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- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 3. |
- Rich, Rebecca L., et al.
(author)
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A global benchmark study using affinity-based biosensors
- 2009
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In: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 386:2, s. 194-216
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Journal article (peer-reviewed)abstract
- To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.
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| 4. |
- Pearse, Rupert M, et al.
(author)
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Mortality after surgery in Europe: a 7 day cohort study.
- 2012
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In: Lancet. - 1474-547X. ; 380:9847, s. 1059-65
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Journal article (peer-reviewed)abstract
- Clinical outcomes after major surgery are poorly described at the national level. Evidence of heterogeneity between hospitals and health-care systems suggests potential to improve care for patients but this potential remains unconfirmed. The European Surgical Outcomes Study was an international study designed to assess outcomes after non-cardiac surgery in Europe.
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| 5. |
- D'Ambruoso, Lucia, et al.
(author)
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Moving from medical to health systems classifications of deaths : extending verbal autopsy to collect information on the circumstances of mortality
- 2016
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In: Global Health Research and Policy. - : BioMed Central. - 2397-0642. ; 1
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Journal article (peer-reviewed)abstract
- Background: Verbal autopsy (VA) is a health surveillance technique used in low and middle-income countries to establish medical causes of death (CODs) for people who die outside hospitals and/or without registration. By virtue of the deaths it investigates, VA is also an opportunity to examine social exclusion from access to health systems. The aims were to develop a system to collect and interpret information on social and health systems determinants of deaths investigated in VA.Methods: A short set of questions on care pathways, circumstances and events at and around the time of death were developed and integrated into the WHO 2012 short form VA (SF-VA). Data were subsequently analysed from two census rounds in the Agincourt Health and Socio-Demographic Surveillance Site (HDSS), South Africa in 2012 and 2013 where the SF-VA had been applied. InterVA and descriptive analysis were used to calculate cause-specific mortality fractions (CSMFs), and to examine responses to the new indicators and whether and how they varied by medical CODs and age/sex sub-groups.Results: One thousand two hundred forty-nine deaths were recorded in the Agincourt HDSS censuses in 2012–13 of which 1,196 (96 %) had complete VA data. Infectious and non-communicable conditions accounted for the majority of deaths (47 % and 39 % respectively) with smaller proportions attributed to external, neonatal and maternal causes (5 %, 2 % and 1 % respectively). 5 % of deaths were of indeterminable cause. The new indicators revealed multiple problems with access to care at the time of death: 39 % of deaths did not call for help, 36 % found care unaffordable overall, and 33 % did not go to a facility. These problems were reported consistently across age and sex sub-groups. Acute conditions and younger age groups had fewer problems with overall costs but more with not calling for help or going to a facility. An illustrative health systems interpretation suggests extending and promoting existing provisions for transport and financial access in this setting.Conclusions: Supplementing VA with questions on the circumstances of mortality provides complementary information to CSMFs relevant for health planning. Further contextualisation of the method and results are underway with health systems stakeholders to develop the interpretation sequence as part of a health policy and systems research approach.
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| 6. |
- D'Ambruoso, Lucia, et al.
(author)
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Rethinking collaboration : developing a learning platform to address under-five mortality in Mpumalanga province, South Africa
- 2019
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In: Health Policy and Planning. - : Oxford University Press. - 0268-1080 .- 1460-2237. ; 34:6, s. 418-429
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Journal article (peer-reviewed)abstract
- Following 50 years of apartheid, South Africa introduced visionary health policy committing to the right to health as part of a primary health care (PHC) approach. Implementation is seriously challenged, however, in an often-dysfunctional health system with scarce resources and a complex burden of avoidable mortality persists. Our aim was to develop a process generating evidence of practical relevance on implementation processes among people excluded from access to health systems. Informed by health policy and systems research, we developed a collaborative learning platform in which we worked as co-researchers with health authorities in a rural province. This article reports on the process and insights brought by health systems stakeholders. Evidence gaps on under-five mortality were identified with a provincial Directorate after which we collected quantitative and qualitative data. We applied verbal autopsy to quantify levels, causes and circumstances of deaths and participatory action research to gain community perspectives on the problem and priorities for action. We then re-convened health systems stakeholders to analyse and interpret these data through which several systems issues were identified as contributory to under-five deaths: staff availability and performance; service organization and infrastructure; multiple parallel initiatives; and capacity to address social determinants. Recommendations were developed ranging from immediate low- and no-cost re-organization of services to those where responses from higher levels of the system or outside were required. The process was viewed as acceptable and relevant for an overburdened system operating 'in the dark' in the absence of local data. Institutional infrastructure for evidence-based decision-making does not exist in many health systems. We developed a process connecting research evidence on rural health priorities with the means for action and enabled new partnerships between communities, authorities and researchers. Further development is planned to understand potential in deliberative processes for rural PHC.
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| 7. |
- Demichev, Vadim, et al.
(author)
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A time-resolved proteomic and prognostic map of COVID-19
- 2021
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In: Cell Systems. - : Elsevier BV. - 2405-4712 .- 2405-4720. ; 12:8, s. 780-794.e7
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Journal article (peer-reviewed)abstract
- COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.
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| 8. |
- Hyde, Kevin D., et al.
(author)
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One stop shop: backbones trees for important phytopathogenic genera: I (2014)
- 2014
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In: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 21-125
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Journal article (peer-reviewed)abstract
- Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.
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| 9. |
- Schuch, R, et al.
(author)
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A first study of dielectronic recombination with the super-expanded electron beam in CRYRING
- 1998
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In: Hyperfine Interactions. - 0304-3843. ; 115:1-4, s. 123-127
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Journal article (peer-reviewed)abstract
- A first temperature measurement of the expanded electron beam from a super-conducting magnet in the cooler of CRYRING is reported. It is based on detection of a dielectronic recombination resonance in C2+. For this measurement C3+ was stored in the ring at 3 MeV/amu energy. A fit to the resonance with free transverse and longitudinal temperatures gave 3.9 x 10(-3) eV and 4.5 x 10(-5) eV,respectively. The result is also compatible with the values of 10(-3) eV for the transverse and 6.7 x 10(-5) eV for the longitudinal component, in good agreement with expected values.
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| 10. |
- Spies, W, et al.
(author)
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Recombination experiments at CRYRING
- 1998
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In: Hyperfine Interactions. - 0304-3843. ; 114:1-4, s. 237-243
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Journal article (peer-reviewed)abstract
- Recent advances in studies of electron-ion recombination processes at low relative energies with the electron cooler of the heavy-ion storage ring CRYRING are shown. Through the use of an adiabatically expanded electron beam, collisions down to 10(-4) eV relative energies were measured with highly charged ions stored in the ring at around 15 MeV/amu energies. Examples of recombination measurements for bare ions of D+, He2+, N7+, Ne10+ and Si14+ are presented. Further on, results of an experiment measuring laser-induced recombination (LIR) into n = 3 states of deuterium with polarized laser light are shown.
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| 11. |
- Wariri, Oghenebrume, et al.
(author)
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Initiating a participatory action research process in the Agincourt health and socio-demographic surveillance site
- 2017
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In: Journal of Global Health. - : Edinburgh University Global Health Society. - 2047-2978 .- 2047-2986. ; 7:1
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Journal article (peer-reviewed)abstract
- Background Despite progressive health policy, disease burdens in South Africa remain patterned by deeply entrenched social inequalities. Accounting for the relationships between context, health and risk can provide important information for equitable service delivery. The aims of the research were to initiate a participatory research process with communities in a low income setting and produce evidence of practical relevance. Methods We initiated a participatory action research (PAR) process in the Agincourt health and socio-demographic surveillance site (HDSS) in rural north-east South Africa. Three village-based discussion groups were convened and consulted about conditions to examine, one of which was under-5 mortality. A series of discussions followed in which routine HDSS data were presented and participants' subjective perspectives were elicited and systematized into collective forms of knowledge using ranking, diagramming and participatory photography. The process concluded with a priority setting exercise. Visual and narrative data were thematically analyzed to complement the participants' analysis. Results A range of social and structural root causes of under-5 mortality were identified: poverty, unemployment, inadequate housing, unsafe environments and shortages of clean water. Despite these constraints, single mothers were often viewed as negligent. A series of mid-level contributory factors in clinics were also identified: overcrowding, poor staffing, delays in treatment and shortages of medications. In a similar sense, pronounced blame and negativity were directed toward clinic nurses in spite of the systems constraints identified. Actions to address these issues were prioritized as: expanding clinics, improving accountability and responsiveness of health workers, improving employment, providing clean water, and expanding community engagement for health promotion. Conclusions We initiated a PAR process to gain local knowledge and prioritise actions. The process was acceptable to those involved, and there was willingness and commitment to continue. The study provided a basis from which to gain support to develop fuller forms of participatory research in this setting. The next steps are to build deeper involvement of participants in the process, expand to include the perspectives of those most marginalized and engage in the health system at different levels to move toward an ongoing process of action and learning from action.
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