Quantifying the psychological properties of words

This thesis explores the psychological properties of words – the idea that words carry links to additional information beyond their dictionary meaning. It does so by presenting three distinct publications and an applied project, the Macroscope. The published research respectively covers: the modelling of language networks to explain lexical growth; the use of high dimensional vector representations of words to discuss language learning; and the collection of a normative dataset of single word humour ratings. The first publication outlines the use of network science in psycholinguistics. The methodology is discussed, providing clear guidelines on the application of networks when answering psychologically motivated questions. A selection of psychological studies is presented as a demonstration of use cases for networks in cognitive psychology. The second publication uses referent feature norms to represent words in a high dimensional vector space. A correlative link between referent distinctiveness and age of acquisition is proposed. The shape bias literature (the idea that children only pay attention to the shape of objects early on) is evaluated in relation to the findings. The third publication collects and shares a normative dataset of single word humour ratings. Descriptive properties of the dataset are outlined and the potential future use in the field of humour is discussed. Finally, the thesis presents the Macroscope, a collaborative project put together with Li Ying. The Macroscope is an online platform, allowing for easy analysis of the psychological properties of target words. The platform is showcased, and its full functionality is presented, including visualisation examples. Overall, the thesis aims to give researchers all that’s necessary to start working with psychological properties of words – the understanding of network science in psycholinguistics, high dimensional vector spaces, normative datasets and the applied use of all the above through the Macroscope

Humor norms for 4,997 English words

Humor ratings are provided for 4,997 English words collected from 821 participants using an online crowd-sourcing platform. Each participant rated 211 words on a scale from 1 (humorless) to 5 (humorous). To provide for comparisons across norms, words were chosen from a set common to a number of previously collected norms (e.g., arousal, valence, dominance, concreteness, age of acquisition, and reaction time). The complete dataset provides researchers with a list of humor ratings and includes information on gender, age, and educational differences. Results of analyses show that the ratings have reliability on a par with previous ratings and are not well predicted by existing norms

The macroscope : a tool for examining the historical structure of language

The recent rise in digitized historical text has made it possible to quantitatively study our psychological past. This involves understanding changes in what words meant, how words were used, and how these changes may have responded to changes in the environment, such as in healthcare, wealth disparity, and war. Here we make available a tool, the Macroscope, for studying historical changes in language over the last two centuries. The Macroscope uses over 155 billion words of historical text, which will grow as we include new historical corpora, and derives word properties from frequency-of-usage and co-occurrence patterns over time. Using co-occurrence patterns, the Macroscope can track changes in semantics, allowing researchers to identify semantically stable and unstable words in historical text and providing quantitative information about changes in a word’s valence, arousal, and concreteness, as well as information about new properties, such as semantic drift. The Macroscope provides information about both the local and global properties of words, as well as information about how these properties change over time, allowing researchers to visualize and download data in order to make inferences about historical psychology. Although quantitative historical psychology represents a largely new field of study, we see this work as complementing a wealth of other historical investigations, offering new insights and new approaches to understanding existing theory. The Macroscope is avail- able online at http://www.macroscope.tech

Integer diagonal forms for subset intersection relations

For integers $0 \leq \ell \leq k_{r} \leq k_{c} \leq n$, we give a description for the Smith group of the incidence matrix with rows (columns) indexed by the size $k_r$ ($k_c$, respectively) subsets of an $n$-element set, where incidence means intersection in a set of size $\ell$. This generalizes work of Wilson and Bier from the 1990s which dealt only with the case where incidence meant inclusion. Our approach also describes the Smith group of any matrix in the $\mathbb{Z}$-linear span of these matrices so includes all integer matrices in the Bose-Mesner algebra of the Johnson association scheme: for example, the association matrices themselves as well as the Laplacian, signless Laplacian, Seidel adjacency matrix, etc. of the associated graphs. In particular, we describe the critical (also known as sandpile) groups of these graphs. The complexity of our formula grows with the $k$ parameters, but is independent of $n$ and $\ell$, which often leads to an efficient algorithm for computing these groups. We illustrate our techniques to give diagonal forms of matrices attached to the Kneser and Johnson graphs for subsets of size $3$, whose invariants have never before been described, and recover results from a variety of papers in the literature in a unified way.Comment: 28 page

Local Population Structure and Patterns of Western Hemisphere Dispersal for Coccidioides spp., the Fungal Cause of Valley Fever.

UnlabelledCoccidioidomycosis (or valley fever) is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year. This infection is caused by two sibling species, Coccidioides immitis and C. posadasii, which are endemic to specific arid locales throughout the Western Hemisphere, particularly the desert southwest of the United States. Recent epidemiological and population genetic data suggest that the geographic range of coccidioidomycosis is expanding, as new endemic clusters have been identified in the state of Washington, well outside the established endemic range. The genetic mechanisms and epidemiological consequences of this expansion are unknown and require better understanding of the population structure and evolutionary history of these pathogens. Here we performed multiple phylogenetic inference and population genomics analyses of 68 new and 18 previously published genomes. The results provide evidence of substantial population structure in C. posadasii and demonstrate the presence of distinct geographic clades in central and southern Arizona as well as dispersed populations in Texas, Mexico, South America, and Central America. Although a smaller number of C. immitis strains were included in the analyses, some evidence of phylogeographic structure was also detected in this species, which has been historically limited to California and Baja, Mexico. Bayesian analyses indicated that C. posadasii is the more ancient of the two species and that Arizona contains the most diverse subpopulations. We propose a southern Arizona-northern Mexico origin for C. posadasii and describe a pathway for dispersal and distribution out of this region.ImportanceCoccidioidomycosis, or valley fever, is caused by the pathogenic fungi Coccidioides posadasii and C. immitis The fungal species and disease are primarily found in the American desert southwest, with spotted distribution throughout the Western Hemisphere. Initial molecular studies suggested a likely anthropogenic movement of C. posadasii from North America to South America. Here we comparatively analyze eighty-six genomes of the two Coccidioides species and establish local and species-wide population structures to not only clarify the earlier dispersal hypothesis but also provide evidence of likely ancestral populations and patterns of dispersal for the known subpopulations of C. posadasii

Dating the Cryptococcus gattii Dispersal to the North American Pacific Northwest.

The emergence of Cryptococcus gattii, previously regarded as a predominantly tropical pathogen, in the temperate climate of the North American Pacific Northwest (PNW) in 1999 prompted several questions. The most prevalent among these was the timing of the introduction of this pathogen to this novel environment. Here, we infer tip-dated timing estimates for the three clonal C. gattii populations observed in the PNW, VGIIa, VGIIb, and VGIIc, based on whole-genome sequencing of 134 C. gattii isolates and using Bayesian evolutionary analysis by sampling trees (BEAST). We estimated the nucleotide substitution rate for each lineage (1.59 × 10-8, 1.59 × 10-8, and 2.70 × 10-8, respectively) to be an order of magnitude higher than common neutral fungal mutation rates (2.0 × 10-9), indicating a microevolutionary rate (e.g., successive clonal generations in a laboratory) in comparison to a species' slower, macroevolutionary rate (e.g., when using fossil records). The clonal nature of the PNW C. gattii emergence over a narrow number of years would therefore possibly explain our higher mutation rates. Our results suggest that the mean time to most recent common ancestor for all three sublineages occurred within the last 60 to 100 years. While the cause of C. gattii dispersal to the PNW is still unclear, our research estimates that the arrival is neither ancient nor very recent (i.e., <25 years ago), making a strong case for an anthropogenic introduction. IMPORTANCE The recent emergence of the pathogenic fungus Cryptococcus gattii in the Pacific Northwest (PNW) resulted in numerous investigations into the epidemiological and enzootic impacts, as well as multiple genomic explorations of the three primary molecular subtypes of the fungus that were discovered. These studies lead to the general conclusion that the subtypes identified likely emerged out of Brazil. Here, we conducted genomic dating analyses to determine the ages of the various lineages seen in the PNW and propose hypothetical causes for the dispersal events. Bayesian evolutionary analysis strongly suggests that these independent fungal populations in the PNW are all 60 to 100 years old, providing a timing that is subsequent to the opening of the Panama Canal, which allowed for more direct shipping between Brazil and the western North American coastline, a possible driving event for these fungal translocation events

Evolution of a pathogen: a comparative genomics analysis identifies a genetic pathway to pathogenesis in acinetobacter.

Acinetobacter baumannii is an emergent and global nosocomial pathogen. In addition to A. baumannii, other Acinetobacter species, especially those in the Acinetobacter calcoaceticus-baumannii (Acb) complex, have also been associated with serious human infection. Although mechanisms of attachment, persistence on abiotic surfaces, and pathogenesis in A. baumannii have been identified, the genetic mechanisms that explain the emergence of A. baumannii as the most widespread and virulent Acinetobacter species are not fully understood. Recent whole genome sequencing has provided insight into the phylogenetic structure of the genus Acinetobacter. However, a global comparison of genomic features between Acinetobacter spp. has not been described in the literature. In this study, 136 Acinetobacter genomes, including 67 sequenced in this study, were compared to identify the acquisition and loss of genes in the expansion of the Acinetobacter genus. A whole genome phylogeny confirmed that A. baumannii is a monophyletic clade and that the larger Acb complex is also a well-supported monophyletic group. The whole genome phylogeny provided the framework for a global genomic comparison based on a blast score ratio (BSR) analysis. The BSR analysis demonstrated that specific genes have been both lost and acquired in the evolution of A. baumannii. In addition, several genes associated with A. baumannii pathogenesis were found to be more conserved in the Acb complex, and especially in A. baumannii, than in other Acinetobacter genomes; until recently, a global analysis of the distribution and conservation of virulence factors across the genus was not possible. The results demonstrate that the acquisition of specific virulence factors has likely contributed to the widespread persistence and virulence of A. baumannii. The identification of novel features associated with transcriptional regulation and acquired by clades in the Acb complex presents targets for better understanding the evolution of pathogenesis and virulence in the expansion of the genus

Genome sequence of Staphylococcus aureus strain CA-347, a USA600 methicillin-resistant isolate

The Staphylococcus aureus clonal lineage CC45 is a predominant colonizer of healthy individuals in northern Europe and constitutes a highly basal cluster of the S. aureus population. Here, we report the complete genome sequence of S. aureus strain CA-347 (NRS648), a representative of the methicillin-resistant USA600 clone predominantly found in the United States