| 1. |
|
|
| 2. |
|
|
| 3. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
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.
|
|
| 4. |
- Jin, Ying-Hui, et al.
(författare)
-
Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
-
Ingår i: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
-
Tidskriftsartikel (refereegranskat)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
|
|
| 5. |
- Hantson, Stijn, et al.
(författare)
-
Quantitative assessment of fire and vegetation properties in simulations with fire-enabled vegetation models from the Fire Model Intercomparison Project
- 2020
-
Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 13:7, s. 3299-3318
-
Tidskriftsartikel (refereegranskat)abstract
- Global fire-vegetation models are widely used to assess impacts of environmental change on fire regimes and the carbon cycle and to infer relationships between climate, land use and fire. However, differences in model structure and parameterizations, in both the vegetation and fire components of these models, could influence overall model performance, and to date there has been limited evaluation of how well different models represent various aspects of fire regimes. The Fire Model Intercomparison Project (FireMIP) is coordinating the evaluation of state-of-the-art global fire models, in order to improve projections of fire characteristics and fire impacts on ecosystems and human societies in the context of global environmental change. Here we perform a systematic evaluation of historical simulations made by nine FireMIP models to quantify their ability to reproduce a range of fire and vegetation benchmarks. The FireMIP models simulate a wide range in global annual total burnt area (39-536 Mha) and global annual fire carbon emission (0.91-4.75 Pg C yr-1) for modern conditions (2002-2012), but most of the range in burnt area is within observational uncertainty (345-468 Mha). Benchmarking scores indicate that seven out of nine FireMIP models are able to represent the spatial pattern in burnt area. The models also reproduce the seasonality in burnt area reasonably well but struggle to simulate fire season length and are largely unable to represent interannual variations in burnt area. However, models that represent cropland fires see improved simulation of fire seasonality in the Northern Hemisphere. The three FireMIP models which explicitly simulate individual fires are able to reproduce the spatial pattern in number of fires, but fire sizes are too small in key regions, and this results in an underestimation of burnt area. The correct representation of spatial and seasonal patterns in vegetation appears to correlate with a better representation of burnt area. The two older fire models included in the FireMIP ensemble (LPJ-GUESS-GlobFIRM, MC2) clearly perform less well globally than other models, but it is difficult to distinguish between the remaining ensemble members; some of these models are better at representing certain aspects of the fire regime; none clearly outperforms all other models across the full range of variables assessed.
|
|
| 6. |
- Hantson, Stijn, et al.
(författare)
-
The status and challenge of global fire modelling
- 2016
-
Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 13:11, s. 3359-3375
-
Tidskriftsartikel (refereegranskat)abstract
- Biomass burning impacts vegetation dynamics, biogeochemical cycling, atmospheric chemistry, and climate, with sometimes deleterious socio-economic impacts. Under future climate projections it is often expected that the risk of wildfires will increase. Our ability to predict the magnitude and geographic pattern of future fire impacts rests on our ability to model fire regimes, using either well-founded empirical relationships or process-based models with good predictive skill. While a large variety of models exist today, it is still unclear which type of model or degree of complexity is required to model fire adequately at regional to global scales. This is the central question underpinning the creation of the Fire Model Intercomparison Project (FireMIP), an international initiative to compare and evaluate existing global fire models against benchmark data sets for present-day and historical conditions. In this paper we review how fires have been represented in fire-enabled dynamic global vegetation models (DGVMs) and give an overview of the current state of the art in fire-regime modelling. We indicate which challenges still remain in global fire modelling and stress the need for a comprehensive model evaluation and outline what lessons may be learned from FireMIP.
|
|
| 7. |
- Pellegrini, Adam F.A., et al.
(författare)
-
Soil carbon storage capacity of drylands under altered fire regimes
- 2023
-
Ingår i: Nature Climate Change. - 1758-678X. ; 13:10, s. 1089-1094
-
Tidskriftsartikel (refereegranskat)abstract
- The determinants of fire-driven changes in soil organic carbon (SOC) across broad environmental gradients remains unclear, especially in global drylands. Here we combined datasets and field sampling of fire-manipulation experiments to evaluate where and why fire changes SOC and compared our statistical model to simulations from ecosystem models. Drier ecosystems experienced larger relative changes in SOC than humid ecosystems—in some cases exceeding losses from plant biomass pools—primarily explained by high fire-driven declines in tree biomass inputs in dry ecosystems. Many ecosystem models underestimated the SOC changes in drier ecosystems. Upscaling our statistical model predicted that soils in savannah–grassland regions may have gained 0.64 PgC due to net-declines in burned area over the past approximately two decades. Consequently, ongoing declines in fire frequencies have probably created an extensive carbon sink in the soils of global drylands that may have been underestimated by ecosystem models.
|
|
| 8. |
- Rabin, Sam S., et al.
(författare)
-
The Fire Modeling Intercomparison Project (FireMIP), phase 1 : Experimental and analytical protocols
- 2016
-
Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X. ; 9:237
-
Tidskriftsartikel (refereegranskat)abstract
- The important role of fire in regulating vegetation community composition and contributions to emissions of greenhouse gases and aerosols make it a critical component of dynamic global vegetation models and Earth system models. Over two decades of development, a wide variety of model structures and mechanisms have been designed and incorporated into global fire models, which have been linked to different vegetation models. However, there has not yet been a systematic examination of how these different strategies contribute to model performance. Here we describe the structure of the first phase of the Fire Model Intercomparison Project (FireMIP), which for the first time seeks to systematically compare a number of models. By combining a standardized set of input data and model experiments with a rigorous comparison of model outputs to each other and to observations, we will improve the understanding of what drives vegetation fire, how it can best be simulated, and what new or improved observational data could allow better constraints on model behavior. Here we introduce the fire models used in the first phase of FireMIP, the simulation protocols applied, and the benchmarking system used to evaluate the models. The works published in this journal are distributed under the Creative Commons Attribution 3.0 License. This license does not affect the Crown copyright work, which is re-usable under the Open Government Licence (OGL). The Creative Commons Attribution 3.0 License and the OGL are interoperable and do not conflict with, reduce, or limit each other.
|
|
| 9. |
- Rabin, Sam S., et al.
(författare)
-
The Fire Modeling Intercomparison Project (FireMIP), phase 1 : Experimental and analytical protocols with detailed model descriptions
- 2017
-
Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 10:3, s. 1175-1197
-
Tidskriftsartikel (refereegranskat)abstract
- The important role of fire in regulating vegetation community composition and contributions to emissions of greenhouse gases and aerosols make it a critical component of dynamic global vegetation models and Earth system models. Over 2 decades of development, a wide variety of model structures and mechanisms have been designed and incorporated into global fire models, which have been linked to different vegetation models. However, there has not yet been a systematic examination of how these different strategies contribute to model performance. Here we describe the structure of the first phase of the Fire Model Intercomparison Project (FireMIP), which for the first time seeks to systematically compare a number of models. By combining a standardized set of input data and model experiments with a rigorous comparison of model outputs to each other and to observations, we will improve the understanding of what drives vegetation fire, how it can best be simulated, and what new or improved observational data could allow better constraints on model behavior. In this paper, we introduce the fire models used in the first phase of FireMIP, the simulation protocols applied, and the benchmarking system used to evaluate the models. We have also created supplementary tables that describe, in thorough mathematical detail, the structure of each model.
|
|
| 10. |
- Uitterlinden, André G, et al.
(författare)
-
The association between common vitamin D receptor gene variations and osteoporosis : a participant-level meta-analysis
- 2006
-
Ingår i: Annals of Internal Medicine. - 0003-4819. ; 145:4, s. 255-264
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Polymorphisms of the vitamin D receptor (VDR) gene have been implicated in the genetic regulation of bone mineral density (BMD). However, the clinical impact of these variants remains unclear.OBJECTIVE: To evaluate the relation between VDR polymorphisms, BMD, and fractures.DESIGN: Prospective multicenter large-scale association study.SETTING: The Genetic Markers for Osteoporosis consortium, involving 9 European research teams.PARTICIPANTS: 26,242 participants (18,405 women).MEASUREMENTS: Cdx2 promoter, FokI, BsmI, ApaI, and TaqI polymorphisms; BMD at the femoral neck and the lumbar spine by dual x-ray absorptiometry; and fractures.RESULTS: Comparisons of BMD at the lumbar spine and femoral neck showed nonsignificant differences less than 0.011 g/cm2 for any genotype with or without adjustments. A total of 6067 participants reported a history of fracture, and 2088 had vertebral fractures. For all VDR alleles, odds ratios for fractures were very close to 1.00 (range, 0.98 to 1.02) and collectively the 95% CIs ranged from 0.94 (lowest) to 1.07 (highest). For vertebral fractures, we observed a 9% (95% CI, 0% to 18%; P = 0.039) risk reduction for the Cdx2 A-allele (13% risk reduction in a dominant model).LIMITATIONS: The authors analyzed only selected VDR polymorphisms. Heterogeneity was detected in some analyses and may reflect some differences in collection of fracture data across cohorts. Not all fractures were related to osteoporosis.CONCLUSIONS: The FokI, BsmI, ApaI, and TaqI VDR polymorphisms are not associated with BMD or with fractures, but the Cdx2 polymorphism may be associated with risk for vertebral fractures.
|
|
