MESH : a flexible manifold-embedded semantic hashing for cross-modal retrieval

Hashing based methods for cross-modal retrieval has been widely explored in recent years. However, most of them mainly focus on the preservation of neighborhood relationship and label consistency, while ignore the proximity of neighbors and proximity of classes, which degrades the discrimination of hash codes. And most of them learn hash codes and hashing functions simultaneously, which limits the flexibility of algorithms. To address these issues, in this article, we propose a two-step cross-modal retrieval method named Manifold-Embedded Semantic Hashing (MESH). It exploits Local Linear Embedding to model the neighborhood proximity and uses class semantic embeddings to consider the proximity of classes. By so doing, MESH can not only extract the manifold structure in different modalities, but also can embed the class semantic information into hash codes to further improve the discrimination of learned hash codes. Moreover, the two-step scheme makes MESH flexible to various hashing functions. Extensive experimental results on three datasets show that MESH is superior to 10 state-of-the-art cross-modal hashing methods. Moreover, MESH also demonstrates superiority on deep features compared with the deep cross-modal hashing method. © 2013 IEEE

A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

Background The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. Results Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. Conclusions These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.info:eu-repo/semantics/publishedVersio

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

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 fl ux 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, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost 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 fi eld 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 delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so 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 autophagy assays, we hope to encourage technical innovation in the field

Rapid Reduction of Ag

Wheat straw is a kind of rich agricultural waste. Resource utilization of wheat straw has received widespread attention. Herein, a novel approach of the rapid reduction of Ag2O into Ag by wheat straw with the production of organic acids under mild hydrothermal conditions is reported. After parameter optimization, almost all Ag2O is converted to Ag at a mild reaction temperature of 150 ℃ and a reaction time of 60 min in sodium hydroxide solution. Meanwhile, wheat straw was converted to organic acid such as formic acid, lactic acid, and acetic acid. This offers a cost-effective approach for Ag recovery and resource utilization of biomass

Diagnostic accuracy of the Xpert MTB/RIF assay for tuberculous pericarditis: A protocol of systematic review and meta-analysis.

BackgroundTuberculous pericarditis (TBP) can lead to serious consequences. Early diagnosis and treatment are very important for TBP, but early diagnosis is still very challenging. This study aims to evaluate the diagnostic accuracy of Xpert MTB/RIF for TBP using meta-analysis method.MethodsWe will search Embase, PubMed, the Cochrane Library, China National Knowledge Infrastructure (CNKI), and the Wanfang database for researches assessing the diagnostic accuracy of Xpert MTB/RIF for TBP until April 2021. Any types of study design with full text will be selected and included. The Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool will be used to assess the risk of bias. We will use version 15.0 of the STATA software with the midas command packages to carry out meta-analyses.ResultsEvidence for diagnostic accuracy of Xpert MTB/RIF for TBP will be provided through the study, and this protocol will be submitted to a peer-reviewed journal for publication.ConclusionThis study will provide evidence of Xpert MTB/RIF for TBP

Anlotinib for refractory advanced non-small-cell lung cancer: A systematic review and meta-analysis.

ObjectiveTo assess the efficacy and toxicity of anlotinib for the treatment of refractory advanced non-small-cell lung cancer (NSCLC).MethodsWe systematically searched databases for randomized controlled trials on anlotinib treatment for patients with advanced NSCLC published until November 6, 2020. Articles were assessed and data were extracted independently by two investigators. Further, we analyzed hazard ratios (HRs) for progression-free and overall survival (PFS and OS, respectively). In addition, we analyzed risk ratio (RR) for overall response and disease control rates (ORR and DCR, respectively) and the odds ratio (OR) for the main adverse events (AEs) using RevMan 5.3 software.ResultsThis analysis included 594 patients from three clinical studies. The pooled HRs for PFS and OS were 0.27 (95% confidence interval (CI): 0.22-0.33, P ConclusionAnlotinib, an effective choice of third- or later line therapy for patients with refractory advanced NSCLC, provides clinical benefits in terms of PFS, OS, ORR, and DCR. AEs associated with anlotinib were tolerable