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- Nelson, G., et al.
(författare)
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QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
- 2021
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 284:1, s. 56-73
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Tidskriftsartikel (refereegranskat)abstract
- A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
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| 2. |
- Boehm, U., et al.
(författare)
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QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy
- 2021
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; :18, s. 1423-1426
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Tidskriftsartikel (refereegranskat)abstract
- The community-driven initiative Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi) wants to improve reproducibility for light microscopy image data through quality control (QC) management of instruments and images. It aims for a common set of QC guidelines for hardware calibration and image acquisition, management and analysis.
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| 4. |
- Lustig, S, et al.
(författare)
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The impact of school-based screening on service use in adolescents at risk for mental health problems and risk-behaviour
- 2023
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Ingår i: European child & adolescent psychiatry. - : Springer Science and Business Media LLC. - 1435-165X .- 1018-8827. ; 32:9, s. 1745-1754
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Tidskriftsartikel (refereegranskat)abstract
- Early detection and intervention can counteract mental disorders and risk behaviours among adolescents. However, help-seeking rates are low. School-based screenings are a promising tool to detect adolescents at risk for mental problems and to improve help-seeking behaviour. We assessed associations between the intervention “Screening by Professionals” (ProfScreen) and the use of mental health services and at-risk state at 12 month follow-up compared to a control group. School students (aged 15 ± 0.9 years) from 11 European countries participating in the “Saving and Empowering Young Lives in Europe” (SEYLE) study completed a self-report questionnaire on mental health problems and risk behaviours. ProfScreen students considered “at-risk” for mental illness or risk behaviour based on the screening were invited for a clinical interview with a mental health professional and, if necessary, referred for subsequent treatment. At follow-up, students completed another self-report, additionally reporting on service use. Of the total sample (N = 4,172), 61.9% were considered at-risk. 40.7% of the ProfScreen at-risk participants invited for the clinical interview attended the interview, and 10.1% of subsequently referred ProfScreen participants engaged in professional treatment. There were no differences between the ProfScreen and control group regarding follow-up service use and at-risk state. Attending the ProfScreen interview was positively associated with follow-up service use (OR = 1.783, 95% CI = 1.038–3.064), but had no effect on follow-up at-risk state. Service use rates of professional care as well as of the ProfScreen intervention itself were low. Future school-based interventions targeting help-seeking need to address barriers to intervention adherence.Clinical Trials Registration: The trial is registered at the US National Institute of Health (NIH) clinical trial registry (NCT00906620, registered on 21 May, 2009), and the German Clinical Trials Register (DRKS00000214, registered on 27 October, 2009).
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| 7. |
- Kaess, M, et al.
(författare)
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Twelve-month service use, suicidality and mental health problems of European adolescents after a school-based screening for current suicidality
- 2022
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Ingår i: European child & adolescent psychiatry. - : Springer Science and Business Media LLC. - 1435-165X .- 1018-8827. ; 31:2, s. 229-238
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Tidskriftsartikel (refereegranskat)abstract
- Suicide is one of the leading causes of death in adolescents and help-seeking behaviour for suicidal behaviour is low. School-based screenings can identify adolescents at risk for suicidal behaviour and might have the potential to facilitate service use and reduce suicidal behaviour. The aim of this study was to assess associations of a two-stage school-based screening with service use and suicidality in adolescents (aged 15 ± 0.9 years) from 11 European countries after one year. Students participating in the ‘Saving and Empowering Young Lives in Europe’ (SEYLE) study completed a self-report questionnaire including items on suicidal behaviour. Those screening positive for current suicidality (first screening stage) were invited to an interview with a mental health professional (second stage) who referred them for treatment, if necessary. At 12-month follow-up, students completed the same self-report questionnaire including questions on service use within the past year. Of the N = 12,395 SEYLE participants, 516 (4.2%) screened positive for current suicidality and were invited to the interview. Of these, 362 completed the 12-month follow-up with 136 (37.6%) self-selecting to attend the interview (screening completers). The majority of both screening completers (81.9%) and non-completers (91.6%) had not received professional treatment within one year, with completers being slightly more likely to receive it (χ2(1) = 8.948, V = 0.157, p ≤ 0.01). Screening completion was associated with higher service use (OR 2.695, se 1.017, p ≤ 0.01) and lower suicidality at follow-up (OR 0.505, se 0.114, p ≤ 0.01) after controlling for potential confounders. This school-based screening offered limited evidence for the improvement of service use for suicidality. Similar future programmes might improve interview attendance rate and address adolescents’ barriers to care.
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| 9. |
- Sorelius, Karl, et al.
(författare)
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The Microbiology of Infective Native Aortic Aneurysms in a Population-Based Setting
- 2022
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Ingår i: Annals of Vascular Surgery. - : Elsevier. - 0890-5096 .- 1615-5947. ; 78, s. 112-122
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Tidskriftsartikel (refereegranskat)abstract
- Objective: The aim was to describe the microbiology of surgically treated infective native (mycotic) aortic aneurysms (INAAs), and associated survival and development of infection-related complications (IRCs). Methods: Data were pooled from 2 nationwide studies on surgically treated patients with INAAs in Sweden, between 1994 - 2016. Patients were grouped and analyzed according to culture results: 1) Staphylococcus aureus, 2) Streptococcus species (sp.), 3) Salmonella sp., 4) Enterococcus sp., 5) Gram-negative intestinal bacteria, 6) Other sp. (all other species found in culture), and 7) Negative cultures. Results: A sum of 182 patients were included, mean age 71 years (standard deviation; SD: 8.9). The median follow-up was 50.3 months (range 0 - 360). 128 (70.3%) patients had positive blood and/or tissue culture; Staphylococcus aureus n = 38 (20.9%), Streptococcus sp. n = 37 (20.3%), Salmonella sp. n = 19 (10.4%), Enterococcus sp. n = 16 (8.8%), Gram-negative intestinal bacteria n = 6, (3.3%), Other sp. n = 12 (6.6%) and Negative cultures n = 54 (29.7%). The estimated survival for the largest groups at 2-years after surgery was: Staphylococcus aureus 62% (95% Confidence interval 53.9 - 70.1), Streptococcus sp. 74.7% (67.4 - 82.0), Salmonella sp. 73.7% (63.6 - 83.8), Enterococcus sp. 61.9% (49.6 - 74.2), and Negative cultures 89.8% (85.5 - 94.1), P =.051. There were 37 IRCs (20.3%), and 19 (51.4%) were fatal, the frequency was insignificant between the groups. The majority of IRCs, 30/37 (81%), developed during the first postoperative year. Conclusion: In this assessment of microbiological findings of INAAs in Sweden, 50% of the pathogens were Staphylococcus aureus, Streptococcus sp., or Salmonella sp.. The overall 20%-frequency of IRCs, and its association with high mortality, motivates long-term antibiotic treatment regardless of microbial findings.
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