| 1. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)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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| 2. |
- ODonnell, Michael, et al.
(author)
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Registered Replication Report: Dijksterhuis and van Knippenberg (1998)
- 2018
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In: Perspectives on Psychological Science. - : SAGE PUBLICATIONS LTD. - 1745-6916 .- 1745-6924. ; 13:2, s. 268-294
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Journal article (peer-reviewed)abstract
- Dijksterhuis and van Knippenberg (1998) reported that participants primed with a category associated with intelligence (professor) subsequently performed 13% better on a trivia test than participants primed with a category associated with a lack of intelligence (soccer hooligans). In two unpublished replications of this study designed to verify the appropriate testing procedures, Dijksterhuis, van Knippenberg, and Holland observed a smaller difference between conditions (2%-3%) as well as a gender difference: Men showed the effect (9.3% and 7.6%), but women did not (0.3% and -0.3%). The procedure used in those replications served as the basis for this multilab Registered Replication Report. A total of 40 laboratories collected data for this project, and 23 of these laboratories met all inclusion criteria. Here we report the meta-analytic results for those 23 direct replications (total N = 4,493), which tested whether performance on a 30-item general-knowledge trivia task differed between these two priming conditions (results of supplementary analyses of the data from all 40 labs, N = 6,454, are also reported). We observed no overall difference in trivia performance between participants primed with the professor category and those primed with the hooligan category (0.14%) and no moderation by gender.
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| 3. |
- Boot-Handford, M. E., et al.
(author)
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Carbon capture and storage update
- 2014
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In: Energy and Environmental Sciences. - : Royal Society of Chemistry (RSC). - 1754-5692 .- 1754-5706. ; 7:1, s. 130-189
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Research review (peer-reviewed)abstract
- In recent years, Carbon Capture and Storage (Sequestration) (CCS) has been proposed as a potential method to allow the continued use of fossil-fuelled power stations whilst preventing emissions of CO2 from reaching the atmosphere. Gas, coat (and biomass)-fired power stations can respond to changes in demand more readily than many other sources of electricity production, hence the importance of retaining them as an option in the energy mix. Here, we review the leading CO2 capture technologies, available in the short and long term, and their technological maturity, before discussing CO2 transport and storage. Current pilot plants and demonstrations are highlighted, as is the importance of optimising the CCS system as a whole. Other topics briefly discussed include the viability of both the capture of CO2 from the air and CO2 reutilisation as climate change mitigation strategies. Finally, we discuss the economic and legal aspects of CCS.
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| 4. |
- Alexandrov, Ludmil B, et al.
(author)
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The repertoire of mutational signatures in human cancer
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 578:7793, s. 94-101
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Journal article (peer-reviewed)abstract
- Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature1. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium2 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses3-15, enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated-but distinct-DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer.
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| 5. |
- Boot, E., et al.
(author)
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Updated clinical practice recommendations for managing adults with 22q11.2 deletion syndrome
- 2023
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In: Genetics in Medicine. - : Elsevier BV. - 1098-3600 .- 1530-0366. ; 25:3
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Journal article (peer-reviewed)abstract
- This review aimed to update the clinical practice guidelines for managing adults with 22q11.2 deletion syndrome (22q11.2DS). The 22q11.2 Society recruited expert clinicians worldwide to revise the original clinical practice guidelines for adults in a stepwise process according to best practices: (1) a systematic literature search (1992-2021), (2) study selection and synthesis by clinical experts from 8 countries, covering 24 subspecialties, and (3) formulation of consensus recommendations based on the literature and further shaped by patient advocate survey results. Of 2441 22q11.2DS-relevant publications initially identified, 2344 received full-text review, with 2318 meeting inclusion criteria (clinical care relevance to 22q11.2DS) including 894 with potential relevance to adults. The evidence base remains limited. Thus multidisciplinary recommendations represent statements of current best practice for this evolving field, informed by the available literature. These recommendations provide guidance for the recognition, evaluation, surveillance, and management of the many emerging and chronic 22q11.2DS-associated multisystem morbidities relevant to adults. The recommendations also address key genetic counseling and psychosocial considerations for the increasing numbers of adults with this complex condition.& COPY; 2023 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
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| 6. |
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| 7. |
- Main, Chris J., et al.
(author)
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Implementation Science and Employer Disability Practices : Embedding Implementation Factors in Research Designs
- 2016
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In: Journal of occupational rehabilitation. - : Springer-Verlag New York. - 1053-0487 .- 1573-3688. ; 26:4, s. 448-464
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Journal article (peer-reviewed)abstract
- Purpose: For work disability research to have an impact on employer policies and practices it is important for such research to acknowledge and incorporate relevant aspects of the workplace. The goal of this article is to summarize recent theoretical and methodological advances in the field of Implementation Science, relate these to research of employer disability management practices, and recommend future research priorities.Methods: The authors participated in a year-long collaboration culminating in an invited 3-day conference, “Improving Research of Employer Practices to Prevent Disability”, held October 14–16, 2015, in Hopkinton, MA, USA. The collaboration included a topical review of the literature, group conference calls to identify key areas and challenges, drafting of initial documents, review of industry publications, and a conference presentation that included feedback from peer researchers and a question/answer session with a special panel of knowledge experts with direct employer experience.Results: A 4-phase implementation model including both outer and inner contexts was adopted as the most appropriate conceptual framework, and aligned well with the set of process evaluation factors described in both the work disability prevention literature and the grey literature. Innovative interventions involving disability risk screening and psychologically-based interventions have been slow to gain traction among employers and insurers. Research recommendations to address this are : (1) to assess organizational culture and readiness for change in addition to individual factors; (2) to conduct process evaluations alongside controlled trials; (3) to analyze decision-making factors among stakeholders; and (4) to solicit input from employers and insurers during early phases of study design.Conclusions: Future research interventions involving workplace support and involvement to prevent disability may be more feasible for implementation if organizational decision-making factors are imbedded in research designs and interventions are developed to take account of these influences.
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| 8. |
- Oskarsdottir, Solveig, 1953, et al.
(author)
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Updated clinical practice recommendations for managing children with 22q11.2 deletion syndrome
- 2023
-
In: Genetics in Medicine. - : Elsevier BV. - 1098-3600 .- 1530-0366. ; 25:3
-
Journal article (peer-reviewed)abstract
- This review aimed to update the clinical practice guidelines for managing children and adolescents with 22q11.2 deletion syndrome (22q11.2DS). The 22q11.2 Society, the international scientific organization studying chromosome 22q11.2 differences and related conditions, recruited expert clinicians worldwide to revise the original 2011 pediatric clinical practice guidelines in a stepwise process: (1) a systematic literature search (1992-2021), (2) study selection and data extraction by clinical experts from 9 different countries, covering 24 subspecialties, and (3) creation of a draft consensus document based on the literature and expert opinion, which was further shaped by survey results from family support organizations regarding perceived needs. Of 2441 22q11.2DS-relevant publications initially identified, 2344 received full-text reviews, including 1545 meeting criteria for potential relevance to clinical care of children and adolescents. Informed by the available literature, recommendations were formulated. Given evidence base limitations, multidisciplinary recommendations represent consensus statements of good practice for this evolving field. These recommendations provide contemporary guidance for evaluation, surveillance, and management of the many 22q11.2DSassociated physical, cognitive, behavioral, and psychiatric morbidities while addressing important genetic counseling and psychosocial issues.& COPY; 2022 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved.
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| 9. |
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| 10. |
- Smeets, C. J. P. P., et al.
(author)
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A wireless subglacial probe for deep ice applications
- 2012
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In: Journal of Glaciology. - 0022-1430 .- 1727-5652. ; 58:211, s. 841-848
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Journal article (peer-reviewed)abstract
- We present the design and first results from two experiments using a wireless subglacial sensor system (WiSe) that is able to transmit data through 2500 m thick ice. Energy consumption of the probes is minimized, enabling the transmission of data for at least 10 years. In July 2010 the first prototype of the system was used to measure subglacial pressure at the base and a temperature profile consisting of 23 probes in two 600 m deep holes at Russell Glacier, a land-terminating part of the West Greenland ice sheet near Kangerlussuaq. The time series of subglacial pressure show very good agreement between data from the WiSe system and the wired reference system. The wireless-measured temperature data were validated by comparison with the theoretical decrease of melting point with water pressure inside the water-filled hole directly after installation. To test the depth range of the WiSe system a second experiment using three different probe types and two different surface antennas was performed inside the 2537 m deep hole at NEEM. It is demonstrated that, with the proper combination of transmission power and surface antenna type, the WiSe system transmits data through 2500 m thick ice.
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| 11. |
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| 12. |
- Vinel, Claire, et al.
(author)
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Comparative epigenetic analysis of tumour initiating cells and syngeneic EPSC-derived neural stem cells in glioblastoma
- 2021
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Journal article (peer-reviewed)abstract
- Epigenetic mechanisms which play an essential role in normal developmental processes, such as self-renewal and fate specification of neural stem cells (NSC) are also responsible for some of the changes in the glioblastoma (GBM) genome. Here we develop a strategy to compare the epigenetic and transcriptional make-up of primary GBM cells (GIC) with patient-matched expanded potential stem cell (EPSC)-derived NSC (iNSC). Using a comparative analysis of the transcriptome of syngeneic GIC/iNSC pairs, we identify a glycosaminoglycan (GAG)-mediated mechanism of recruitment of regulatory T cells (Tregs) in GBM. Integrated analysis of the transcriptome and DNA methylome of GBM cells identifies druggable target genes and patient-specific prediction of drug response in primary GIC cultures, which is validated in 3D and in vivo models. Taken together, we provide a proof of principle that this experimental pipeline has the potential to identify patient-specific disease mechanisms and druggable targets in GBM. The identification of patient-specific disease mechanisms and druggable targets is crucial for precision medicine in glioblastoma. Here, the authors show that comparing patients-matched glioma-initiating cells with neural stem cells enables the discovery of patient-specific mechanisms of disease and the identification of effective drugs
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| 13. |
- von Scheibler, Emma N.M.M., et al.
(author)
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Parkinsonism in Genetic Neurodevelopmental Disorders : A Systematic Review
- 2023
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In: Movement Disorders Clinical Practice. - : Wiley. - 2330-1619. ; 10:1, s. 17-31
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Research review (peer-reviewed)abstract
- Background: With advances in clinical genetic testing, associations between genetic neurodevelopmental disorders and parkinsonism are increasingly recognized. In this review, we aimed to provide a comprehensive overview of reports on parkinsonism in genetic neurodevelopmental disorders and summarize findings related to genetic diagnosis, clinical features and proposed disease mechanisms. Methods: A systematic literature review was conducted in PubMed and Embase on June 15, 2021. Search terms for parkinsonism and genetic neurodevelopmental disorders, using generic terms and the Human Phenotype Ontology, were combined. Study characteristics and descriptive data were extracted from the articles using a modified version of the Cochrane Consumers and Communication Review Group's data extraction template. The protocol was registered in PROSPERO (CRD42020191035). Results: The literature search yielded 208 reports for data-extraction, describing 69 genetic disorders in 422 patients. The five most reported from most to least frequent were: 22q11.2 deletion syndrome, beta-propeller protein-associated neurodegeneration, Down syndrome, cerebrotendinous xanthomatosis, and Rett syndrome. Notable findings were an almost equal male to female ratio, an early median age of motor onset (26 years old) and rigidity being more common than rest tremor. Results of dopaminergic imaging and response to antiparkinsonian medication often supported the neurodegenerative nature of parkinsonism. Moreover, neuropathology results showed neuronal loss in the majority of cases. Proposed disease mechanisms included aberrant mitochondrial function and disruptions in neurotransmitter metabolism, endosomal trafficking, and the autophagic-lysosomal and ubiquitin-proteasome system. Conclusion: Parkinsonism has been reported in many GNDs. Findings from this study may provide clues for further research and improve management of patients with GNDs and/or parkinsonism.
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| 14. |
- Blagowidow, N., et al.
(author)
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Prenatal Screening and Diagnostic Considerations for 22q11.2 Microdeletions
- 2023
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In: Genes. - : MDPI AG. - 2073-4425. ; 14:1
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Journal article (peer-reviewed)abstract
- Diagnosis of a chromosome 22q11.2 microdeletion and its associated deletion syndrome (22q11.2DS) is optimally made early. We reviewed the available literature to provide contemporary guidance and recommendations related to the prenatal period. Indications for prenatal diagnostic testing include a parent or child with the 22q11.2 microdeletion or suggestive prenatal screening results. Definitive diagnosis by genetic testing of chorionic villi or amniocytes using a chromosomal microarray will detect clinically relevant microdeletions. Screening options include noninvasive prenatal screening (NIPS) and imaging. The potential benefits and limitations of each screening method should be clearly conveyed. NIPS, a genetic option available from 10 weeks gestational age, has a 70-83% detection rate and a 40-50% PPV for most associated 22q11.2 microdeletions. Prenatal imaging, usually by ultrasound, can detect several physical features associated with 22q11.2DS. Findings vary, related to detection methods, gestational age, and relative specificity. Conotruncal cardiac anomalies are more strongly associated than skeletal, urinary tract, or other congenital anomalies such as thymic hypoplasia or cavum septi pellucidi dilatation. Among others, intrauterine growth restriction and polyhydramnios are additional associated, prenatally detectable signs. Preconception genetic counselling should be offered to males and females with 22q11.2DS, as there is a 50% risk of transmission in each pregnancy. A previous history of a de novo 22q11.2 microdeletion conveys a low risk of recurrence. Prenatal genetic counselling includes an offer of screening or diagnostic testing and discussion of results. The goal is to facilitate optimal perinatal care.
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| 15. |
- Den Ouden, M. A. G., et al.
(author)
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Stand-alone single-frequency GPS ice velocity observations on Nordenskiöldbreen, Svalbard
- 2010
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In: The Cryosphere. - : Copernicus GmbH. - 1994-0416 .- 1994-0424. ; 4:4, s. 593-604
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Journal article (peer-reviewed)abstract
- Precise measurements of ice-flow velocities are necessary for a proper understanding of the dynamics of glaciers and their response to climate change. We use stand-alone single-frequency GPS receivers for this purpose. They are designed to operate unattended for 1–3 years, allowing uninterrupted measurements for long periods with hourly temporal resolution. We present the system and illustrate its functioning using data from 9 GPS receivers deployed on Nordenskiöldbreen, Svalbard, for the period 2006–2009. The accuracy of the receivers is 1.62 m based on the standard deviation in the average location of a stationary reference station (NBRef). Both the location of NBRef and the observed flow velocities agree within one standard deviation with DGPS measurements. Periodicity (6, 8, 12, 24 h) in the NBRef data is largely explained by the atmospheric, mainly ionospheric, influence on the GPS signal. A (weighed) running-average on the observed locations significantly reduces the standard deviation and removes high frequency periodicities, but also reduces the temporal resolution. Results show annual average velocities varying between 40 and 55 m yr−1 at stations on the central flow-line. On weekly to monthly time-scales we observe a peak in the flow velocities (from 60 to 90 m yr−1) at the beginning of July related to increased melt-rates. No significant lag is observed between the timing of the maximum speed between different stations. This is likely due to the limited temporal resolution after averaging in combination with the relatively small distance (max. ±13 km) between the stations.
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| 16. |
- Marques, André R A, et al.
(author)
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Glucosylated cholesterol in mammalian cells and tissues: formation and degradation by multiple cellular β-glucosidases.
- 2016
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In: Journal of Lipid Research. - 1539-7262. ; 57, s. 451-463
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Journal article (peer-reviewed)abstract
- The membrane lipid glucosylceramide (GlcCer) is continuously formed and degraded. Cells express two GlcCer-degrading β-glucosidases, GBA and GBA2, located in and outside the lysosome, respectively. Here we demonstrate that through transglucosylation both GBA and GBA2 are able to catalyze in vitro the transfer of glucosyl-moieties from GlcCer to cholesterol, and vice versa. Furthermore, the natural occurrence of 1-O-cholesteryl-β-D-glucopyranoside (GlcChol) in mouse tissues and human plasma is demonstrated using LC-MS/MS and 13C6-labelled GlcChol as internal standard. In cells the inhibition of GBA increases GlcChol, whereas inhibition of GBA2 decreases glucosylated sterol. Similarly, in GBA2-deficient mice GlcChol is reduced. Depletion of GlcCer by inhibition of GlcCer synthase decreases GlcChol in cells and likewise in plasma of inhibitor-treated Gaucher disease patients. In tissues of mice with Niemann-Pick type C, a condition characterized by intralysosomal accumulation of cholesterol, marked elevations in GlcChol occur as well. When lysosomal accumulation of cholesterol is induced in cultured cells, GlcChol is formed via lysosomal GBA. This illustrates that reversible transglucosylation reactions are highly dependent on local availability of suitable acceptors. In conclusion, mammalian tissues contain GlcChol formed by transglucosylation through β-glucosidases using GlcCer as donor. Our findings reveal a novel metabolic function for GlcCer.
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| 17. |
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| 18. |
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| 19. |
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| 20. |
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| 21. |
- Young, Amanda E., et al.
(author)
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Workplace Outcomes in Work-Disability Prevention Research : A Review with Recommendations for Future Research
- 2016
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In: Journal of occupational rehabilitation. - New York, USA : Springer. - 1053-0487 .- 1573-3688. ; 26:4, s. 434-447
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Research review (peer-reviewed)abstract
- Introduction: Outcome assessment is a central issue in work disability prevention research. The goal of this paper was to (1) ascertain the most salient workplace outcomes; (2) evaluate the congruence between business and science perspectives; (3) illustrate new perspectives on assessing longitudinal outcomes; and (4) provide recommendations for advancing outcome evaluation in this area of research.Methods: The authors participated in a year-long collaboration that culminated in a sponsored 3-day conference, "Improving Research of Employer Practices to Prevent Disability", held October 14-16, 2015, in Hopkinton, MA, USA. The collaboration included a topical review of the literature, group conference calls to identify key areas and challenges, drafting of initial documents, review of industry publications, and a conference presentation that included feedback from peer researchers and a question/answer session with a special panel of knowledge experts with direct employer experience.Results: Numerous workplace work-disability prevention outcome measures were identified. Analysis indicated that their applicability varied depending on the type of work disability the worker was experiencing. For those who were working, but with health-related work limitations (Type 1), predominant outcomes were measures of productivity, presenteeism, and work-related limitations. For those who were off work due to a health condition (Type 2), predominant outcomes were measures of time off work, supervisor/employee interactions, and return-to-work (RTW) preparation. For those who had returned to work (Type 3), predominant outcomes were measures of presenteeism, time until RTW, percentage of work resumption, employment characteristics, stigma, work engagement, co-worker interactions, and sustained or durable RTW. For those who had withdrawn from the labor force (Type 4), predominant outcomes were cost and vocational status.Discussion: Currently available measures provide a good basis to use more consistent outcomes in disability prevention in the future. The research area would also benefit from more involvement of employers as stakeholders, and multilevel conceptualizations of disability outcomes.
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| 22. |
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| 23. |
- Zuiker, Rob G J A, et al.
(author)
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Kinetics of TH2 biomarkers in sputum of asthmatics following inhaled allergen.
- 2015
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In: European clinical respiratory journal. - : Informa UK Limited. - 2001-8525. ; 2
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Journal article (peer-reviewed)abstract
- Allergen-induced late airway response offers important pharmacodynamic targets, including T helper 2 (TH2) biomarkers. However, detection of inflammatory markers has been limited in dithiothreitol-processed sputum.
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