Extending Hidden Structure Learning: Features, Opacity, and Exceptions

This dissertation explores new perspectives in phonological hidden structure learning (inferring structure not present in the speech signal that is necessary for phonological analysis; Tesar 1998, Jarosz 2013a, Boersma and Pater 2016), and extends this type of learning towards the domain of phonological features, towards derivations in Stratal OT (Bermúdez-Otero 1999), and towards exceptionality indices in probabilistic OT. Two more specific themes also come out: the possibility of inducing instead of pre-specifying the space of possible hidden structures, and the importance of cues in the data for triggering the use of hidden structure. In chapters 2 and 4, phonological features and exception groupings are induced by an unsupervised procedure that finds units not explicitly given to the learner. In chapters 2 and 3, there is an effect of non-specification or underspecification on the hidden level whenever the data does not give enough cues for that hidden level to be used. When features are hidden structure (chapter 2), they are only used for patterns that generalize across multiple segments. When intermediate derivational levels are hidden structure (chapter 3), the hidden structure necessary for opaque interactions is found more often when additional cues for the stratal affiliation of the opaque process are present in the data. Chapter 1 motivates and explains the central questions in this dissertation. Chapter 2 shows that phonological features can be induced from groupings of segments (which is motivated by phonetic non-transparency of feature assignment, see, e.g., Anderson 1981), and that patterns that do not generalize across segments are formulated in terms of segments in such a model. Chapter 3 implements a version of Stratal OT (Bermúdez-Otero 1999), and confirms Kiparsky’s (2000) hypothesis that evidence for an opaque process’ stratal affiliation makes it easier to learn an opaque interaction, even when opaque interactions are more difficult to learn than their transparent counterparts. Chapter 4 proposes a probabilistic (instead of non-probabilistic; e.g. Pater 2010) learner for lexically indexed constraints (Pater 2000) in Expectation Driven Learning (Jarosz submitted), and demonstrates its effectiveness on Dutch stress (van der Hulst 1984, Kager 1989, Nouveau 1994, van Oostendorp 1997)

A Half-Century History of Applications of Antisense Oligonucleotides in Medicine, Agriculture and Forestry: We Should Continue the Journey

Antisense oligonucleotides (ASO), short single-stranded polymers based on DNA or RNA chemistries and synthesized in vitro, regulate gene expression by binding in a sequence-specific manner to an RNA target. The functional activity and selectivity in the action of ASOs largely depends on the combination of nitrogenous bases in a target sequence. This simple and natural property of nucleic acids provides an attractive route by which scientists can create different ASO-based techniques. Over the last 50 years, planned and realized applications in the field of antisense and nucleic acid nanotechnologies have produced astonishing results and posed new challenges for further developments, exemplifying the essence of the post-genomic era. Today the majority of ASOs are chemically modified and/or incorporated within nanoparticles to enhance their stability and cellular uptake. This review critically analyzes some successful cases using the antisense approach in medicine to address severe diseases, such as Duchenne muscular dystrophy and spinal muscular atrophy, and suggests some prospective directions for future research. We also examine in detail the elaboration of unmodified insect-specific DNA insecticides and RNA preparations in the areas of agriculture and forestry, a relatively new branch of ASO that allows circumvention of the use of non-selective chemical insecticides. When considering the variety of successful ASO modifications with an efficient signal-to-noise ratio of action, coupled with the affordability of in vitro oligonucleotide synthesis and post-synthesis procedures, we predict that the next half-century will produce a fruitful yield of tools created from effective ASO-based end products