| 1. |
- Ederle, Joerg, et al.
(author)
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Carotid artery stenting compared with endarterectomy in patients with symptomatic carotid stenosis (International Carotid Stenting Study): an interim analysis of a randomised controlled trial
- 2010
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In: The Lancet. - 1474-547X. ; 375:9719, s. 985-997
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Journal article (peer-reviewed)abstract
- Background Stents are an alternative treatment to carotid endarterectomy for symptomatic carotid stenosis, but previous trials have not established equivalent safety and efficacy. We compared the safety of carotid artery stenting with that of carotid endarterectomy. Methods The International Carotid Stenting Study (ICSS) is a multicentre, international, randomised controlled trial with blinded adjudication of outcomes. Patients with recently symptomatic carotid artery stenosis were randomly assigned in a 1:1 ratio to receive carotid artery stenting or carotid endarterectomy. Randomisation was by telephone call or fax to a central computerised service and was stratified by centre with minimisation for sex, age, contralateral occlusion, and side of the randomised artery. Patients and investigators were not masked to treatment assignment. Patients were followed up by independent clinicians not directly involved in delivering the randomised treatment. The primary outcome measure of the trial is the 3-year rate of fatal or disabling stroke in any territory, which has not been analysed yet. The main outcome measure for the interim safety analysis was the 120-day rate of stroke, death, or procedural myocardial infarction. Analysis was by intention to treat (ITT). This study is registered, number ISRCTN25337470. Findings The trial enrolled 1713 patients (stenting group, n=855; endarterectomy group, n=858). Two patients in the stenting group and one in the endarterectomy group withdrew immediately after randomisation, and were not included in the ITT analysis. Between randomisation and 120 days, there were 34 (Kaplan-Meier estimate 4.0%) events of disabling stroke or death in the stenting group compared with 27 (3.2%) events in the endarterectomy group (hazard ratio [HR] 1.28, 95% CI 0.77-2.11). The incidence of stroke, death, or procedural myocardial infarction was 8.5% in the stenting group compared with 5.2% in the endarterectomy group (72 vs 44 events; HR 1.69, 1.16-2.45, p=0.006), Risks of any stroke (65 vs 35 events; HR 1.92, 1.27-2.89) and all-cause death (19 vs seven events; HR 2.76, 1.16-6.56) were higher in the stenting group than in the endarterectomy group. Three procedural myocardial infarctions were recorded in the stenting group, all of which were fatal, compared with four, all non-fatal, in the endarterectomy group. There was one event of cranial nerve palsy in the stenting group compared with 45 in the endarterectomy group. There were also fewer haematomas of any severity in the stenting group than in the endarterectomy group (31 vs 50 events; p=0.0197). Interpretation Completion of long-term follow-up is needed to establish the efficacy of carotid artery stenting compared with endarterectomy. In the meantime, carotid endarterectomy should remain the treatment of choice for patients suitable for surgery.
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| 2. |
- Herber, O. R., et al.
(author)
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What feedback do reviewers give when reviewing qualitative manuscripts? A focused mapping review and synthesis
- 2020
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In: BMC Medical Research Methodology. - : Springer Science and Business Media LLC. - 1471-2288. ; 20:1
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Journal article (peer-reviewed)abstract
- Background Peer review is at the heart of the scientific process. With the advent of digitisation, journals started to offer electronic articles or publishing online only. A new philosophy regarding the peer review process found its way into academia: the open peer review. Open peer review as practiced by BioMed Central (BMC) is a type of peer review where the names of authors and reviewers are disclosed and reviewer comments are published alongside the article. A number of articles have been published to assess peer reviews using quantitative research. However, no studies exist that used qualitative methods to analyse the content of reviewers' comments. Methods A focused mapping review and synthesis (FMRS) was undertaken of manuscripts reporting qualitative research submitted to BMC open access journals from 1 January - 31 March 2018. Free-text reviewer comments were extracted from peer review reports using a 77-item classification system organised according to three key dimensions that represented common themes and sub-themes. A two stage analysis process was employed. First, frequency counts were undertaken that allowed revealing patterns across themes/sub-themes. Second, thematic analysis was conducted on selected themes of the narrative portion of reviewer reports. Results A total of 107 manuscripts submitted to nine open-access journals were included in the FMRS. The frequency analysis revealed that among the 30 most frequently employed themes "writing criteria" (dimension II) is the top ranking theme, followed by comments in relation to the "methods" (dimension I). Besides that, some results suggest an underlying quantitative mindset of reviewers. Results are compared and contrasted in relation to established reporting guidelines for qualitative research to inform reviewers and authors of frequent feedback offered to enhance the quality of manuscripts. Conclusions This FMRS has highlighted some important issues that hold lessons for authors, reviewers and editors. We suggest modifying the current reporting guidelines by including a further item called "Degree of data transformation" to prompt authors and reviewers to make a judgment about the appropriateness of the degree of data transformation in relation to the chosen analysis method. Besides, we suggest that completion of a reporting checklist on submission becomes a requirement.
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| 3. |
- Andersson, Jan O., et al.
(author)
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A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution
- 2007
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 8, s. 51-
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Research review (peer-reviewed)abstract
- Background: Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey project resulting in 2341 expressed sequence tags (EST) corresponding to 853 unique clones, 5275 genome survey sequences (GSS), and eleven finished contigs from the diplomonad fish parasite Spironucleus salmonicida (previously described as S. barkhanus). Results: The analyses revealed a compact genome with few, if any, introns and very short 3′ untranslated regions. Strikingly different patterns of codon usage were observed in genes corresponding to frequently sampled ESTs versus genes poorly sampled, indicating that translational selection is influencing the codon usage of highly expressed genes. Rigorous phylogenomic analyses identified 84 genes - mostly encoding metabolic proteins - that have been acquired by diplomonads or their relatively close ancestors via lateral gene transfer (LGT). Although most acquisitions were from prokaryotes, more than a dozen represent likely transfers of genes between eukaryotic lineages. Many genes that provide novel insights into the genetic basis of the biology and pathogenicity of this parasitic protist were identified including 149 that putatively encode variant-surface cysteine-rich proteins which are candidate virulence factors. A number of genomic properties that distinguish S. salmonicida from its human parasitic relative G. lamblia were identified such as nineteen putative lineage-specific gene acquisitions, distinct mutational biases and codon usage and distinct polyadenylation signals. Conclusion: Our results highlight the power of comparative genomic studies to yield insights into the biology of parasitic protists and the evolution of their genomes, and suggest that genetic exchange between distantly-related protist lineages may be occurring at an appreciable rate in eukaryote genome evolution.
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| 4. |
- Andersson, Jan O., et al.
(author)
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Evolution of four gene families with patchy phylogenetic distributions : influx of genes into protist genomes
- 2006
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In: BMC Evolutionary Biology. - 1471-2148. ; 6
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Journal article (peer-reviewed)abstract
- BACKGROUND: Lateral gene transfer (LGT) in eukaryotes from non-organellar sources is a controversial subject in need of further study. Here we present gene distribution and phylogenetic analyses of the genes encoding the hybrid-cluster protein, A-type flavoprotein, glucosamine-6-phosphate isomerase, and alcohol dehydrogenase E. These four genes have a limited distribution among sequenced prokaryotic and eukaryotic genomes and were previously implicated in gene transfer events affecting eukaryotes. If our previous contention that these genes were introduced by LGT independently into the diplomonad and Entamoeba lineages were true, we expect that the number of putative transfers and the phylogenetic signal supporting LGT should be stable or increase, rather than decrease, when novel eukaryotic and prokaryotic homologs are added to the analyses. RESULTS: The addition of homologs from phagotrophic protists, including several Entamoeba species, the pelobiont Mastigamoeba balamuthi, and the parabasalid Trichomonas vaginalis, and a large quantity of sequences from genome projects resulted in an apparent increase in the number of putative transfer events affecting all three domains of life. Some of the eukaryotic transfers affect a wide range of protists, such as three divergent lineages of Amoebozoa, represented by Entamoeba, Mastigamoeba, and Dictyostelium, while other transfers only affect a limited diversity, for example only the Entamoeba lineage. These observations are consistent with a model where these genes have been introduced into protist genomes independently from various sources over a long evolutionary time. CONCLUSION: Phylogenetic analyses of the updated datasets using more sophisticated phylogenetic methods, in combination with the gene distribution analyses, strengthened, rather than weakened, the support for LGT as an important mechanism affecting the evolution of these gene families. Thus, gene transfer seems to be an on-going evolutionary mechanism by which genes are spread between unrelated lineages of all three domains of life, further indicating the importance of LGT from non-organellar sources into eukaryotic genomes.
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| 5. |
- Bill, O, et al.
(author)
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Predictors of the pulsatility index in the middle cerebral artery of acute stroke patients
- 2020
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In: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1, s. 17110-
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Journal article (peer-reviewed)abstract
- Cervical and transcranial Doppler (TCD) are widely used as non-invasive methods in the evaluation of acute ischemic stroke (AIS) patients. High-grade carotid artery stenosis induces haemodynamic changes such as collateral flow and a so-called post-stenotic flow pattern of the middle cerebral artery (MCA), which appears flattened, with a reduction of the velocity difference between systole and diastole. We studied the influence of carotid artery stenosis and other variables on the flow pattern in the MCA using the pulsatility index (PI), a quantitative TCD parameter reflecting the flow spectrum in a large of cohort AIS patients. We performed ultrasound examinations of 1825 AIS patients at the CHUV from October 2004 to December 2014. We extracted patient characteristics from the ASTRAL registry. Carotid stenosis severity was classified as < 50%, 50–70%, 70–90% and > 90%, or occlusion, according to Doppler velocity criteria. We first determined variables associated with stenosis grade. Then we performed a multivariate analysis after adjusting for baseline differences, using MCA PI as dependent variable. Carotid stenosis > 70% (− 0.07) and carotid stenosis > 90%, or occlusion (− 0.14) and left side (− 0.02) are associated with lower MCA PI values. Age (+0.006 PI units per decade), diabetes (+0.07), acute ischemic changes on initial CT (+0.03) and severe plaque morphology (+0.18) are associated with higher MCA PI values. We found a number of clinical and radiological conditions that significantly influence the PI of the MCA, including high-grade ipsilateral carotid stenosis in AIS patients. We provide for the first time a quantitative evaluation of the effect of these influencing factors from a large cohort of AIS patients.
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| 6. |
- Brose, Ulrich, et al.
(author)
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Predicting the consequences of species lossusing size-structured biodiversity approaches
- 2017
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In: Biological Reviews. - : Wiley-Blackwell. - 1464-7931 .- 1469-185X. ; 92:2, s. 684-697
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Research review (peer-reviewed)abstract
- Understanding the consequences of species loss in complex ecological communities is one of the great challenges in current biodiversity research. For a long time, this topic has been addressed by traditional biodiversity experiments. Most of these approaches treat species as trait-free, taxonomic units characterizing communities only by species number without accounting for species traits. However, extinctions do not occur at random as there is a clear correlation between extinction risk and species traits. In this review, we assume that large species will be most threatened by extinction and use novel allometric and size-spectrum concepts that include body mass as a primary species trait at the levels of populations and individuals, respectively, to re-assess three classic debates on the relationships between biodiversity and (i) food-web structural complexity, (ii) community dynamic stability, and (iii) ecosystem functioning. Contrasting current expectations, size-structured approaches suggest that the loss of large species, that typically exploit most resource species, may lead to future food webs that are less interwoven and more structured by chains of interactions and compartments. The disruption of natural body-mass distributions maintaining food-web stability may trigger avalanches of secondary extinctions and strong trophic cascades with expected knock-on effects on the functionality of the ecosystems. Therefore, we argue that it is crucial to take into account body size as a species trait when analysing the consequences of biodiversity loss for natural ecosystems. Applying size-structured approaches provides an integrative ecological concept that enables a better understanding of each species' unique role across communities and the causes and consequences of biodiversity loss.
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| 7. |
- Ergeneman, O., et al.
(author)
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Morphology, structure and magnetic properties of cobalt-nickel films obtained from acidic electrolytes containing glycine
- 2011
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In: Electrochimica Acta. - : Elsevier BV. - 0013-4686 .- 1873-3859. ; 56:3, s. 1399-1408
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Journal article (peer-reviewed)abstract
- This paper focuses on the development and optimization of electroplated cobalt-nickel (CoNi) alloys for use in biomedical microdevices. CoNi films were electrodeposited from glycine-containing electrolyte solutions at acidic pH. The influence of pH (2.5-5), temperature (55 and 80 degrees C). current density (from -5 to -40 mA cm(-2)), glycine concentration (0.5 and 1 mol dm(-3)) and the nature of the metal salts (chlorides or sulphates) on the composition and the magnetic properties of the films were systematically analyzed. The cobalt content varied between 50 and 83 wt% depending on the applied conditions. As a result, deposits showed variable morphologies, different structures (either hexagonal close-packed (hcp) or mixed hcp and face-centered cubic phases) and tunable magnetic properties, ranging from semi-hard (18.51 kA m(-1). i.e. 233 Oe) to very soft (1.43 kA m(-1), i.e. 18 Oe). To understand the role of glycine in this system, a comparison of the electrochemical processes, and the structural and magnetic properties is made for samples produced in glycine-containing and glycine-free baths. (C) 2010 Elsevier Ltd. All rights reserved.
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| 8. |
- Lewis, William H, et al.
(author)
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Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss
- 2020
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In: Molecular biology and evolution. - : OXFORD UNIV PRESS. - 0737-4038 .- 1537-1719. ; 37:2, s. 524-539
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Journal article (peer-reviewed)abstract
- Hydrogenosomes are H-2-producing mitochondrial homologs found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H-2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition, we generated genomic and transcriptomic data sets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H-2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.
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| 9. |
- Sotiriou, Georgios A., et al.
(author)
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Thermal Energy Dissipation by SiO2-Coated Plasmonic-Superpararnagnetic Nanoparticles in Alternating Magnetic Fields
- 2013
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In: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 25:22, s. 4603-4612
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Journal article (peer-reviewed)abstract
- Multifunctional nanoparticles show great potential in the biomedical field and may help the diagnosis and therapy of diseases. Superparamagnetic nanoparticles are especially attractive because of their ability to dissipate thermal energy in an alternating magnetic field. Furthermore, plasmonic nanoparticles can be effectively used in non- or minimally invasive therapy of tumors exploiting their plasmonic photothermal effect. Here, hybrid plasmonicmagnetic Ag/Fe2O3 nanoparticles are made by flame aerosol technology. These nanoparticles can be in situ encapsulated with an amorphous nanothin SiO2 film to facilitate their dispersion and block any toxicity from Ag/Fe2O3. Detailed physicochemical characterization, including electron microscopy, electron dispersive X-ray spectroscopy, and X-ray diffraction, is performed. Furthermore, their magnetic properties are characterized in detail by monitoring their hysteresis, first-order-reversal-curves, and isothermal remanent magnetization. Finally, the effect of SiO2 and Agcontent on the specific absorption rate (SAR) of the hybrid Ag/Fe2O3 nanoparticles is investigated. The obtained understanding will help the rational design and engineering of multifunctional hybrid nanoprobes targeting specific biomedical applications.
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