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.

For example, 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 versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase 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. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy.

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. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. 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 assays, we hope to encourage technical innovation in the field.

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Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

The Smart Grid, regarded as the next generation power grid, uses two-way flows of electricity and information to create a widely distributed automated energy delivery network. In this article, we survey the literature till 2011 on the enabling technologies for the Smart Grid. We explore three major systems, namely the smart infrastructure system, the smart management system, and the smart protection system. We also propose possible future directions in each system. colorred{Specifically, for the smart infrastructure system, we explore the smart energy subsystem, the smart information subsystem, and the smart communication subsystem.} For the smart management system, we explore various management objectives, such as improving energy efficiency, profiling demand, maximizing utility, reducing cost, and controlling emission. We also explore various management methods to achieve these objectives. For the smart protection system, we explore various failure protection mechanisms which improve the reliability of the Smart Grid, and explore the security and privacy issues in the Smart Grid.

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Smart Grid — The New and Improved Power Grid: A Survey

Smart Grid - The New and Improved Power Grid:

In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes contain a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with Shared Information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different level of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems. This special issue aims at gathering the recent advances in learning with shared information methods and their applications in computer vision and multimedia analysis. Both state-of-the-art works, as well as literature reviews, are welcome for submission. Papers addressing interesting real-world computer vision and multimedia applications are especially encouraged. Topics of interest include, but are not limited to:  • Multi-task learning or transfer learning for large-scale computer vision and multimedia analysis • Deep learning for large-scale computer vision and multimedia analysis • Multi-modal approach for large-scale computer vision and multimedia analysis • Different sharing strategies, e.g., sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, • Real-world computer vision and multimedia applications based on learning with shared information, e.g., event detection, object recognition, object detection, action recognition, human head pose estimation, object tracking, location-based services, semantic indexing. • New datasets and metrics to evaluate the benefit of the proposed sharing ability for the specific computer vision or multimedia problem. • Survey papers regarding the topic of learning with shared information.  Authors who are unsure whether their planned submission is in scope may contact the guest editors prior to the submission deadline with an abstract, in order to receive feedback.

IEEE transactions on pattern analysis and machine intelligence

Social network analysis has attracted much attention in recent years. Link prediction is a key research directions within this area. In this research, we study link prediction as a supervised learning task. Along the way, we identify a set of features that are key to the superior performance under the supervised learning setup. The identified features are very easy to compute, and at the same time surprisingly effective in solving the link prediction problem. We also explain the effectiveness of the features from their class density distribution. Then we compare different classes of supervised learning algorithms in terms of their prediction performance using various performance metrics, such as accuracy, precision-recall, F-values, squared error etc. with a 5-fold cross validation. Our results on two practical social network datasets shows that most of the well-known classification algorithms (decision tree, k-nn,multilayer perceptron, SVM, rbf network) can predict link with surpassing performances, but SVM defeats all of them with narrow margin in all different performance measures. Again, ranking of features with popular feature ranking algorithms shows that a small subset of features always plays a significant role in the link prediction job.

/pdf/link-prediction-using-supervised-learning-3wdct6dn9f.pdf

Link prediction using supervised learning

During atherogenesis and vascular inflammation quiescent platelets are activated to increase the surface expression and ligand affinity of the integrin αIIbβ3 via inside-out signaling. Diverse signals such as thrombin, ADP and epinephrine transduce signals through their respective GPCRs to activate protein kinases that ultimately lead to the phosphorylation of the cytoplasmic tail of the integrin αIIbβ3 and augment its function. The signaling pathways that transmit signals from the GPCR to the cytosolic domain of the integrin are not well defined. In an effort to better understand these pathways, we employed a combination of proteomic profiling and computational analyses of isolated human platelets. We analyzed ten independent human samples and identified a total of 1507 unique proteins in platelets. This is the most comprehensive platelet proteome assembled to date and includes 190 membrane-associated and 262 phosphorylated proteins, which were identified via independent proteomic and phospho-proteomic profiling. We used this proteomic dataset to create a platelet protein-protein interaction (PPI) network and applied novel contextual information about the phosphorylation step to introduce limited directionality in the PPI graph. This newly developed contextual PPI network computationally recapitulated an integrin signaling pathway. Most importantly, our approach not only provided insights into the mechanism of integrin αIIbβ3 activation in resting platelets but also provides an improved model for analysis and discovery of PPI dynamics and signaling pathways in the future.

/pdf/proteomic-and-phospho-proteomic-profile-of-human-platelets-51m9x9ij0f.pdf

Proteomic and phospho-proteomic profile of human platelets in basal, resting state: Insights into integrin signaling

In this paper, we introduce the concept of alpha-orthogonal patterns to mine a representative set of graph patterns. Intuitively, two graph patterns are alpha-orthogonal if their similarity is bounded above by alpha. Each alpha-orthogonal pattern is also a representative for those patterns that are at least beta similar to it. Given user defined alpha, beta isin [0,1], the goal is to mine an alpha-orthogonal, beta-representative set that minimizes the set of unrepresented patterns. We present ORIGAMI, an effective algorithm for mining the set of representative orthogonal patterns. ORIGAMI first uses a randomized algorithm to randomly traverse the pattern space, seeking previously unexplored regions, to return a set of maximal patterns. ORIGAMI then extracts an alpha-orthogonal, beta-representative set from the mined maximal patterns. We show the effectiveness of our algorithm on a number of real and synthetic datasets. In particular, we show that our method is able to extract high quality patterns even in cases where existing enumerative graph mining methods fail to do so.

/pdf/origami-mining-representative-orthogonal-graph-patterns-2l4aho7v67.pdf

ORIGAMI: Mining Representative Orthogonal Graph Patterns

Electrical grids are highly complex and dynamic systems that can be unreliable, insecure, and inefficient in serving end consumers The promise of Smart Grids lies in the architecting and developing of intelligent distributed and networked systems for automated monitoring and controlling of the grid to improve performance We have designed an agent-oriented architecture for a simulation which can help in understanding Smart Grid issues and in identifying ways to improve the electrical grid We focus primarily on the self-healing problem, which concerns methodologies for activating control solutions to take preventative actions or to handle problems after they occur We present software design issues that must be considered in producing a system that is flexible, adaptable and scalable Agent-based systems provide a paradigm for conceptualizing, designing, and implementing software systems Agents are sophisticated computer programs that can act autonomously and communicate with each other across open and distributed environments We present design issues that are appropriate in developing a Multi-agent System (MAS) for the grid Our MAS is implemented in the Java Agent Development Framework (JADE) Our Smart Grid Simulation uses many types of agents to acquire and monitor data, support decision making, and represent devices, controls, alternative power sources, the environment, management functions, and user interfaces

Agent-Oriented Designs for a Self Healing Smart Grid

http://www.cs.rpi.edu/~zaki/PaperDir/PRL09.pdf

Saeed Salem

Papers

Link prediction using supervised learning

Proteomic and phospho-proteomic profile of human platelets in basal, resting state: Insights into integrin signaling

ORIGAMI: Mining Representative Orthogonal Graph Patterns

Agent-Oriented Designs for a Self Healing Smart Grid

Robust partitional clustering by outlier and density insensitive seeding