
  • Variability in white blood cell count during uncomplicated malaria and implications for parasite density estimation : a WorldWide Antimalarial Resistance Network individual patient data meta-analysis
  • 2023
  • In: Malaria Journal. - : Springer Nature. - 1475-2875. ; 22
  • Journal article (peer-reviewed)abstract
    • Background: The World Health Organization (WHO) recommends that when peripheral malarial parasitaemia is quantified by thick film microscopy, an actual white blood cell (WBC) count from a concurrently collected blood sample is used in calculations. However, in resource-limited settings an assumed WBC count is often used instead. The aim of this study was to describe the variability in WBC count during acute uncomplicated malaria, and estimate the impact of using an assumed value of WBC on estimates of parasite density and clearance.Methods: Uncomplicated malaria drug efficacy studies that measured WBC count were selected from the WorldWide Antimalarial Resistance Network data repository for an individual patient data meta-analysis of WBC counts. Regression models with random intercepts for study-site were used to assess WBC count variability at presentation and during follow-up. Inflation factors for parasitaemia density, and clearance estimates were calculated for methods using assumed WBC counts (8000 cells/mu L and age-stratified values) using estimates derived from the measured WBC value as reference.Results: Eighty-four studies enrolling 27,656 patients with clinically uncomplicated malaria were included. Geometric mean WBC counts (x 1000 cells/mu L) in age groups < 1, 1-4, 5-14 and >= 15 years were 10.5, 8.3, 7.1, 5.7 and 7.5, 7.0, 6.5, 6.0 for individuals with falciparum (n = 24,978) and vivax (n = 2678) malaria, respectively. At presentation, higher WBC counts were seen among patients with higher parasitaemia, severe anaemia and, for individuals with vivax malaria, in regions with shorter regional relapse periodicity. Among falciparum malaria patients, using an assumed WBC count of 8000 cells/mu L resulted in parasite density underestimation by a median (IQR) of 26% (4-41%) in infants < 1 year old but an overestimation by 50% (16-91%) in adults aged = 15 years. Use of age-stratified assumed WBC values removed systematic bias but did not improve precision of parasitaemia estimation. Imprecision of parasite clearance estimates was only affected by the within-patient WBC variability over time, and remained < 10% for 79% of patients.Conclusions: Using an assumed WBC value for parasite density estimation from a thick smear may lead to underdiagnosis of hyperparasitaemia and could adversely affect clinical management; but does not result in clinically consequential inaccuracies in the estimation of the prevalence of prolonged parasite clearance and artemisinin resistance.
  •  
45.
  • Zaremba-Niedzwiedzka, Katarzyna, et al. (author)
  • Asgard archaea illuminate the origin of eukaryotic cellular complexity
  • 2017
  • In: Nature. - : NATURE PUBLISHING GROUP. - 0028-0836 .- 1476-4687. ; 541:7637, s. 353-
  • Journal article (peer-reviewed)abstract
    • The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.
  •  
46.
  • Aad, G., et al. (author)
  • 2015
  • In: Physical Review C (Nuclear Physics). - 0556-2813 .- 1089-490X. ; 92:3
  • Journal article (peer-reviewed)
  •  
47.
  • Aad, G., et al. (author)
  • 2015
  • In: Physical Review C (Nuclear Physics). - 0556-2813 .- 1089-490X. ; 92:3
  • Journal article (peer-reviewed)
  •  
48.
  • Aad, G., et al. (author)
  • 2015
  • Journal article (peer-reviewed)
  •  
49.
  • Aad, G., et al. (author)
  • 2015
  • In: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368 .- 1550-7998. ; 91:11, s. 112011-
  • Journal article (peer-reviewed)
  •  
50.
  • Aad, G., et al. (author)
  • 2015
  • In: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 115:9
  • Journal article (peer-reviewed)
  •  
Skapa referenser, mejla, bekava och länka
  • Result 1-50 of 60
Type of publication
journal article (54)
other publication (2)
conference paper (2)
doctoral thesis (1)
research review (1)
Type of content
peer-reviewed (57)
other academic/artistic (3)
Author/Editor
Chen, L (32)
Aad, G (32)
Abbott, B. (32)
Abdinov, O (32)
Zwalinski, L. (32)
Gregersen, K. (32)
show more...
Kalderon, C.W. (32)
Poettgen, R. (32)
Lundberg, Olof (32)
Aben, R. (32)
Abreu, H. (32)
Abreu, R. (32)
Adye, T. (32)
Agatonovic-Jovin, T. (32)
Ahmadov, F. (32)
Aielli, G. (32)
Alberghi, G. L. (32)
Albert, J. (32)
Albrand, S. (32)
Aleksa, M. (32)
Aleksandrov, I. N. (32)
Alexander, G. (32)
Alexopoulos, T. (32)
Alhroob, M. (32)
Alimonti, G. (32)
Alio, L. (32)
Aloisio, A. (32)
Alonso, A. (32)
Alonso, F. (32)
Alpigiani, C. (32)
Altheimer, A. (32)
Alviggi, M. G. (32)
Amako, K. (32)
Amelung, C. (32)
Amidei, D. (32)
Amorim, A. (32)
Amoroso, S. (32)
Amram, N. (32)
Amundsen, G. (32)
Anastopoulos, C. (32)
Ancu, L. S. (32)
Andari, N. (32)
Andeen, T. (32)
Anders, G. (32)
Anderson, K. J. (32)
Andreazza, A. (32)
Andrei, V. (32)
Angelidakis, S. (32)
Anger, P. (32)
Angerami, A. (32)
show less...
University
Uppsala University (44)
Lund University (41)
Stockholm University (36)
Royal Institute of Technology (32)
University of Gothenburg (9)
Karolinska Institutet (9)
show more...
Linköping University (2)
Umeå University (1)
Halmstad University (1)
Örebro University (1)
Chalmers University of Technology (1)
Swedish University of Agricultural Sciences (1)
show less...
Language
English (60)
Research subject (UKÄ/SCB)
Natural sciences (46)
Medical and Health Sciences (10)
Engineering and Technology (2)

Year

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

 
pil uppåt Close

Copy and save the link in order to return to this view