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The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both(More)
Recent work has shown that recurrent neural networks have the ability to learn finite state automata from examples. In particular, networks using second-order units have been successful at this task. In studying the performance and learning behavior of such networks we have found that the second-order network model attempts to form clusters in activation(More)
The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids(More)
We discuss several important issues specific to Web caching for content dynamically generated from database applications. We present the techniques employed by Oracle Web Cache to address these issues. They include: content disambiguation based on information in addition to the URL, transparent session management, partial-page caching for personalization,(More)
A recent genome-wide study showed that the single nucleotide polymorphisms (SNPs) in the HLA-DP region were associated with chronic hepatitis B virus (HBV) infection in Japanese and Thai persons. We tested the effects of HLA-DP SNPs for all major HBV outcomes in Han Chinese (n = 1742): HBV resistance, clearance, chronic infection, cirrhosis, and(More)
We propose a class of complex population dynamic models that combines new time-varying parameters and second-order time lags for describing univariate ecological time series data. The Kalman filter and likelihood function were used to estimate parameters of all models in the class for 31 data sets, and Schwarz’s information criterion (SIC) was used to(More)
Describes a novel neural architecture for learning deterministic context-free grammars, or equivalently, deterministic pushdown automata. The unique feature of the proposed network is that it forms stable state representations during learning-previous work has shown that conventional analog recurrent networks can be inherently unstable in that they cannot(More)
Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced mRNA from a pool of forty-three different tissues. From(More)
Diabetic cardiomyopathy (DCM) is characterized by cardiac dysfunction and cardiomyocyte apoptosis. Oxidative stress is suggested to be the major contributor to the development of DCM. This study was intended to evaluate the protective effect of low molecular weight fucoidan (LMWF) against cardiac dysfunction in diabetic rats. Type 2 diabetic goto-kakizaki(More)