| 1. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 2. |
- Hill, M. S., et al.
(författare)
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Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:1, s. e50437-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A well-supported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance: These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets.
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| 3. |
- Gundersen, P., et al.
(författare)
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The response of methane and nitrous oxide fluxes to forest change in Europe
- 2012
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 9:10, s. 3999-4012
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Tidskriftsartikel (refereegranskat)abstract
- Forests in Europe are changing due to interactions between climate change, nitrogen (N) deposition and new forest management practices. The concurrent impact on the forest greenhouse gas (GHG) balance is at present difficult to predict due to a lack of knowledge on controlling factors of GHG fluxes and response to changes in these factors. To improve the mechanistic understanding of the ongoing changes, we studied the response of soil–atmosphere exchange of nitrous oxide (N2O) and methane (CH4) at twelve experimental or natural gradient forest sites, representing anticipated future forest change. The experimental manipulations, one or more per site, included N addition (4 sites), changes of climate (temperature, 1 site; precipitation, 2 sites), soil hydrology (3 sites), harvest intensity (1 site), wood ash fertilisation (1 site), pH gradient in organic soil (1 site) and afforestation of cropland (1 site). On average, N2O emissions increased by 0.06 ± 0.03 (range 0–0.3) g N2O-N m−2 yr−1 across all treatments on mineral soils, but the increase was up to 10 times higher in an acidic organic soil. Soil moisture together with mineral soil C / N ratio and pH were found to significantly influence N2O emissions across all treatments. Emissions were increased by elevated N deposition, especially in interaction with increased soil moisture. High pH reduced the formation of N2O, even under otherwise favourable soil conditions. Oxidation (uptake) of CH4 was on average reduced from 0.16 ± 0.02 to 0.04 ± 0.05 g CH4-C m−2 yr−1 by the investigated treatments. The CH4 exchange was significantly influenced by soil moisture and soil C / N ratio across all treatments, and CH4 emissions occurred only in wet or water-saturated conditions. For most of the investigated forest manipulations or natural gradients, the response of both N2O and CH4 fluxes was towards reducing the overall GHG forest sink. The most resilient forests were dry Mediterranean forests, as well as forests with high soil C / N ratio or high soil pH. Mitigation strategies may focus on (i) sustainable management of wet forest areas and forested peatlands, (ii) continuous forest cover management, (iii) reducing atmospheric N input and, thus, N availability, and (iv) improving neutralisation capacity of acid soils (e.g. wood ash application).
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| 4. |
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| 5. |
- Bjork, J., et al.
(författare)
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STM fingerprint of molecule-adatom interactions in a self-assembled metal-organic surface coordination network on Cu(111)
- 2010
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 12:31, s. 8815-8821
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Tidskriftsartikel (refereegranskat)abstract
- A novel approach of identifying metal atoms within a metal-organic surface coordination network using scanning tunnelling microscopy (STM) is presented. The Cu adatoms coordinated in the porous surface network of 1,3,8,10-tetraazaperopyrene (TAPP) molecules on a Cu(111) surface give rise to a characteristic electronic resonance in STM experiments. Using density functional theory calculations, we provide strong evidence that this resonance is a fingerprint of the interaction between the molecules and the Cu adatoms. We also show that the bonding of the Cu adatoms to the organic exodentate ligands is characterised by both the mixing of the nitrogen lone-pair orbitals of TAPP with states on the Cu adatoms and the partial filling of the lowest unoccupied molecular orbital (LUMO) of the TAPP molecule. Furthermore, the key interactions determining the surface unit cell of the network are discussed.
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| 6. |
- Björk, Jonas, et al.
(författare)
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STM fingerprint of molecule-adatom interactions in a self-assembled metal-organic surface coordination network on Cu(111)
- 2010
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : R S C Publications. - 1463-9076 .- 1463-9084. ; 12, s. 8815-8821
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Tidskriftsartikel (refereegranskat)abstract
- A novel approach of identifying metal atoms within a metal-organic surface coordination network using scanning tunnelling microscopy (STM) is presented. The Cu adatoms coordinated in the porous surface network of 1,3,8,10-tetraazaperopyrene (TAPP) molecules on a Cu(111) surface give rise to a characteristic electronic resonance in STM experiments. Using density functional theory calculations, we provide strong evidence that this resonance is a fingerprint of the interaction between the molecules and the Cu adatoms. We also show that the bonding of the Cu adatoms to the organic exodentate ligands is characterised by both the mixing of the nitrogen lone-pair orbitals of TAPP with states on the Cu adatoms and the partial filling of the lowest unoccupied molecular orbital (LUMO) of the TAPP molecule. Furthermore, the key interactions determining the surface unit cell of the network are discussed.
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| 7. |
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| 8. |
- Gustafsson, U. O., et al.
(författare)
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Guidelines for perioperative care in elective colonic surgery : enhanced recovery after surgery (ERAS(®)) society recommendations
- 2013
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Ingår i: World Journal of Surgery. - : Springer. - 0364-2313 .- 1432-2323. ; 37:2, s. 259-284
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Forskningsöversikt (refereegranskat)abstract
- BACKGROUND: This review aims to present a consensus for optimal perioperative care in colonic surgery and to provide graded recommendations for items for an evidenced-based enhanced perioperative protocol.METHODS: Studies were selected with particular attention paid to meta-analyses, randomised controlled trials and large prospective cohorts. For each item of the perioperative treatment pathway, available English-language literature was examined, reviewed and graded. A consensus recommendation was reached after critical appraisal of the literature by the group.RESULTS: For most of the protocol items, recommendations are based on good-quality trials or meta-analyses of good-quality trials (quality of evidence and recommendations according to the GRADE system).CONCLUSIONS: Based on the evidence available for each item of the multimodal perioperative care pathway, the Enhanced Recovery After Surgery (ERAS) Society, International Association for Surgical Metabolism and Nutrition (IASMEN) and European Society for Clinical Nutrition and Metabolism (ESPEN) present a comprehensive evidence-based consensus review of perioperative care for colonic surgery.
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| 9. |
- Gustafsson, U. O., et al.
(författare)
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Guidelines for perioperative care in elective colonic surgery : enhanced recovery after surgery (ERAS®) society recommendations
- 2012
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Ingår i: Clinical Nutrition. - Amsterdam, Netherlands : Elsevier. - 0261-5614 .- 1532-1983. ; 31:6, s. 783-800
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Forskningsöversikt (refereegranskat)abstract
- Background: This review aims to present a consensus for optimal perioperative care in colonic surgery and to provide graded recommendations for items for an evidenced-based enhanced perioperative protocol.Methods: Studies were selected with particular attention paid to meta-analyses, randomised controlled trials and large prospective cohorts. For each item of the perioperative treatment pathway, available English-language literature was examined, reviewed and graded. A consensus recommendation was reached after critical appraisal of the literature by the group.Results: For most of the protocol items, recommendations are based on good-quality trials or meta-analyses of good-quality trials (quality of evidence and recommendations according to the GRADE system).Conclusions: Based on the evidence available for each item of the multimodal perioperative-care pathway, the Enhanced Recovery After Surgery (ERAS) Society, International Association for Surgical Metabolism and Nutrition (IASMEN) and European Society for Clinical Nutrition and Metabolism (ESPEN) present a comprehensive evidence-based consensus review of perioperative care for colonic surgery.
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| 10. |
- Matena, Manfred, et al.
(författare)
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Aggregation and contingent metal/surface reactivity of 1,3,8,10-tetraazaperopyrene (TAPP) on Cu(111)
- 2010
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Ingår i: Chemistry - A European Journal. - : Wiley-VCH Verlagsgesellschaft. - 0947-6539 .- 1521-3765. ; 16:7, s. 2079-2091
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Tidskriftsartikel (refereegranskat)abstract
- The structural chemistry and reactivity of 1,3,8,10-tetraazaperopyrene (TAPP) on Cu(111) under ultra-high-vacuum (UHV) conditions has been studied by a combination of experimental techniques (scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy, XPS) and DFT calculations. Depending on the deposition conditions, TAPP forms three main assemblies, which result from initial submonolayer coverages based on different intermolecular interactions: a close-packed assembly similar to a projection of the bulk structure of TAPP, in which the molecules interact mainly through van der Waals (vDW) forces and weak hydrogen bonds; a porous copper surface coordination network; and covalently linked molecular chains. The Cu substrate is of crucial importance in determining the structures of the aggregates and available reaction channels on the surface, both in the formation of the porous network for which it provides the Cu atoms for surface metal coordination and in the covalent coupling of the TAPP molecules at elevated temperature. Apart from their role in the kinetics of surface transformations, the available metal adatoms may also profoundly influence the thermodynamics of transformations by coordination to the reaction product, as shown in this work for the case of the Cu-decorated covalent poly(TAPP-Cu) chains.
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