Memory-enhanced Decoder for Neural Machine Translation

We propose to enhance the RNN decoder in a neural machine translator (NMT) with external memory, as a natural but powerful extension to the state in the decoding RNN. This memory-enhanced RNN decoder is called \textsc{MemDec}. At each time during decoding, \textsc{MemDec} will read from this memory and write to this memory once, both with content-based addressing. Unlike the unbounded memory in previous work\cite{RNNsearch} to store the representation of source sentence, the memory in \textsc{MemDec} is a matrix with pre-determined size designed to better capture the information important for the decoding process at each time step. Our empirical study on Chinese-English translation shows that it can improve by $4.8$ BLEU upon Groundhog and $5.3$ BLEU upon on Moses, yielding the best performance achieved with the same training set.Comment: 11 page

Deep Neural Machine Translation with Linear Associative Unit

Deep Neural Networks (DNNs) have provably enhanced the state-of-the-art Neural Machine Translation (NMT) with their capability in modeling complex functions and capturing complex linguistic structures. However NMT systems with deep architecture in their encoder or decoder RNNs often suffer from severe gradient diffusion due to the non-linear recurrent activations, which often make the optimization much more difficult. To address this problem we propose novel linear associative units (LAU) to reduce the gradient propagation length inside the recurrent unit. Different from conventional approaches (LSTM unit and GRU), LAUs utilizes linear associative connections between input and output of the recurrent unit, which allows unimpeded information flow through both space and time direction. The model is quite simple, but it is surprisingly effective. Our empirical study on Chinese-English translation shows that our model with proper configuration can improve by 11.7 BLEU upon Groundhog and the best reported results in the same setting. On WMT14 English-German task and a larger WMT14 English-French task, our model achieves comparable results with the state-of-the-art.Comment: 10 pages, ACL 201

Composite electrospun nanomembranes of fish scale collagen peptides/chito-oligosaccharides: antibacterial properties and potential for wound dressing

Yan Wang1, Chen-lu Zhang2, Qun Zhang1, Ping Li1,31School of Life Sciences and Technology, Tongji University, Shanghai, People’s Republic of China; 2College of Life Sciences, Nanjing Agricultural University, Nanjing, People’s Republic of China; 3Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, People’s Republic of ChinaPurpose: The objective of the present investigation was to evaluate the antibacterial properties and the biocompatibility of composite electrospun nanofibrous membranes (NFMs) with low-molecular-weight fish scale collagen peptides (FSCP) and chito-oligosaccharide (COS), to determine their potential for use as wound dressings.Methods: Low-molecular-weight FSCP were combined with COS to prepare nanofibers by electrospinning, and polyvinyl alcohol (PVA) was used for enhancing fiber-forming ability. Transmission electron microscope and scanning electron microscope methods were used to observe bacterial adhesion and the bacterial cell membrane. Fibroblast cell viability was determined using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay.Results: The best FSCP/COS mass ratio for electrospinning was 2:1, and the nanofibers had small dimensions ranging from 50 to 100 nm. The NFM showed good antibacterial activities against Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli. The antibacterial activity against S. aureus was higher than against E. coli. The pili and adhesive fimbriae of E. coli promoted bacterial adhesion to the NFM surfaces, and S. aureus biofilms aided S. aureus adhesion on the surface of NFMs. Damage to the bacterial cell membrane indicates that the NFMs could lead to the release of intracellular materials, particularly with S. aureus. In addition, FSCP/COS NFM rapidly increased the permeability of the outer membranes of E. coli. The electrospun NFM with FSCP and COS had good biocompatibility in vitro and supported proliferation of human skin fibroblasts.Conclusion: FSCP are superior to mammalian collagen, and have feasibility and potency for wound dressings. FSCP/COS NFMs had good anti-bactericidal activity that improved with increased COS, and showed good biocompatibility in vitro and supported the proliferation of fibroblasts.Keywords: composite electrospun nanomembranes, fish scale collagen peptides, bacterial adhesion, bacterial cell membrane, wound dressin

Injectable PLGA based Colloidal Gels for Zero-order Dexamethasone Release in Cranial Defects

Bone fillers have emerged as an alternative to the invasive surgery often required to repair skeletal defects. Achieving controlled release from these materials is desired for accelerating healing. Here, oppositely-charged Poly (d,l-lactic-co-glycolic acid) (PLGA) nanoparticles were used to create a cohesive colloidal gel as an injectable drug-loaded filler to promote healing in bone defects. The colloid self-assembled through electrostatic forces resulting in a stable 3-D network that may be extruded or molded to the desired shape. The colloidal gel demonstrated shear-thinning behavior due to the disruption of interparticle interactions as the applied shear force was increased. Once the external force was removed, the cohesive property of the colloidal gel was recovered. Similar reversibility and shear-thinning behavior were also observed in colloidal gels loaded with dexamethasone. Near zero-order dexamethasone release was observed over two months when the drug was encapsulated in PLGA nanoparticles and simply blending the drug with the colloidal gel showed similar kinetics for one month. Surgical placement was facilitated by the pseudoplastic material properties and in vivo observations demonstrated that the PLGA colloidal gels stimulated osteoconductive bone formation in rat cranial bone defects

TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are a class of important gene regulators. The number of identified miRNAs has been increasing dramatically in recent years. An emerging major challenge is the interpretation of the genome-scale miRNA datasets, including those derived from microarray and deep-sequencing. It is interesting and important to know the common rules or patterns behind a list of miRNAs, (i.e. the deregulated miRNAs resulted from an experiment of miRNA microarray or deep-sequencing).</p> <p>Results</p> <p>For the above purpose, this study presents a method and develops a tool (TAM) for annotations of meaningful human miRNAs categories. We first integrated miRNAs into various meaningful categories according to prior knowledge, such as miRNA family, miRNA cluster, miRNA function, miRNA associated diseases, and tissue specificity. Using TAM, given lists of miRNAs can be rapidly annotated and summarized according to the integrated miRNA categorical data. Moreover, given a list of miRNAs, TAM can be used to predict novel related miRNAs. Finally, we confirmed the usefulness and reliability of TAM by applying it to deregulated miRNAs in acute myocardial infarction (AMI) from two independent experiments.</p> <p>Conclusion</p> <p>TAM can efficiently identify meaningful categories for given miRNAs. In addition, TAM can be used to identify novel miRNA biomarkers. TAM tool, source codes, and miRNA category data are freely available at <url>http://cmbi.bjmu.edu.cn/tam</url>.</p

Lifshitz effects on holographic pp-wave superfluid

In the probe limit, we numerically build a holographic $p$-wave superfluid model in the four-dimensional Lifshitz black hole coupled to a Maxwell-complex vector field. We observe the rich phase structure and find that the Lifshitz dynamical exponent $z$ contributes evidently to the effective mass of the matter field and dimension of the gravitational background. Concretely, we obtain the Cave of Winds appeared only in the five-dimensional anti-de Sitter~(AdS) spacetime, and the increasing $z$ hinders not only the condensate but also the appearance of the first-order phase transition. Furthermore, our results agree with the Ginzburg-Landau results near the critical temperature. In addition, the previous AdS superfluid model is generalized to the Lifshitz spacetime.Comment: 14 pages,5 figures, and 1 table, accepted by Phys. Lett.