| 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. |
- Ahmed, Jawwad, et al.
(författare)
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Efficient Inter-Thread Scheduling Scheme for Long-Reach Passive Optical Networks
- 2013
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Ingår i: IEEE Communications Magazine. - 0163-6804 .- 1558-1896. ; 51:2, s. S35-S43
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Tidskriftsartikel (refereegranskat)abstract
- These days there is a clear trend toward extending the reach of passive optical networks to cover large geographical areas, which enables reduction of the number of central offices and hence has the potential of cost saving in network operation. On the other hand, this reach extension necessitates the design of efficient dynamic bandwidth allocation schemes in order to tackle performance degradation caused by the increased propagation delay in long reach PONs. Among many existing approaches, the multi-thread-based DBA scheme where several bandwidth allocation processes are performed in parallel is considered one of the most effective options to improve network performance in LRPONs. We have found that without proper intercommunication between the overlapped threads, multi-thread DBA may lose efficiency and even perform worse than the conventional single-thread algorithm. With this in mind, this article reviews different inter-thread scheduling schemes for LR-PONs, and proposes a novel approach of integrating the key ideas of the existing ones. Extensive simulation results confirm that our proposed scheme can significantly improve DBA performance for LR-PONs under a variety of scenarios with consideration of different values of network load and reach.
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| 3. |
- Skubic, Björn, et al.
(författare)
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Dynamic Bandwidth Allocation for Long-Reach PON : Overcoming Performance Degradation
- 2010
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Ingår i: IEEE Communications Magazine. - 0163-6804 .- 1558-1896. ; 48:11, s. 100-108
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Tidskriftsartikel (refereegranskat)abstract
- A passive optical network, with its inherent point to multi-point structure, allows for centralized placement of active equipment and possible extension of its boundary towards core networks. This property of the PON can be exploited for node consolidation where multiple central offices are replaced by a single one covering a larger service area. Such node consolidation is being particularly driven by the need for network operational cost saving, and is offering significant challenges to PONs. The degree of node consolidation that can be achieved is limited by the reach of conventional PON systems. In order to achieve a larger degree of node consolidation, an extension of the PON reach, beyond the conventional 20 km, is required. This article addresses the challenges of the dynamic bandwidth allocation, where increased reach results in a degradation of DBA performance and quality of service support. This degradation is a consequence of the increased propagation delay of the DBA messages exchanged between different PON elements. A potential solution to the performance degradation is the introduction of a multi-threaded DBA. In this article, we examine for both Gigabit PON and Ethernet PON, the extent to which DBA performance degradation can be reduced by exploiting multi-threading. It is found that for both standards, multi-threading, if done properly, can be used to mitigate the performance degradation due to the increased reach. To make bandwidth allocation efficient, new schemes for coordinating the multiple threads are required in long reach PON.
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| 4. |
- Skubic, Björn, et al.
(författare)
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Dynamic bandwidth allocation in EPON and GPON
- 2010
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Ingår i: Convergence of Mobile and Stationary Next-Generation Networks. - Hoboken, NJ, USA : John Wiley & Sons. - 9780470543566 - 9780470630976
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Bokkapitel (refereegranskat)
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| 5. |
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| 6. |
- Yang, Yang, et al.
(författare)
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Structure-based prediction of the effects of a missense variant on protein stability
- 2013
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Ingår i: Amino Acids. - : Springer Science and Business Media LLC. - 0939-4451 .- 1438-2199. ; 44:3, s. 847-855
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Tidskriftsartikel (refereegranskat)abstract
- Predicting the effects of amino acid substitutions on protein stability provides invaluable information for protein design, the assignment of biological function, and for understanding disease-associated variations. To understand the effects of substitutions, computational models are preferred to time-consuming and expensive experimental methods. Several methods have been proposed for this task including machine learning-based approaches. However, models trained using limited data have performance problems and many model parameters tend to be over-fitted. To decrease the number of model parameters and to improve the generalization potential, we calculated the amino acid contact energy change for point variations using a structure-based coarse-grained model. Based on the structural properties including contact energy (CE) and further physicochemical properties of the amino acids as input features, we developed two support vector machine classifiers. M47 predicted the stability of variant proteins with an accuracy of 87 % and a Matthews correlation coefficient of 0.68 for a large dataset of 1925 variants, whereas M8 performed better when a relatively small dataset of 388 variants was used for 20-fold cross-validation. The performance of the M47 classifier on all six tested contingency table evaluation parameters is better than that of existing machine learning-based models or energy function-based protein stability classifiers.
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| 7. |
- Yi, Peng, et al.
(författare)
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Circulation of water masses in the Baltic Proper revealed through iodine isotopes
- 2013
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Ingår i: Applied Geochemistry. - : Elsevier BV. - 0883-2927 .- 1872-9134. ; 36, s. 118-124
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Tidskriftsartikel (refereegranskat)abstract
- Tracer technology has been used to understand water circulation in marine systems where the tracer dose is commonly injected into the marine waters through controlled experiments, accidental releases or waste discharges. Anthropogenic discharges of I-129 have been used to trace water circulation in the Arctic and North Atlantic Ocean. Here, I-129, together with I-127, is utilized as a tracer of water pathways and circulation in the Baltic Sea through collection of seawater depth profiles. The results indicate the presence of I-129 signatures which are distinct for each water mass and provide evidence for: (1) inflow water masses through the Drogden Sill that may reach as far as the SW of the Arkona Sea, (2) a portion of North Atlantic water in the bottom of Arkona basin, (3) cyclonic upwelling which breaks through the halocline in a pattern similar to the Baltic haline conveyor belt and (4) more influx of fresher water from the Gulf of Finland and Bothnian Sea in August relative to April. These findings provide advances in labeling and understanding water pathways in the Baltic Sea.
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| 8. |
- Yi, Peng, et al.
(författare)
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Model simulation of inflow water to the Baltic Sea based on I-129
- 2013
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Ingår i: Applied Radiation and Isotopes. - : Elsevier BV. - 0969-8043 .- 1872-9800. ; 82, s. 223-231
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Tidskriftsartikel (refereegranskat)abstract
- The semi-enclosed Baltic Sea represents a vital economic and recreational resource for more than 90 million people inhabiting its coasts. Extensive contamination of this sea by a variety of anthropogenic pollutants has raised the concern of the people in the region. Quantifying seawater inflow is crucial for estimating potential environmental risks as well as to find the best remedial strategy. We present here a model to estimate water inflow from the North Sea to the Baltic Sea by utilizing 1291 as a tracer. The results predicted inflow range of 230-450 km(3)/y with best fit value around 330 km(3)/y from the North Sea to the Baltic Sea during 1980-1999. Despite limited time series data on I-129, the model presented here demonstrates a new management tool for the Baltic Sea to calculate inflow water compared to conventional methods (such as salinity, temperature and hydrographic models).
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