Personalising synthetic voices for individuals with severe speech impairment.

Speech technology can help individuals with speech disorders to interact more easily. Many individuals with severe speech impairment, due to conditions such as Parkinson's disease or motor neurone disease, use voice output communication aids (VOCAs), which have synthesised or pre-recorded voice output. This voice output effectively becomes the voice of the individual and should therefore represent the user accurately. Currently available personalisation of speech synthesis techniques require a large amount of data input, which is difficult to produce for individuals with severe speech impairment. These techniques also do not provide a solution for those individuals whose voices have begun to show the effects of dysarthria. The thesis shows that Hidden Markov Model (HMM)-based speech synthesis is a promising approach for 'voice banking' for individuals before their condition causes deterioration of the speech and once deterioration has begun. Data input requirements for building personalised voices with this technique using human listener judgement evaluation is investigated. It shows that 100 sentences is the minimum required to build a significantly different voice from an average voice model and show some resemblance to the target speaker. This amount depends on the speaker and the average model used. A neural network analysis trained on extracted acoustic features revealed that spectral features had the most influence for predicting human listener judgements of similarity of synthesised speech to a target speaker. Accuracy of prediction significantly improves if other acoustic features are introduced and combined non-linearly. These results were used to inform the reconstruction of personalised synthetic voices for speakers whose voices had begun to show the effects of their conditions. Using HMM-based synthesis, personalised synthetic voices were built using dysarthric speech showing similarity to target speakers without recreating the impairment in the synthesised speech output

Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes

Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size - 0.6pg to 4.4 pg per haploid cell. Firstly, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree - the first between 43-49 Mya (95% highest posterior density (HPD) 36.2-68.1 Mya) and the second at ~19 Mya (95% HPD 15.3-30.14 Mya). Secondly, RAD sequencing was used to identify potential WGD events and quantify transposable element abundance in different lineages. Evidence of two lineage scale WGDs were identified across the phylogeny, the first event occurring between 54-66 Mya (95% HPD 42.56-99.5 Mya) and the second at 20-30 Mya (95% HPD 15.3-45 Mya) based on haplotype numbers per contig and between 35-44 Mya (95% HPD 30.29-64.51 Mya) and 20-30 Mya (95% HPD 15.3-45 Mya) based on SNP read ratios. Transposable element abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20-30 Mya (95% HPD 15.3-45 Mya) and an older event at 35-44 Mya (95% HPD 30.29-64.51 Mya). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution

A Multi-Proxy Approach to Archaeobotanical Research: Archaic and Fremont Diets, Utah

New analytical techniques in archaeobotany allow researchers to examine human plant use by developing interrelated, yet independent lines of evidence. Here we outline the results of a two-method archaeobotanical approach to investigate Archaic and Fremont Great Basin diets. We conducted both macro- and microbotanical (starch granule) analyses at nine archaeological sites located in central and southwestern Utah. Our results show that in contexts where macrobotanical remains are poorly preserved, the application of microbotanical methods can produce additional sets of information, thus improving interpretations about past human diets. In this study, macrobotanical remains represented seed-based dietary contributions, while microbotanical remains came primarily from geophytes. Results suggest largely overlapping diets for Archaic and Fremont residents of Utah

Provision of powered communication aids in the United Kingdom

AAC service provision in the United Kingdom (UK) has evolved since the first service dedicated to the provision of communication aids opened in 1986. Within the UK, many health and care services are provided via government funding; however, the assessment and provision of AAC and specifically of speech-generating devices (SGDs) is inconsistent and inequitable. The study reported in this paper aimed to collect information on levels of current provision of powered communication aids (the term used in the study to refer to SGDs) by UK service providers in 2013 with the intention of improving future estimates for need of services. A questionnaire survey was designed and data were obtained from 98 AAC services across the UK. Service providers reported the number of individuals known to be using powered communication aids and the mean value reported was 0.0155% of the services? catchment populations. However levels of service provision reported were highly variable. Although the data reported must be treated with caution, it adds to the sparse literature on the topic, informs AAC service design and delivery in the UK, and acts as an indicative baseline measure for future service development

Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics?: a case study within spiders (Arthropoda: Araneae)

The development of second generation sequencing technology has resulted in the rapid production of large volumes of sequence data for relatively little cost, thereby substantially increasing the quantity of data available for phylogenetic studies. Despite these technological advances, assembling longer sequences, such as that of entire mitochondrial genomes, has not been straightforward. Existing studies have been limited to using only incomplete or nominally intra-specific datasets resulting in a bottleneck between mitogenome amplification and downstream high-throughput sequencing. Here we assess the effectiveness of a wide range of targeted long-range PCR strategies, encapsulating single and dual fragment primer design approaches to provide full mitogenomic coverage within the Araneae (Spiders). Despite extensive rounds of optimisation, full mitochondrial genome PCR amplifications were stochastic in most taxa, although 454 Roche sequencing confirmed the successful amplification of 10 mitochondrial genomes out of the 33 trialled species. The low success rates of amplification using long-Range PCR highlights the difficulties in consistently obtaining genomic amplifications using currently available DNA polymerases optimised for large genomic amplifications and suggests that there may be opportunities for the use of alternative amplification methods

Domestication-induced reduction in eye size revealed in multiple common garden experiments: The case of Atlantic salmon (Salmo salar L.)

Domestication leads to changes in traits that are under directional selection in breeding programmes, though unintentional changes in nonproduction traits can also arise. In offspring of escaping fish and any hybrid progeny, such unintentionally altered traits may reduce fitness in the wild. Atlantic salmon breeding programmes were established in the early 1970s, resulting in genetic changes in multiple traits. However, the impact of domestication on eye size has not been studied. We measured body size corrected eye size in 4000 salmon from six common garden experiments conducted under artificial and natural conditions, in freshwater and saltwater environments, in two countries. Within these common gardens, offspring of domesticated and wild parents were crossed to produce 11 strains, with varying genetic backgrounds (wild, domesticated, F1 hybrids, F2 hybrids and backcrosses). Size-adjusted eye size was influenced by both genetic and environmental factors. Domesticated fish reared under artificial conditions had smaller adjusted eye size when compared to wild fish reared under identical conditions, in both the freshwater and marine environments, and in both Irish and Norwegian experiments. However, in parr that had been introduced into a river environment shortly after hatching and sampled at the end of their first summer, differences in adjusted eye size observed among genetic groups were of a reduced magnitude and were nonsignificant in 2-year-old sea migrating smolts sampled in the river immediately prior to sea entry. Collectively, our findings could suggest that where natural selection is present, individuals with reduced eye size are maladapted and consequently have reduced fitness, building on our understanding of the mechanisms that underlie a well-documented reduction in the fitness of the progeny of domesticated salmon, including hybrid progeny, in the wild

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity