| 1. |
- 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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| 2. |
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| 3. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 4. |
- Ahlberg, Simon, et al.
(author)
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An information fusion demonstrator for tactical intelligence processing in network-based defense
- 2007
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In: Information Fusion. - : Elsevier BV. - 1566-2535 .- 1872-6305. ; 8:1, s. 84-107
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Journal article (peer-reviewed)abstract
- The Swedish Defence Research Agency (FOI) has developed a concept demonstrator called the Information Fusion Demonstrator 2003 (IFD03) for demonstrating information fusion methodology suitable for a future Network Based Defense (NBD) C4ISR system. The focus of the demonstrator is on real-time tactical intelligence processing at the division level in a ground warfare scenario. The demonstrator integrates novel force aggregation, particle filtering, and sensor allocation methods to create, dynamically update, and maintain components of a tactical situation picture. This is achieved by fusing physically modelled and numerically simulated sensor reports from several different sensor types with realistic a priori information sampled from both a high-resolution terrain model and an enemy organizational and behavioral model. This represents a key step toward the goal of creating in real time a dynamic, high fidelity representation of a moving battalion-sized organization, based on sensor data as well as a priori intelligence and terrain information, employing fusion, tracking, aggregation, and resource allocation methods all built on well-founded theories of uncertainty. The motives behind this project, the fusion methods developed for the system, as well as its scenario model and simulator architecture are described. The main services of the demonstrator are discussed and early experience from using the system is shared.
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| 5. |
- Ahlberg, Simon, et al.
(author)
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The IFD03 information fusion demonstrator
- 2004
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In: Proceedings of the Seventh International Conference on Information Fusion, FUSION 2004. - 917056115X ; , s. 936-943
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Conference paper (peer-reviewed)abstract
- The paper discusses a recently developed demonstrator system where new ideas in tactical information fusion may be tested and demonstrated. The main services of the demonstrator are discussed, and essential experience from the use and development of the system is shared.
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| 6. |
- Berglund, Johan, et al.
(author)
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5-y follow-up study of patients with neuroborreliosis
- 2002
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In: Scandinavian Journal of Infectious Diseases. - : Taylor & Francis. - 0036-5548 .- 1651-1980. ; 34:6, s. 421-425
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Journal article (peer-reviewed)abstract
- The objective of this follow-up study was to determine the long-term outcome of strictly classified cases of neuroborreliosis treated with antibiotics. A one-year prospective population-based survey of Lyme borreliosis was conducted in southern Sweden, between 1992 and 1993. A total of 349 identified cases with suspected neuroborreliosis were followed up 5 years later. Medical records were reviewed and all participants filled in a questionnaire. Of those classified with definite neuroborreliosis 114/130 completed the follow-up, of whom 111 had completed the initial antibiotic treatment. Of the 114 patients followed up, 86 (75%) had recovered completely and 70 (61%) had recovered within 6 months. Residual neurological symptoms such as facial palsy, concentration disorder, paresthesia and/or neuropathy were reported by 28/114. No significant differences between different antibiotic treatments were observed in terms of occurrence of sequelae. To conclude, we found that 25% (95% confidence interval 17-33%) of the patients suffered from residual neurological symptoms 5 years post-treatment. However, the clinical outcome of treated neuroborreliosis is favourable as only 14/114 (12%) of the patients had sequelae that influenced their daily activity post-treatment. Early diagnosis and treatment would seem to be of great importance in order to avoid such sequelae.
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| 7. |
- Berglund, Johan, et al.
(author)
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A 5-years follow-up of patients with neuroborreliosis.
- 2002
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Conference paper (peer-reviewed)abstract
- The objective of this follow-up study was to determine the long-term outcome in patients treated with antibiotics for strictly classified cases of neuroborreliosis. A one-year prospective population-based survey of Lyme borreliosis was conducted in southern Sweden, 1992-1993. Totally 349 identified cases with suspected neuroborreliosis were registered. Of those, 130 were classified as definitively neuroborreliosis and followed up five years later. Medical records were reviewed and all participants filled in a questionnaire. Totally, 114/130 (88%) completed the follow-up of whom 111/114 (97%) had fulfilled the initial antibiotic treatment. Of these, 86/114 (75%) had recovered completely and 70 (61%) recovered within six months. However 28/114 (25%) suffered from remaining neurological symptoms such as facial palsy, concentration disorder, paresthesia and/or neuropathy. The longer the duration from the neurological symptoms onset to antibiotic treatment the higher was the rate of sequelae. Of those who were treated within 30 days 5/32 (16%) and of those who were treated after 30 days 16/41 (39%) respectively, reported sequelae. Women suffered significantly more from sequelae compared to men, this difference was not seen among the children. No significant differences between the different antibiotic treatments given and experience of sequelae were seen. To conclude, we found that 25% (95% CI 17% to 33%) of the patients suffered from remaining neurological symptoms five years post treatment. However, the clinical outcome of treated neuroborreliosis is favourable as only 14/114 (12%) of the patients had sequelae that influenced their daily activity post treatment and early diagnosis and treatment seems to be of great importance to possibly avoid also these cases.
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| 8. |
- Dodd, Seetal, et al.
(author)
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Application of the Gradient Boosted method in randomised clinical trials: Participant variables that contribute to depression treatment efficacy of duloxetine, SSRIs or placebo.
- 2014
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In: Journal of affective disorders. - : Elsevier BV. - 1573-2517 .- 0165-0327. ; 168, s. 284-93
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Journal article (peer-reviewed)abstract
- Randomised, placebo-controlled trials of treatments for depression typically collect outcomes data but traditionally only analyse data to demonstrate efficacy and safety. Additional post-hoc statistical techniques may reveal important insights about treatment variables useful when considering inter-individual differences amongst depressed patients. This paper aims to examine the Gradient Boosted Model (GBM), a statistical technique that uses regression tree analyses and can be applied to clinical trial data to identify and measure variables that may influence treatment outcomes.
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| 9. |
- Hvidtfeldt, Ulla A., et al.
(author)
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Alcohol Intake and Risk of Coronary Heart Disease in Younger, Middle-Aged, and Older Adults
- 2010
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In: Circulation. - : LIPPINCOTT WILLIAMS & WILKINS. - 0009-7322 .- 1524-4539. ; 121:14, s. 1589-1597
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Journal article (peer-reviewed)abstract
- Background-Light to moderate alcohol consumption is associated with a reduced risk of coronary heart disease. This protective effect of alcohol, however, may be confined to middle-aged or older individuals. Coronary heart disease incidence is low in men <40 years of age and in women <50 years of age; for this reason, study cohorts rarely have the power to investigate the effects of alcohol on coronary heart disease risk in younger adults. This study examined whether the beneficial effect of alcohol on coronary heart disease depends on age. Methods and Results-In this pooled analysis of 8 prospective studies from North America and Europe including 192 067 women and 74 919 men free of cardiovascular diseases, diabetes, and cancers at baseline, average daily alcohol intake was assessed at baseline with a food frequency or diet history questionnaire. An inverse association between alcohol and risk of coronary heart disease was observed in all age groups; hazard ratios among moderately drinking men (5.0 to 29.9 g/d) 39 to 50, 50 to 59, and >= 60 years of age were 0.58 (95% confidence interval [CI], 0.36 to 0.93), 0.72 (95% CI, 0.60 to 0.86), and 0.85 (95% CI, 0.75 to 0.97) compared with abstainers. However, the analyses indicated a smaller incidence rate difference between abstainers and moderate consumers in younger adults (incidence rate difference, 45 per 100 000; 90% CI, 8 to 84) than in middle-aged (incidence rate difference, 64 per 100 000; 90% CI, 24 to 102) and older (incidence rate difference, 89 per 100 000; 90% CI, 44 to 140) adults. Similar results were observed in women. Conclusion-Alcohol is also associated with a decreased risk of coronary heart disease in younger adults; however, the absolute risk was small compared with middle-aged and older adults. (Circulation. 2010; 121: 1589-1597.)
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| 10. |
- Jakobsen, Marianne U, et al.
(author)
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Major types of dietary fat and risk of coronary heart disease : a pooled analysis of 11 cohort studies.
- 2009
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In: American Journal of Clinical Nutrition. - : Elsevier BV. - 0002-9165 .- 1938-3207. ; 89:5, s. 1425-1432
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Journal article (peer-reviewed)abstract
- BACKGROUND: Saturated fatty acid (SFA) intake increases plasma LDL-cholesterol concentrations; therefore, intake should be reduced to prevent coronary heart disease (CHD). Lower habitual intakes of SFAs, however, require substitution of other macronutrients to maintain energy balance. OBJECTIVE: We investigated associations between energy intake from monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), and carbohydrates and risk of CHD while assessing the potential effect-modifying role of sex and age. Using substitution models, our aim was to clarify whether energy from unsaturated fatty acids or carbohydrates should replace energy from SFAs to prevent CHD. DESIGN: This was a follow-up study in which data from 11 American and European cohort studies were pooled. The outcome measure was incident CHD. RESULTS: During 4-10 y of follow-up, 5249 coronary events and 2155 coronary deaths occurred among 344,696 persons. For a 5% lower energy intake from SFAs and a concomitant higher energy intake from PUFAs, there was a significant inverse association between PUFAs and risk of coronary events (hazard ratio: 0.87; 95% CI: 0.77, 0.97); the hazard ratio for coronary deaths was 0.74 (95% CI: 0.61, 0.89). For a 5% lower energy intake from SFAs and a concomitant higher energy intake from carbohydrates, there was a modest significant direct association between carbohydrates and coronary events (hazard ratio: 1.07; 95% CI: 1.01, 1.14); the hazard ratio for coronary deaths was 0.96 (95% CI: 0.82, 1.13). MUFA intake was not associated with CHD. No effect modification by sex or age was found. CONCLUSION: The associations suggest that replacing SFAs with PUFAs rather than MUFAs or carbohydrates prevents CHD over a wide range of intakes.
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