| 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. |
- Alves, G.R., et al.
(författare)
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Using VISIR in a large undergraduate course : Preliminary assessment results
- 2011
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Konferensbidrag (refereegranskat)abstract
- The use of remote labs in undergraduate courses has been reported in literature several times since the mid 90's. Nevertheless, very few articles present results about the learning gains obtained by students using them, especially with a large number of students, thus suggesting a lack of data concerning their pedagogical effectiveness. This paper addresses such a gap by presenting some preliminary results concerning the use of a remote laboratory, known as VISIR, in a large undergraduate course on Applied Physics, with over 500 students enrolled.
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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. |
- A.V., Fidalgo, et al.
(författare)
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Adapting remote labs to learning scenarios : Case studies using VISIR and remotElectLab
- 2014
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Ingår i: Revista Iberoamericana de Tecnologias del Aprendizaje. - : Education Society of IEEE (Spanish Chapter). - 1932-8540. ; 9:1, s. 33-39
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Tidskriftsartikel (refereegranskat)abstract
- Remote laboratories are an emergent technological and pedagogical tool at all education levels, and their widespread use is an important part of their own improvement and evolution. This paper describes several issues encountered on laboratorial classes, on higher education courses, when using remote laboratories based on PXI systems, either using the VISIR system or an alternate in-house solution. Three main issues are presented and explained, all reported by teachers, that gave support to students' use of remote laboratories. The first issue deals with the need to allow students to select the actual place where an ammeter is to be inserted on electric circuits, even incorrectly, therefore emulating real-world difficulties. The second one deals with problems with timing when several measurements are required at short intervals, as in the discharge cycle of a capacitor. In addition, the last issue deals with the use of a multimeter in dc mode when reading ac values, a use that collides with the lab settings. All scenarios are presented and discussed, including the solution found for each case. The conclusion derived from the described work is that the remote laboratories area is an expanding field, where practical use leads to improvement and evolution of the available solutions, requiring a strict cooperation and information-sharing between all actors, i.e., developers, teachers, and students.
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| 5. |
- Braam, Arjan W, et al.
(författare)
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Depression and parkinsonism in older Europeans: results from the EURODEP concerted action.
- 2010
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Ingår i: International journal of geriatric psychiatry. - : Wiley. - 1099-1166 .- 0885-6230. ; 25:7, s. 679-87
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: The prevalence rate of depression among patients with Parkinson's disease (PD) has been estimated at 25%, although prevalence figures range between 7-76%. Relatively few studies on PD and depression are based on random samples in the general population. Some depressive symptoms can also be understood as symptoms of parkinsonism, and the current study aims to describe which 'overlap' symptoms can be identified in a community sample. METHODS: Data are employed from the EURODEP collaboration. Nine study centres, from eight western European countries, provided data on depression (most GMS-AGECAT), depressive symptoms (EURO-D items and anxiety), parkinsonism (self-report of PD or clinical signs of PD), functional disability and dementia diagnosis. RESULTS: Data were complete for 16 313 respondents, aged 65 and older; 306 (1.9%) reported or had signs of parkinsonism. The rate of depression was about twice as high among respondents with parkinsonism (unadjusted Odds Ratio 2.44, 95% Confidence Interval 1.88-3.17), also among those without functional disability. 'Overlap' symptoms between parkinsonism and depression, were represented by motivation and concentration problems, appetite problems and especially the symptom of fatigue (energy loss). However, principal component analysis showed that these 'overlap' symptoms loaded on different factors of the EURO-D scale. CONCLUSIONS: As among clinical patients with PD, depression is highly common in community dwelling older people with parkinsonism, even among those without functional disability. Although fatigue did not strongly relate to motivational symptoms, both types of 'overlap' symptoms possibly trigger a final common pathway towards a full depressive syndrome. Copyright (c) 2009 John Wiley & Sons, Ltd.
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| 6. |
- Braam, A. W., et al.
(författare)
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Depression, subthreshold depression and comorbid anxiety symptoms in older Europeans: Results from the EURODEP concerted action
- 2014
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Ingår i: Journal of Affective Disorders. - : Elsevier BV. - 0165-0327. ; 155, s. 266-272
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Tidskriftsartikel (refereegranskat)abstract
- Background: In the epidemiology of late life depression, few insights are available on the co-occurrence of subthreshold depression and comorbicl symptoms of anxiety. The current study aims to describe prevalence patterns of comorbid anxiety symptoms across different levels of depression in old age, and to describe the burden of depressive symptoms and functional disability across patterns of comorbidity. Methods: Respondents were older adults in the community, age 65-104 (N=14,200), from seven European countries, with in total nine study centres, collaborating in the EURODEP concerted action. Depression and anxiety were assessed using the Geriatric Mental State examination (GMS-AGECAT package), providing subthreshold level and case level diagnoses. Presence of anxiety symptoms was defined as at least three distinct symptoms of anxiety. Number of depressive symptoms was assessed with the EURO-D scale. Results: The prevalence of anxiety symptoms amounts to 32% for respondents without depression, 67% for those with subthreshold depression, and 87% for those with case level depression. The number of depressive symptoms is similar for those with subthreshold level depression with cornorbid anxiety, compared to case level depression without symptoms of anxiety. In turn, at case level, comorbid symptoms of anxiety are associated with higher levels of depressive symptoms and more functional disability. Limitations: GMS-AGECAT is insufficiently cciuipped with diagnostic procedures to identify specific types of anxiety disorders. conclusions: Anxiety symptoms in late life depression are highly prevalent, and are likely to contribute to the burden of symptoms of the depression, even at subthreshold level. (C) 2013 Elsevier By. All rights reserved.
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| 7. |
- 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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| 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
- 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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| 9. |
- 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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| 10. |
- Lassen, K., et al.
(författare)
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Pancreaticoduodenectomy : ERAS recommendations.
- 2013
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Ingår i: Clinical Nutrition. - Edinburgh, UK : Churchill-Livingstone. - 0261-5614 .- 1532-1983. ; 32:5, s. 870-871
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Tidskriftsartikel (refereegranskat)
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