Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Towards a hybrid model of speech prosody

Speech is conveyed through a richly detailed acoustic signal, and each spoken instance of a word varies. Yet humans recognize words quickly, with few errors and typically with no conscious effort. Linguists hypothesize that abstract categories aid the process of speech comprehension because complex details can be mapped to a category, after which the detail of an instance can be forgotten. At the same time, research shows acoustic detail guides comprehension in real time and is retained in implicit memory. This dissertation addresses language processing for speech prosody. This study consists of five perception experiments that test the representation of pitch accents in memory, and directly compares memory for pitch accents to memory for phonemes. Results show that (1) explicit memory for prosody is more accurate for categorical differences, rather than equivalently large within-category differences, and (2) that, unlike phoneme categories, listeners are able to explicitly remember within-category detail for pitch accents, but that this memory decays quickly. Based on these results, I propose a hybrid model of comprehension of prosody that involves activating both previously proposed abstract categories and gradient detail

Towards a hybrid model of speech prosody

Speech is conveyed through a richly detailed acoustic signal, and each spoken instance of a word varies. Yet humans recognize words quickly, with few errors and typically with no conscious effort. Linguists hypothesize that abstract categories aid the process of speech comprehension because complex details can be mapped to a category, after which the detail of an instance can be forgotten. At the same time, research shows acoustic detail guides comprehension in real time and is retained in implicit memory. This dissertation addresses language processing for speech prosody. This study consists of five perception experiments that test the representation of pitch accents in memory, and directly compares memory for pitch accents to memory for phonemes. Results show that (1) explicit memory for prosody is more accurate for categorical differences, rather than equivalently large within-category differences, and (2) that, unlike phoneme categories, listeners are able to explicitly remember within-category detail for pitch accents, but that this memory decays quickly. Based on these results, I propose a hybrid model of comprehension of prosody that involves activating both previously proposed abstract categories and gradient detail.LimitedAuthor requested closed access (OA after 2yrs) in Vireo ETD syste

Kimball_Yiu_Watson

Word Recall is Affected by Surrounding Metrical Context Forthcoming in Language Cognition, Neuroscienc

Quasi-Separation in Linguistic Data

Code, data and summary tables for paper examining quasi-separation in different kinds of linguistic data

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field