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- Wilkinson, Mark D., et al.
(författare)
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Comment : The FAIR Guiding Principles for scientific data management and stewardship
- 2016
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
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| 2. |
- Hubers, Anna A M, et al.
(författare)
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Suicidal ideation in a European Huntington's disease population
- 2013
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Ingår i: Journal of Affective Disorders. - : Elsevier BV. - 1573-2517 .- 0165-0327. ; 151:1, s. 58-248
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Previous studies indicate increased prevalences of suicidal ideation, suicide attempts, and completed suicide in Huntington's disease (HD) compared with the general population. This study investigates correlates and predictors of suicidal ideation in HD.METHODS: The study cohort consisted of 2106 HD mutation carriers, all participating in the REGISTRY study of the European Huntington's Disease Network. Of the 1937 participants without suicidal ideation at baseline, 945 had one or more follow-up measurements. Participants were assessed for suicidal ideation by the behavioural subscale of the Unified Huntington's Disease Rating Scale (UHDRS). Correlates of suicidal ideation were analyzed using logistic regression analysis and predictors were analyzed using Cox regression analysis.RESULTS: At baseline, 169 (8.0%) mutation carriers endorsed suicidal ideation. Disease duration (odds ratio [OR]=0.96; 95% confidence interval [CI]: 0.9-1.0), anxiety (OR=2.14; 95%CI: 1.4-3.3), aggression (OR=2.41; 95%CI: 1.5-3.8), a previous suicide attempt (OR=3.95; 95%CI: 2.4-6.6), and a depressed mood (OR=13.71; 95%CI: 6.7-28.0) were independently correlated to suicidal ideation at baseline. The 4-year cumulative incidence of suicidal ideation was 9.9%. Longitudinally, the presence of a depressed mood (hazard ratio [HR]=2.05; 95%CI: 1.1-4.0) and use of benzodiazepines (HR=2.44; 95%CI: 1.2-5.0) at baseline were independent predictors of incident suicidal ideation, whereas a previous suicide attempt was not predictive.LIMITATIONS: As suicidal ideation was assessed by only one item, and participants were a selection of all HD mutation carriers, the prevalence of suicidal ideation was likely underestimated.CONCLUSIONS: Suicidal ideation in HD frequently occurs. Assessment of suicidal ideation is a priority in mutation carriers with a depressed mood and in those using benzodiazepines.
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| 3. |
- In ’t Veld, Sjors G.J.G., et al.
(författare)
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Detection and localization of early- and late-stage cancers using platelet RNA
- 2022
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Ingår i: Cancer Cell. - : Elsevier. - 1535-6108 .- 1878-3686. ; 40:9, s. 999-1009.e6
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Tidskriftsartikel (refereegranskat)abstract
- Cancer patients benefit from early tumor detection since treatment outcomes are more favorable for less advanced cancers. Platelets are involved in cancer progression and are considered a promising biosource for cancer detection, as they alter their RNA content upon local and systemic cues. We show that tumor-educated platelet (TEP) RNA-based blood tests enable the detection of 18 cancer types. With 99% specificity in asymptomatic controls, thromboSeq correctly detected the presence of cancer in two-thirds of 1,096 blood samples from stage I–IV cancer patients and in half of 352 stage I–III tumors. Symptomatic controls, including inflammatory and cardiovascular diseases, and benign tumors had increased false-positive test results with an average specificity of 78%. Moreover, thromboSeq determined the tumor site of origin in five different tumor types correctly in over 80% of the cancer patients. These results highlight the potential properties of TEP-derived RNA panels to supplement current approaches for blood-based cancer screening.
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| 4. |
- Klingström, Tomas, et al.
(författare)
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Workshop on laboratory protocol standards for the molecular methods database
- 2013
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Ingår i: New Biotechnology. - : Elsevier BV. - 1871-6784 .- 1876-4347. ; 30:2, s. 109-113
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Tidskriftsartikel (refereegranskat)abstract
- Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.
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| 8. |
- Brahme, Anders, et al.
(författare)
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Solution of an integral equation encountered in rotation therapy
- 1982
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Ingår i: Physics in Medicine and Biology. - : IOP Publishing. - 0031-9155 .- 1361-6560. ; 27:10, s. 1221-1229
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Tidskriftsartikel (refereegranskat)abstract
- An integral equation relating the lateral absorbed dose profile of a photon beam to the resultant absorbed dose distribution during single-turn rotating-beam therapy has been set up and solved for the case of a cylindrical phantom with the axis of rotation coinciding with the axis of symmetry of the cylinder. In the first approximation the results obtained are also valid when the axis of rotation is somewhat off-centred, even in a phantom that deviates from circular symmetry, provided the rotation is performed in both clockwise and counter clockwise directions. The calculated dose profiles indicate that improved dose uniformity can be achieved using a new type of non-linear wedge-shaped filter, which can easily be designed using the derived general analytic solution to the integral equation.
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| 9. |
- de Wit, Cynthia A., et al.
(författare)
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Organohalogen compounds of emerging concern in Baltic Sea biota : Levels, biomagnification potential and comparisons with legacy contaminants
- 2020
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Ingår i: Environment International. - : Elsevier BV. - 0160-4120 .- 1873-6750. ; 144
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Tidskriftsartikel (refereegranskat)abstract
- While new chemicals have replaced major toxic legacy contaminants such as polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDT), knowledge of their current levels and biomagnification potential in Baltic Sea biota is lacking. Therefore, a suite of chemicals of emerging concern, including organophosphate esters (OPEs), short-chain, medium-chain and long-chain chlorinated paraffins (SCCPs, MCCPs, LCCPs), halogenated flame retardants (HFRs), and per- and polyfluoroalkyl substances (PFAS), were analysed in blue mussel (Mytilus edulis), viviparous eelpout (Zoarces viviparus), Atlantic herring (Clupea harengus), grey seal (Halichoerus grypus), harbor seal (Phoca vitulina), harbor porpoise (Phocoena phocoena), common eider (Somateria mollissima), common guillemot (Uria aalge) and white-tailed eagle (Haliaeetus albicilla) from the Baltic Proper, sampled between 2006 and 2016. Results were benchmarked with existing data for legacy contaminants. The mean concentrations for Sigma OPEs ranged from 57 to 550 ng g(-1) lipid weight (lw), for Sigma CPs from 110 to 640 ng g(-1) lw for Sigma HFRs from 0.42 to 80 ng g(-1) lw, and for Sigma PFAS from 1.1 to 450 ng g(-1) wet weight. Perfluoro-4-ethyl-cyclohexanesulfonate (PFECHS) was detected in most species. Levels of OPEs, CPs and HFRs were generally similar or higher than those of polybrominated diphenyl ethers (PBDEs) and/or hexabromocyclododecane (HBCDD). OPE, CP and HFR concentrations were also similar to PCBs and DDTs in blue mussel, viviparous eelpout and Atlantic herring. In marine mammals and birds, PCB and DDT concentrations remained orders of magnitude higher than those of OPEs, CPs, HFRs and PFAS. Predator-prey ratios for individual OPEs (0.28-3.9) and CPs (0.40-5.0) were similar or somewhat lower than those seen for BDE-47 (5.0-29) and HBCDD (2.4-13). Ratios for individual HFRs (0.010-37) and PFAS (0.15-47) were, however, of the same order of magnitude as seen for p,p'-DDE (4.7-66) and CB-153 (31-190), indicating biomagnification potential for many of the emerging contaminants. Lack of toxicity data, including for complex mixtures, makes it difficult to assess the risks emerging contaminants pose. Their occurence and biomagnification potential should trigger risk management measures, particularly for MCCPs, HFRs and PFAS.
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