| 1. |
- 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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| 2. |
- Batra, Gorav, et al.
(författare)
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Biomarker-Based Prediction of Recurrent Ischemic Events in Patients With Acute Coronary Syndromes
- 2022
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Ingår i: Journal of the American College of Cardiology. - : Elsevier. - 0735-1097 .- 1558-3597. ; 80:18, s. 1735-1747
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: In patients with acute coronary syndrome (ACS), there is residual and variable risk of recurrent ischemic events.OBJECTIVES: This study aimed to develop biomarker-based prediction models for 1-year risk of cardiovascular (CV) death and myocardial infarction (MI) in patients with ACS undergoing percutaneous coronary intervention.METHODS: We included 10,713 patients from the PLATO (A Comparison of Ticagrelor [AZD6140] and Clopidogrel in Patients With Acute Coronary Syndrome) trial in the development cohort and externally validated in 3,508 patients from the TRACER (Thrombin Receptor Antagonist for Clinical Event Reduction in Acute Coronary Syndrome) trial. Variables contributing to risk of CV death/MI were assessed using Cox regression models, and a score was derived using subsets of variables approximating the full model.RESULTS: There were 632 and 190 episodes of CV death/MI in the development and validation cohorts. The most important predictors of CV death/MI were the biomarkers, growth differentiation factor 15, and N-terminal pro-B-type natriuretic peptide, which had greater prognostic value than all candidate variables. The final model included 8 items: age (A), biomarkers (B) (growth differentiation factor 15 and N-terminal pro-B-type natriuretic peptide), and clinical variables (C) (extent of coronary artery disease, previous vascular disease, Killip class, ACS type, P2Y12 inhibitor). The model, named ABC-ACS ischemia, was well calibrated and showed good discriminatory ability for 1-year risk of CV death/MI with C-indices of 0.71 and 0.72 in the development and validation cohorts, respectively. For CV death, the score performed better, with C-indices of 0.80 and 0.84 in the development and validation cohorts, respectively.CONCLUSIONS: An 8-item score for the prediction of CV death/MI was developed and validated for patients with ACS undergoing percutaneous coronary intervention. The ABC-ACS ischemia score showed good calibration and discrimination and might be useful for risk prediction and decision support in patients with ACS. (A Comparison of Ticagrelor [AZD6140] and Clopidogrel in Patients With Acute Coronary Syndrome [PLATO]; NCT00391872; Trial to Assess the Effects of Vorapaxar [SCH 530348; MK-5348] in Preventing Heart Attack and Stroke in Participants With Acute Coronary Syndrome [TRACER]; NCT00527943)
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| 3. |
- Pavlović, Tomislav, et al.
(författare)
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Predicting attitudinal and behavioral responses to COVID-19 pandemic using machine learning
- 2022
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Ingår i: PNAS Nexus. - : Oxford University Press (OUP). - 2752-6542 .- 2752-6542. ; 1:3
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- At the beginning of 2020, COVID-19 became a global problem. Despite all the efforts to emphasize the relevance of preventive measures, not everyone adhered to them. Thus, learning more about the characteristics determining attitudinal and behavioral responses to the pandemic is crucial to improving future interventions. In this study, we applied machine learning on the multinational data collected by the International Collaboration on the Social and Moral Psychology of COVID-19 ( = 51,404) to test the predictive efficacy of constructs from social, moral, cognitive, and personality psychology, as well as socio-demographic factors, in the attitudinal and behavioral responses to the pandemic. The results point to several valuable insights. Internalized moral identity provided the most consistent predictive contribution-individuals perceiving moral traits as central to their self-concept reported higher adherence to preventive measures. Similar results were found for morality as cooperation, symbolized moral identity, self-control, open-mindedness, and collective narcissism, while the inverse relationship was evident for the endorsement of conspiracy theories. However, we also found a non-neglible variability in the explained variance and predictive contributions with respect to macro-level factors such as the pandemic stage or cultural region. Overall, the results underscore the importance of morality-related and contextual factors in understanding adherence to public health recommendations during the pandemic.
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| 4. |
- Azevedo, Flavio, et al.
(författare)
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Social and moral psychology of COVID-19 across 69 countries
- 2023
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Ingår i: Scientific Data. - : NATURE PORTFOLIO. - 2052-4463. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The COVID-19 pandemic has affected all domains of human life, including the economic and social fabric of societies. One of the central strategies for managing public health throughout the pandemic has been through persuasive messaging and collective behaviour change. To help scholars better understand the social and moral psychology behind public health behaviour, we present a dataset comprising of 51,404 individuals from 69 countries. This dataset was collected for the International Collaboration on Social & Moral Psychology of COVID-19 project (ICSMP COVID-19). This social science survey invited participants around the world to complete a series of moral and psychological measures and public health attitudes about COVID-19 during an early phase of the COVID-19 pandemic (between April and June 2020). The survey included seven broad categories of questions: COVID-19 beliefs and compliance behaviours; identity and social attitudes; ideology; health and well-being; moral beliefs and motivation; personality traits; and demographic variables. We report both raw and cleaned data, along with all survey materials, data visualisations, and psychometric evaluations of key variables.
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| 5. |
- Eilertsen, Gabriel, et al.
(författare)
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Evaluation of Tone Mapping Operators for HDR-Video
- 2013
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Ingår i: Computer graphics forum (Print). - : Wiley. - 0167-7055 .- 1467-8659. ; 32:7, s. 275-284
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Tidskriftsartikel (refereegranskat)abstract
- Eleven tone-mapping operators intended for video processing are analyzed and evaluated with camera-captured and computer-generated high-dynamic-range content. After optimizing the parameters of the operators in a formal experiment, we inspect and rate the artifacts (flickering, ghosting, temporal color consistency) and color rendition problems (brightness, contrast and color saturation) they produce. This allows us to identify major problems and challenges that video tone-mapping needs to address. Then, we compare the tone-mapping results in a pair-wise comparison experiment to identify the operators that, on average, can be expected to perform better than the others and to assess the magnitude of differences between the best performing operators.
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| 6. |
- Eilertsen, Gabriel, et al.
(författare)
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Perceptually based parameter adjustments for video processing operations
- 2014
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Ingår i: ACM SIGGRAPH Talks 2014. - : ACM Press.
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Konferensbidrag (refereegranskat)abstract
- Extensive post processing plays a central role in modern video production pipelines. A problem in this context is that many filters and processing operators are very sensitive to parameter settings and that the filter responses in most cases are highly non-linear. Since there is no general solution for performing perceptual calibration of image and video operators automatically, it is often necessary to manually perform tweaking of multiple parameters. This is an iterative process which requires instant visual feedback of the result in both the spatial and temporal domains. Due to large filter kernels, computational complexity, high frame rate, and image resolution it is, however, often very time consuming to iteratively re-process and tweak long video sequences.We present a new method for rapidly finding the perceptual minima in high-dimensional parameter spaces of general video operators. The key idea of our algorithm is that the characteristics of an operator can be accurately described by interpolating between a small set of pre-computed parameter settings. By computing a perceptual linearization of the parameter space of a video operator, the user can explore this interpolated space to find the best set of parameters in a robust way. Since many operators are dependent on two or more parameters, we formulate this as a general optimization problem where we let the objective function be determined by the user’s image assessments. To demonstrate the usefulness of our approach we show a set of use cases (see the supplementary material) where our algorithm is applied to computationally expensive video operations.
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| 7. |
- Eilertsen, Gabriel, et al.
(författare)
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Survey and Evaluation of Tone Mapping Operators for HDR-video
- 2013
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Ingår i: Siggraph 2013 Talks. - New York, NY, USA : ACM Press. - 9781450323444
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- This work presents a survey and a user evaluation of tone mapping operators (TMOs) for high dynamic range (HDR) video, i.e. TMOs that explicitly include a temporal model for processing of variations in the input HDR images in the time domain. The main motivations behind this work is that: robust tone mapping is one of the key aspects of HDR imaging [Reinhard et al. 2006]; recent developments in sensor and computing technologies have now made it possible to capture HDR-video, e.g. [Unger and Gustavson 2007; Tocci et al. 2011]; and, as shown by our survey, tone mapping for HDR video poses a set of completely new challenges compared to tone mapping for still HDR images. Furthermore, video tone mapping, though less studied, is highly important for a multitude of applications including gaming, cameras in mobile devices, adaptive display devices and movie post-processing. Our survey is meant to summarize the state-of-the-art in video tonemapping and, as exemplified in Figure 1 (right), analyze differences in their response to temporal variations. In contrast to other studies, we evaluate TMOs performance according to their actual intent, such as producing the image that best resembles the real world scene, that subjectively looks best to the viewer, or fulfills a certain artistic requirement. The unique strength of this work is that we use real high quality HDR video sequences, see Figure 1 (left), as opposed to synthetic images or footage generated from still HDR images.
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| 8. |
- Gorgolewski, Krzysztof J., et al.
(författare)
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BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
- 2017
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Ingår i: PloS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the comprehensiveness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi-tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.
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| 9. |
- Hollenberg, Jacob, et al.
(författare)
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Dual dispatch early defibrillation in out-of-hospital cardiac arrest: the SALSA-pilot
- 2009
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Ingår i: European Heart Journal. - : Oxford University Press. - 0195-668X .- 1522-9645. ; 30:14, s. 1781-9
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Tidskriftsartikel (refereegranskat)abstract
- AIMS: Out-of-hospital cardiac arrest (OHCA) is a major public health problem. The objective of this study is to explore the effects of a dual dispatch early defibrillation programme. METHODS AND RESULTS: In this pilot study, automated external defibrillators (AEDs) were provided to all 43 fire stations in Stockholm during 2005. Fire-fighters were dispatched in parallel with traditional emergency medical responders (EMS) to all suspected cases of OHCA. Additionally, 65 larger public venues were equipped with AEDs. All 863 OHCA from December 2005 to December 2006 were included during the intervention, whereas all 657 OHCA from 2004 served as historical controls. Among dual dispatches, fire-fighters assisted with cardiopulmonary resuscitation (CPR) in 94% of the cases and arrived first on scene in 36%. The median time from call to arrival of first responder decreased from 7.5 min during the control period to 7.1 min during the intervention (P = 0.004). The proportion of patients in shockable rhythm remained unchanged. The proportion of patients alive 1 month after OHCA rose from 4.4 to 6.8% [adjusted odds ratio (OR): 1.6; 95% confidence interval (CI): 0.9-2.9]. One-month survival in witnessed cases rose from 5.7 to 9.7% (adjusted OR: 2.0; 95% CI: 1.1-3.7). Survival after OHCA in the rest of Sweden (Stockholm excluded) declined from 8.3 to 6.6% during the corresponding time period (unadjusted OR: 0.8; 95% CI: 0.6-1.0). Only three OHCA occurred at public venues equipped with AEDs. CONCLUSION: An introduction of a dual dispatch early defibrillation programme in Stockholm has shortened response times and is likely to have improved survival in patients with OHCA, especially in the group of witnessed cardiac arrests. The increase in survival is believed to be associated with improved CPR and shortened time intervals.
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| 10. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.
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