Jiangsu University

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. 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.

Abstract: Recently, multiple graph regularizer based methods have shown promising performances in data representation However, the parameter choice of the regularizer is crucial to the performance of clustering and its optimal value changes for different real datasets To deal with this problem, we propose a novel method called Parameter-less Auto-weighted Multiple Graph regularized Nonnegative Matrix Factorization (PAMGNMF) in this paper PAMGNMF employs the linear combination of multiple simple graphs to approximate the manifold structure of data as previous methods do Moreover, the proposed method can automatically learn an optimal weight for each graph without introducing an additive parameter Therefore, the proposed PAMGNMF method is easily applied to practical problems Extensive experimental results on different real-world datasets have demonstrated that the proposed method achieves better performance than the state-of-the-art approaches

Abstract: The uncontrolled discharge of large amounts of food waste (FW) causes severe environmental pollution in many countries. Within different possible treatment routes, anaerobic digestion (AD) of FW into biogas, is a proven and effective solution for FW treatment and valorization. The present paper reviews the characteristics of FW, the principles of AD, the process parameters, and two approaches (pretreatment and co-digestion) for enhancing AD of food waste. Among the successive digestion reactions, hydrolysis is considered to be the rate-limiting step. To enhance the performance of AD, several physical, thermo-chemical, biological or combined pretreatments are reviewed. Moreover, a promising way for improving the performance of AD is the co-digestion of FW with other organic substrates, as confirmed by numerous studies, where a higher buffer capacity and an optimum nutrient balance enhance the biogas/methane yields of the co-digestion system.

Abstract: We develop a novel maximum neighborhood margin discriminant projection (MNMDP) technique for dimensionality reduction of high-dimensional data. It utilizes both the local information and class information to model the intraclass and interclass neighborhood scatters. By maximizing the margin between intraclass and interclass neighborhoods of all points, MNMDP cannot only detect the true intrinsic manifold structure of the data but also strengthen the pattern discrimination among different classes. To verify the classification performance of the proposed MNMDP, it is applied to the PolyU HRF and FKP databases, the AR face database, and the UCI Musk database, in comparison with the competing methods such as PCA and LDA. The experimental results demonstrate the effectiveness of our MNMDP in pattern classification.

Abstract: Near-infrared (NIR) spectroscopy has increasingly been adopted as an analytical tool in various fields, such as the petrochemical, pharmaceutical, environmental, clinical, agricultural, food and biomedical sectors during the past 15 years. A NIR spectrum of a sample is typically measured by modern scanning instruments at hundreds of equally spaced wavelengths. The large number of spectral variables in most data sets encountered in NIR spectral chemometrics often renders the prediction of a dependent variable unreliable. Recently, considerable effort has been directed towards developing and evaluating different procedures that objectively identify variables which contribute useful information and/or eliminate variables containing mostly noise. This review focuses on the variable selection methods in NIR spectroscopy. Selection methods include some classical approaches, such as manual approach (knowledge based selection), "Univariate" and "Sequential" selection methods; sophisticated methods such as successive projections algorithm (SPA) and uninformative variable elimination (UVE), elaborate search-based strategies such as simulated annealing (SA), artificial neural networks (ANN) and genetic algorithms (GAs) and interval base algorithms such as interval partial least squares (iPLS), windows PLS and iterative PLS. Wavelength selection with B-spline, Kalman filtering, Fisher's weights and Bayesian are also mentioned. Finally, the websites of some variable selection software and toolboxes for non-commercial use are given.