Improved Name-Recognition with Meta-data Dependent Name Networks

A transcription system that requires accurate general name transcription is faced with the problem of covering the large number of names it may encounter. Without any prior knowledge, this requires a large increase in the size and complexity of the system due to the expansion of the lexicon. Furthermore, this increase will adversely affect the system performance due to the increased confusability. Here we propose a method that uses meta-data, available at runtime to ensure better name coverage without significantly increasing the system complexity. We tested this approach on a voicemail transcription task and assumed meta-data to be available in the form of a caller ID string (as it would show up on a caller ID enabled phone) and the name of the mailbox owner. Networks representing possible spoken realization of those names are generated at runtime and included in network of the decoder. The decoder network is built at training time using a class-dependent language model, with caller and mailbox name instances modeled as class tokens. The class tokens are replaced at test time with the name networks built from the meta-data. The proposed algorithm showed a reduction in the error rate of name tokens of 22.1%

Probabilistic approaches for modeling text structure and their application to text-to-text generation

Since the early days of generation research, it has been acknowledged that modeling the global structure of a document is crucial for producing coherent, readable output. However, traditional knowledge-intensive approaches have been of limited utility in addressing this problem since they cannot be effectively scaled to operate in domain-independent, large-scale applications. Due to this difficulty, existing text-to-text generation systems rarely rely on such structural information when producing an output text. Consequently, texts generated by these methods do not match the quality of those written by humans – they are often fraught with severe coherence violations and disfluencies. In this chapter, I will present probabilistic models of document structure that can be effectively learned from raw document collections. This feature distinguishes these new models from traditional knowledge intensive approaches used in symbolic concept-to-text generation. Our results demonstrate that these probabilistic models can be directly applied to content organization, and suggest that these models can prove useful in an even broader range of text-to-text applications than we have considered here.National Science Foundation (U.S.) (CAREER grant IIS- 0448168)Microsoft Research. New Faculty Fellowshi

A Brief History, Status, and Perspective of Modified Oligonucleotides for Chemotherapeutic Applications

The advent of rapid and efficient methods of oligonucleotide synthesis has allowed the design of modified oligonucleotides that are complementary to specific nucleotide sequences in mRNA targets. Such modified oligonucleotides can be used to disrupt the flow of genetic information from transcribed mRNAs to proteins. This antisense strategy has been used to develop therapeutic oligonucleotides against cancer and various infectious diseases in humans. This overview reports recent advances in the application of oligonucleotides as drug candidates, describes the relationship between oligonucleotide modifications and their therapeutic profiles, and provides general guidelines for enhancing oligonucleotide drug properties.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143788/1/cpnc0401.pd

Sequential NMR assignments of labile protons in DNA using two-dimensional nuclear-Overhauser-enhancement spectroscopy with three jump-and-return pulse sequences

Two-dimensional nuclear Overhauser enhancement (NOESY) spectra of labile protons were recorded in H2O solutions of a protein and of a DNA duplex, using a modification of the standard NOESY experiment with all three 90 degree pulses replaced by jump-and-return sequences. For the protein as well as the DNA fragment the strategically important spectral regions could be recorded with good sensitivity and free of artifacts. Using this procedure, sequence-specific assignments were obtained for the imino protons, C2H of adenine, and C4NH2 of cytosine in a 23-base-pair DNA duplex which includes the 17-base-pair OR3 repressor binding site of bacteriophage lambda. Based on comparison with previously published results on the isolated OR3 binding site, these data were used for a study of chain termination effects on the chemical shifts of imino proton resonances of DNA duplexes

Patent Politics: Intellectual Property, the Railroad Industry, and the Problem of Monopoly

As winter descended on Washington in December 1878, the Forty-fifth Congress gathered for what promised to be a hectic third and final session. At this critical juncture in American politics, the Senate found itself embroiled in a long and complex discussion of the virtues and deficiencies of the patent system. Patent policy resonated with powerfully felt ideologies and tapped into strongly felt beliefs. Patents were exclusive privileges that the federal government granted to certain individuals for a limited period of time, and, like all monopoly grants, their regulation raised some of the most fundamental questions of the age. The monopoly issue confronted every branch of nineteenth-century American government as well as every jurisdiction: federal, state, and local. In essence, the issue boiled down to two interrelated questions: Did the government have the authority to regulate the monopolies it had created? And, if so, how? The ramifications of the patent issue were practical as well as ideological. At its core, it posed a special challenge for two groups of economic actors, namely, farmers and railroads, who were often at odds not only with Congress but also with each other

Combination of surgical excision and custom designed silicon pressure splint therapy for keloids on the helical rim

Keloids are defined as dermal fibrotic lesions which are considered an aberration of the wound healing process. Their etiology and pathogenesis are poorly understood. Different treatment modalities are described in the literature depending on the morphology and size of the keloid. We report a case of a large ear keloid on the helical rim which was successfully treated with surgery and a custom designed silicon pressure clip

Enzymatic Activities and DNA Substrate Specificity of Mycobacterium tuberculosis DNA Helicase XPB

XPB, also known as ERCC3 and RAD25, is a 3′→5′ DNA repair helicase belonging to the superfamily 2 of helicases. XPB is an essential core subunit of the eukaryotic basal transcription factor complex TFIIH. It has two well-established functions: in the context of damaged DNA, XPB facilitates nucleotide excision repair by unwinding double stranded DNA (dsDNA) surrounding a DNA lesion; while in the context of actively transcribing genes, XPB facilitates initiation of RNA polymerase II transcription at gene promoters. Human and other eukaryotic XPB homologs are relatively well characterized compared to conserved homologs found in mycobacteria and archaea. However, more insight into the function of bacterial helicases is central to understanding the mechanism of DNA metabolism and pathogenesis in general. Here, we characterized Mycobacterium tuberculosis XPB (Mtb XPB), a 3′→5′ DNA helicase with DNA-dependent ATPase activity. Mtb XPB efficiently catalyzed DNA unwinding in the presence of significant excess of enzyme. The unwinding activity was fueled by ATP or dATP in the presence of Mg2+/Mn2+. Consistent with the 3′→5′ polarity of this bacterial XPB helicase, the enzyme required a DNA substrate with a 3′ overhang of 15 nucleotides or more. Although Mtb XPB efficiently unwound DNA model substrates with a 3′ DNA tail, it was not active on substrates containing a 3′ RNA tail. We also found that Mtb XPB efficiently catalyzed ATP-independent annealing of complementary DNA strands. These observations significantly enhance our understanding of the biological roles of Mtb XPB