Sequence-dependent histone variant positioning signatures

Background: Nucleosome, the fundamental unit of chromatin, is formed by wrapping nearly 147bp of DNA around an octamer of histone proteins. This histone core has many variants that are different from each other by their biochemical compositions as well as biological functions. Although the deposition of histone variants onto chromatin has been implicated in many important biological processes, such as transcription and replication, themechanisms of how they are deposited on target sites are still obscure. Results: By analyzing genomic sequences of nucleosomes bearing different histone variants from human, including H2A.Z, H3.3 and both (H3.3/H2A.Z, so-called double variant histones), we found that genomic sequencecontributes in part to determining target sites for different histone variants. Moreover, dinucleotides CA/TG are remarkably important in distinguishing target sites of H2A.Z-only nucleosomes with those of H3.3-containing (both H3.3-only and double variant) nucleosomes. Conclusions: There exists a DNA-related mechanism regulating the deposition of different histone variants onto chromatin and biological outcomes thereof. This provides additional insights into epigenetic regulatory mechanisms of many important cellular processes

A Practice-Based Study into the Composition and Performance of Polytemporal Music

This practice-based research explores the composition and performance of polytemporal music, culminating in ten new works in audio/visual format with accompanying commentaries and notation. Research is undertaken into concepts of rhythm and pulse in order to develop new techniques for composing music in multiple simultaneous tempi, particularly methods for managing rhythmic consonance and dissonance in the compositional process. Attention is also given to the practicalities and implications of performance, investigating issues of accessibility and ensemble in reference to the use of click tracks and headphones, as well as the form and function of notation. The approaches within this research stem from my experience as a commercial rock/studio musician fused with contemporary classical influences. As well as these musical influences, a background in visual art and design also contributes to the visual presentation of works and scores; musical works are presented in video format which is shown to enhance temporal perception, and a new form of rhythmically accurate western notation for polytemporal music is developed. Composing and performing in a strictly polytemporal setting has at the time of writing not been widely researched, and it is hoped this work displays new knowledge and approaches important for the development of composition in this area

Motive-Directed Meter

This dissertation isolates, defines, and explores the phenomenon of Motive-Directed Meter (MDM), which has hitherto received little scholarly attention. MDM is a listening experience evoked by music that is temporally regular enough to encourage metric listening and prediction, but irregular enough to frustrate these behaviors. MDM arises when recurring musical motives suggest parallel metric hearings, but shifting durational spans make metrical parallelism difficult to achieve. Listeners are therefore caught in a state of expectational limbo, urged to continually revise predictions that are recurrently thwarted. To approach this phenomenon, Chapter 1 describes the model of musical meter that undergirds this project, in which meter is viewed as an experiential process of temporal orientation taking place in the mind and body of a listener. Central to this dissertation is the notion that, like temporal orientation itself, the category “metric music” is not binary but graded, permitting degrees of inclusion; this removes the need to determine whether MDM can be considered “metric.” In order to accommodate this fluid conception, a flexible model of meter is introduced, which assesses the entrained listening experience according to four continua: timepoint specificity, pulse periodicity, hierarchic depth, and motivic saturation. These criteria are combined to create the multidimensional Flexible Metric Space, which accommodates all metric experiences, including Motive-Directed Meter, traditionally deep meter, and any other listening experience arising from synchronization with felt pulsation. This graded approach to membership in “metric music” allows analysts to compare and contrast musics from diverse repertoires. After Chapter 1 defines Motive-Directed Meter and the model of meter in which it is situated, Chapter 2 introduces five analytic tools appropriate to MDM. Some of these are adapted, some are newly developed, and each captures a different aspect of real-time listening. First, motive maps provide visual representations that summarize and highlight relationships between motives and durational spans, providing an overview of the interplay between these domains. Second, the variability index ranks categories of meter according to entrainment difficulty in isolation. Taken together, these two methods provide a rough picture of the shifting levels of unpredictability across a given passage of MDM. Third, Mark Gotham’s metric relations describe the relative difficulty and quality of connections between adjacent meters, further refining the processual approach undertaken here. Fourth, the metric displacement technique assesses the degree of mismatch between a listener’s expectations and realized musical events, comparing the expected metric depth—roughly, the metric strength—of certain important musical events with the “actual,” realized metric depth of those moments. This technique thereby describes the magnitude of the entrainment shift a listener must undertake in order to adjust to musical events at unexpected temporal positions. Fifth and finally, three expectation-generation methods are used to produce hypothetical sets of predictions intended to roughly approximate listener expectations at various stages of the learning process; these are local inertia, motivic inertia, and prototype methods. The utility of these analytic techniques is highlighted by way of a diverse series of analyses. Chapters 2 and 3 focus on the music of Igor Stravinsky: Chapter 2 analyzes brief passages from the Rite of Spring, the Soldier’s Tale, and Petrushka, while Chapter 3 delves deeply into three large works: the “Sacrificial Dance” and “Glorification of the Chosen One” from the Rite of Spring, and the “Feast at the Emperor’s Palace” from the Song of the Nightingale. Chapter 4 then moves beyond Stravinsky to explore the music of a large number of late twentieth- and early twenty-first century composers and popular music artists working in diverse styles and genres. The artists studied in this chapter include the composers Meredith Monk and Julia Wolfe, and the groups Rolo Tomassi and Mayors of Miyazaki. The analyses comprising this dissertation employ an experiential perspective, combining the techniques outlined above in order to better understand how we as listeners may work to orient ourselves to these pieces of music. In contrast to traditional structuralist approaches, all of the analyses presented in chapters 2-4, as well as the tools supporting them, are directed at the listening experience. Indeed, this dissertation—from its conceptions about meter and the tools it introduces, to the analyses that stem from both—is driven by a belief that the experience of the listener must lie at the heart of the analytic process. Central to all of the analyses is thus this aim: to illustrate how Motive-Directed Meter arises and to elucidate what it feels like to listen to it. With hope, this experience-driven approach may serve as a starting point for others seeking to similarly represent musical meter

Social Network Limits Language Complexity

Natural languages vary widely in the degree to which they make use of nested compositional structure in their grammars. It has long been noted by linguists that the languages historically spoken in small communities develop much deeper levels of compositional embedding than those spoken by larger groups. Recently, this observation has been confirmed by a robust statistical analysis of the World Atlas of Language Structures. In order to examine this connection mechanistically, we propose an agent\u2010based model that accounts for key cultural evolutionary features of language transfer and language change. We identify transitivity as a physical parameter of social networks critical for the evolution of compositional structure and the hierarchical patterning of scale\u2010free distributions as inhibitory

Understanding the Structure-Function Relationship in Peptide-Enabled High Entropy Alloy Nanocatalysts

The structural complexity in high entropy alloy nanocatalysts (HEAs), afforded by the homogeneous mixing of five or more elements, has resulted in a limited understanding about the origin of their promising electrocatalytic properties. This thesis investigates the structure-function relationship in HEAs using advanced material characterization techniques. At first, a methodology for resolving the atomic-scale structure of peptide-enabled HEAs was developed using high-energy X-ray diffraction (HE-XRD) coupled with atomic pair distribution function (PDF) and reverse Monte Carlo (RMC) simulations, yielding structure models over the length scale of HEAs. Coordination analysis of the structure models revealed a multifunctional interplay of geometric and electronic attributes of surface atoms in HEAs that was responsible for the catalytic activity enhancement during the methanol electrooxidation reaction. Using the methodology for resolving the atomic scale structure of HEAs and peptide sequence engineering, the structure-function relationship of model PtPdAuCoSn HEAs during ethanol electrooxidation reaction (EOR) was studied. Compositional analysis of the PtPdAuCoSn HEA structure models revealed distinct miscibility characteristics that were attributed to the unique biotic-abiotic interactions. Analysis of the structure models identified the rapid dehydrogenation of CH3CHO intermediate into CH3COads in an optimized adsorption configuration as the contributing factor for the high selectivity towards CH3COO- in PtPdAuCoSn HEAs. Armed with these insights, a study was designed for understanding the effect of changing the concentration of Pt in the structure-function relationship of PtPdAuCoSn HEAs using spatiotemporal structural insights from in-situ PDF. The structure models demonstrated a degree of metastability as a function of their corresponding configurational entropy. Analysis of the structure models revealed that high selectivity towards CH3COO- in PtPdAuCoSn HEAs during EOR originates from the enhanced distribution of Pd and Co surface atoms. In summary, this thesis uses atomic PDF and RMC simulations to draw structure-function correlations in HEAs, presenting a path forward for developing strategies for the rational design of HEAs. Through collaborative efforts from theoreticians and experimentalists, the methodology presented here can form the basis for accelerating the discovery of promising HEA configurations for emerging electrocatalytic applications

Modeling, Predicting and Capturing Human Mobility

Realistic models of human mobility are critical for modern day applications, specifically for recommendation systems, resource planning and process optimization domains. Given the rapid proliferation of mobile devices equipped with Internet connectivity and GPS functionality today, aggregating large sums of individual geolocation data is feasible. The thesis focuses on methodologies to facilitate data-driven mobility modeling by drawing parallels between the inherent nature of mobility trajectories, statistical physics and information theory. On the applied side, the thesis contributions lie in leveraging the formulated mobility models to construct prediction workflows by adopting a privacy-by-design perspective. This enables end users to derive utility from location-based services while preserving their location privacy. Finally, the thesis presents several approaches to generate large-scale synthetic mobility datasets by applying machine learning approaches to facilitate experimental reproducibility

Portfolio of compositions

The essay briefly contextualizes the field of my compositional interest and accordingly proceeds to examine sound, space, and time from different grounds. The intention of this preliminary exercise is to derive a revised notion of onkyō (sound) in relation to time, which will be useful to comment on my works. The compositional approaches presented here do not only involve the use of computers, but also the acoustic and physical shaping of sound and attempts at incorporating yet more complex historical and cultural aspects of sound in composition. Where necessary, hard- and software technologies specific to the works have been devised and research papers published. These are also discussed

Empirical evidence for musical syntax processing? Computer simulations reveal the contribution of auditory short-term memory

During the last decade, it has been argued that (1) music processing involves syntactic representations similar to those observed in language, and (2) that music and language share similar syntactic-like processes and neural resources. This claim is important for understanding the origin of music and language abilities and, furthermore, it has clinical implications. The Western musical system, however, is rooted in psychoacoustic properties of sound, and this is not the case for linguistic syntax. Accordingly, musical syntax processing could be parsimoniously understood as an emergent property of auditory memory rather than a property of abstract processing similar to linguistic processing. To support this view, we simulated numerous empirical studies that investigated the processing of harmonic structures, using a model based on the accumulation of sensory information in auditory memory. The simulations revealed that most of the musical syntax manipulations used with behavioral and neurophysiological methods as well as with developmental and cross-cultural approaches can be accounted for by the auditory memory model. This led us to question whether current research on musical syntax can really be compared with linguistic processing. Our simulation also raises methodological and theoretical challenges to study musical syntax while disentangling the confounded low-level sensory influences. In order to investigate syntactic abilities in music comparable to language, research should preferentially use musical material with structures that circumvent the tonal effect exerted by psychoacoustic properties of sounds