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- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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- Arvidsson, Patrik, et al.
(författare)
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Structural validity and internal consistency of Picture My Participation : A measure for children with disability
- 2021
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Ingår i: African Journal of Disability. - : OASIS. - 2226-7220 .- 2223-9170. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Background: Picture My Participation (PMP) intended to measure participation, defined as attendance and involvement in everyday situations, of children with disabilities, particularly in low- and middle-income settings.Objectives: To explore structural validity of PMP by identifying possible subcomponents in the attendance scale and examining internal consistency of the total score and each subcomponent.Method: A picture-supported interview was conducted with 182 children, 7–18 years, with and without intellectual disability (ID). Frequency of attendance in 20 activities was rated on a four-point Likert scale (never, seldom, sometimes and always).Results: An exploratory principal component analysis extracted four subcomponents: (1) organised activities, (2) social activities and taking care of others, (3) family life activities and 4) personal care and development activities. Internal consistency for the total scale (alpha = 0.85) and the first two subcomponents (alpha = 0.72 and 0.75) was acceptable. The two last subcomponents alpha values were 0.57 and 0.49.Conclusion: The four possible subcomponents of PMP can be used to provide information about possible domains in which participation and participation restrictions exist. This study provided further psychometric evidence about PMP as a measure of participation. The stability and the utility of these subcomponents needed further exploration.
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- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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- Kang, Lin-Ju, et al.
(författare)
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Development and usability of an app-based instrument of participation in children with disabilities
- 2023
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Ingår i: Scandinavian Journal of Occupational Therapy. - : Taylor & Francis. - 1103-8128 .- 1651-2014. ; 30:3, s. 322-333
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Tidskriftsartikel (refereegranskat)abstract
- Background: Picture My Participation (PmP) is a picture-supported child-report instrument of participation of children with disabilities.Aims: This study described the development of a mobile application of the PmP Traditional Chinese version (PmP-C) and evaluated its usability.Methods: The PmP-C App includes features that allow the input of a child’s demographics, identification of frequency and involvement of 22 culturally appropriate activities, selection of the three most important activities and the specification of the environmental facilitators and barriers. The usability test was conducted with 10 healthcare workers, who interviewed 10 children with disabilities aged 6–12 years. The healthcare workers completed a usability questionnaire and were asked to provide feedback on the ease of use, learning, satisfaction and perceived usefulness.Results: The mean score for the usability questionnaire ranged from 2.7 to 4.6 out of 5.0. The feedback indicated that the interface was simple to operate by the healthcare workers and was attractive and motivating to children. Improvements of layout design, operation instructions and technical problems were recommended, which contributed to the app program optimization.Conclusions: The PmP-C App provides a practical tool with initial support for usability to enable active engagement and communication of children with disabilities with healthcare providers.
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- Hwang, Ai-Wen, et al.
(författare)
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Linkage of ICF-CY codes with environmental factors in studies of developmental outcomes of infants and toddlers with or at risk for motor delays
- 2014
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Ingår i: Disability and Rehabilitation. - : Informa UK Limited. - 0963-8288 .- 1464-5165. ; 36:2, s. 89-104
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Forskningsöversikt (refereegranskat)abstract
- Purpose: Environmental variables have been explored in studies of the development of young children with motor delays. Linking environmental variables to the International Classification of Functioning, Disability and Health – Children and Youth (ICF-CY), environmental factors (EFs) categories can provide a common language for documenting their contribution to developmental outcomes. This review of studies aimed to (1) link EFs for developmental outcomes in infants with or at risk for motor delays to ICF-CY categories and (2) synthesize the influences of EFs (with ICF-CY linkage) on developmental outcomes.Method: A systematic literature search was performed of multiple databases. After applying selection criteria, environmental variables in 28 articles were linked to ICF-CY categories and underwent qualitative synthesis.Results: Results indicated that physical environmental variables could be linked successfully to ICF-CY EFs categories, but not social environmental variables. Multiple environmental variables were associated with motor and other developmental outcomes.Conclusion: Difficulties in linking social factors to ICF-CY categories indicate that additional EFs codes may need to be considered in the ICF-CY revision processes. The review provides empirical data on relationships between EFs and developmental outcomes in children with or at risk for motor delay.
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