Дисертації з теми "Generational variation"

Thanks to the evolution of modern audiovisual technology, film audiences nowadays can enjoy the flexibility of watching movies at venues ranging from multiplex theatres to living rooms and bedrooms at home through various film-viewing platforms from broadcast television, cable movie channels, VCR, VCD, and DVD to internet downloading. With the increased amount of transnational audiovisual products imported over the years, Taiwanese audiences can also consume different types of films from different places in these ways. This thesis focuses on the relationship between different generations of film audiences and their 'film-viewing' practices via various viewing platforms, attempting to reveal the social, cultural and economic significance of their everyday practices, and frame them in the structure of the local film industry and the increasingly transnational local cinema culture. The project employs various qualitative research techniques to collect Taipei film audiences' own accounts of their quotidian film-viewing practices through currently available viewing platforms. This multi-platform approach to contemporary film audiences in today's digital-rich media environment contributes to this understudied field of film audience research. Furthermore, the empirical data on the 'film-viewing' practices of five age groups yields an understanding of the complicated interrelationships among film audiences, film texts and viewing platforms. On this basis, it is argued that the conventional 'audience-film' relationship studied in audience research should be reframed as the study of the 'audience-film-viewing platform' relationship.

Phenotypic variation, or the total variation in a trait, and its components are of great importance in the fields of evolutionary and behavioral ecology. Phenotypic variation can be broken down into both environmental and genetic influences on that particular trait. However, due to an increasing trend of quantitative genetics in behavioral studies, researchers have begun to consider lesser studied components of phenotypic variation in addition to the commonly studied direct environmental and genetic influences. Some of these lesser studied components include maternal and paternal effects, or the effect that parental phenotype has on their offspring’s phenotype. In Chapter 1, I examine the impacts of direct environmental manipulation on cricket song production. For Chapter 2 however, instead of examining the direct environmental influence at the individual level, I examine, through meta-analysis, how the indirect environmental influences that occur at both the maternal and paternal level impact offspring phenotype across taxa.
North Dakota State University. College of Science and Mathematics

There is some evidence from scholarship that politeness norms in China are diversified. I maintain that a study aiming to provide systematic evidence of this would require an approach to politeness phenomena that is able to address such diversity. Drawing upon the insights of recent scholarship on the distinction between the modernist and postmodernist approaches to politeness, I survey relevant literature. I show that many current works on politeness argue that the modernist approach (Lakoff 1973/1975, Brown and Levinson 1987[1978], Leech 1983) generally tends to assume that society is relatively homogeneous with regard to politeness norms. By contrast, I demonstrate that the postmodernist approach to politeness (e.g. Eelen 2001, Mills 2003, Watts 2003) foregrounds the heterogeneity of society and the rich variability of politeness norms within a given culture. I argue that, by using a postmodernist approach to politeness, it is possible to show evidence of differences between groups of the Chinese in their politeness behaviour and the informing norms of politeness. I then explore this issue in depth by focusing on compliments and compliment responses (CRs). I show that studies on these speech acts in Chinese have to date tended to adopt a modernist approach to politeness and often assume a compliment and a CR to be easily identifiable. Moreover, I show that they do not address the heterogeneity of Chinese society and generally assume interactants to be homogeneous in terms of politeness norms that inform compliment and CR behaviours. On this basis, I raise the questions as to whether, by adopting a postmodernist rather than modernist approach, there is empirical evidence that politeness norms informing compliments and CRs vary among the Chinese, and whether these norms correlate with generation. v To this end, by audio-recording both spontaneous naturally occurring conversations and follow-up interviews, I construct a corpus of compliments and CRs generated by two generations of the Chinese brought up before and after the launch of China's reform. Quantitative and qualitative analyses of these data show that there is variation in compliment and CR behaviours in Chinese and the informing politeness norms. Furthermore, the result shows that this variation is correlated with generation. I then show how, by using a research methodology which emphasizes the interactants' perceptions obtained through follow-up interviews, my study brings to light problems with previous studies on compliments and CRs which hitherto are not addressed. By showing evidence that compliments and CRs are not as easy to identify as many previous researchers have indicated. I argue that my emic approach to data analysis provides a useful perspective on the complexity of intention in studies on speech acts and perhaps beyond. My study, therefore, makes an interesting contribution to the debate over this notion central to politeness research. Moreover, I argue my methodology which is able to categorize and analyze data according to participants' self-reported perceptions allows me to draw out differences in the two generations' compliment and CR behaviours and the informing politeness norms.

Alpine ecosystems are particularly sensitive to the effects of global warming because they are characterized by species adapted to low temperatures. Although adapted to low temperatures, alpine plants may still be capable of persisting under a changing climate and this will largely be dependent on the ability of their seeds to germinate, establish and reproduce in situ, or after dispersal to new sites. The effects of climate change on regeneration from seeds may be influenced by intrinsic factors such as seed longevity (how long seeds remain viable and able to germinate after dispersal), or germination success (the proportion of a seed population that will germinate following exposure to future climate scenarios), and the seasonal timing of germination. Germination strategy, among the earliest life history traits expressed, reflects germination timing and pattern across the progression of seasons after seed dispersal and I therefore expected germination strategy would be a key trait affecting the responses of species to climate change. To examine seed longevity, which reflects the potential for survival in a soil seed bank or in ex situ conservation, I explored the seed intrinsic lifespan (longevity) and its correlates across 56 species (Chapter 2). I showed that Australian alpine seeds are short-lived, similar to alpine seeds elsewhere and relatively shorter-lived compared to non-alpine Australian seeds. Although relatively short-lived, the seeds do survive long enough to form persistent soil seed banks. However, it is unclear whether the conditions required for germination will still be present in future climate scenarios. Thus, I conducted experimental studies that investigated how germination success in future climate scenarios will differ from germination in ambient climate scenarios, and whether germination strategy moderates the germination responses across 39 species (Chapter 3). This study highlights that when comparing across species, germination strategy moderates the effect of changing climate on germination success such that species with immediate germination strategy that germinate readily after dispersal are less sensitive to changing temperature and winter duration compared to species with dormant seed components (staggered and postponed strategies). Since germination strategy is a significant factor in determining the responses of species to climate change I also examined how within-species variation in germination strategy might affect the adaptability or plasticity of species in response to climate change. I examined the germination strategy variation within-species to specify the climate variables driving variation in germination strategy in wild populations (Chapter 4). I found that within the alpine herb Oreomyrrhis eriopoda, variation in germination strategies is mainly determined by temperature variability in the climate of origin. I also examined the consequences of germination strategy on not just germination but the whole plant life cycle, including early establishment, vegetative and reproductive traits and phenology, under ambient and future climate scenarios (Chapter 5). Under warmer soil temperatures, survival was reduced, and lifetime (time to senesce) and reproductive period were both condensed. Several vegetative and reproductive traits were affected by warming and the response indeed differed across germination strategies. This reveals that within-species variation in germination strategy may also enable species to express different patterns in life history traits across development, not just germination timing. Lastly, I also tested whether germination strategy is plastic across generations. Intraspecific germination strategies in O. eriopoda were not plastic across generations, even though labile in the species. The results highlight that across scales immediate species and immediate populations are less constrained by changing climate. What is interesting is the staggered germination strategy that maintained seasonal variations in seedling emergence, at current climate but also under future climate scenarios. Postponed strategy also tend to maintain germination under warmer germination temperatures, and hence, no shift in germination as reported in alpine seed elsewhere is observed across Australian alpine seeds. The germination strategy within species that is observed to be a conserved trait and did not change with maternal condition raises some questions. If germination strategy is not plastic across generations, then why does recent climate matter? Will germination strategy change when maternal conditions they are exposed to repeated over a few more generations? And how do the adult traits differ among the mothers? Together, the findings of this thesis contribute to improved understanding of alpine seed and seedling ecology, in particular how among- and within-species variation in germination strategy may influence species’ responses to climate change by affecting germination success and contributing to the persistence of species and/or populations. These findings have applied and pure ecological and evolutionary relevance to Australia and will make a substantive contribution to our global understanding of alpine plants.

La présente thèse consiste en une étude en diachronie de la terminologie du prêt-à-porter féminin dans des catalogues français de vente par correspondance depuis l’introduction du concept en France au début des années 1950. Notre travail est centré sur les emprunts à l’anglais et les créations sous influence anglaise comparativement à la néologie dans l’ensemble de notre corpus.Notre objectif est, d’une part, d’apprécier l’influence de l’anglais dans cette terminologie et, d’autre part, d’appréhender les tendances et mécanismes propres à ce domaine. Par l’étude des néologismes, des nécrologismes et des termes stables de notre corpus, nous examinons le renouvellement terminologique, ses mécanismes et ses motivations.Nous avons travaillé par comparaison de sous-corpus distants de cinq ans environ, chacun composé des catalogues des collections Printemps-Été et Automne-Hiver d’une année donnée. Les termes, collectés et traités manuellement, ont dans un premier temps fait l’objet d’une étude synchronique, à l’aide de sources secondaires, pour établir leur étymologie, leur définition et les catégoriser selon une typologie adaptée de la typologie des emprunts proposée par l’Office québécois de la langue française. Dans un second temps, les analyses diachroniques se sont fondées sur un trépied méthodologique formé des termes du corpus, des visuels des catalogues et d’avis d’experts. Sur le plan théorique, ces analyses se sont appuyées sur des théories issues de la linguistique et de la sociologie, en tenant compte de logiques économiques et d’autres facteurs, tels que des évènements historiques et sociétaux.Ces analyses nous ont permis d’étayer la place de l’anglais dans ce domaine ainsi que l’importance du renouvellement terminologique, fréquemment citées dans la littérature. De plus, au-delà de logiques propres au fonctionnement de la mode, notre corpus a révélé une régularité dans l’activité néologique permettant d’appuyer l’hypothèse d’un renouvellement à fréquence générationnelle. Enfin, nous proposons une réflexion sur la nécessité de travaux – en linguistique notamment – dans le domaine de la mode, compte tenu du manque d’étude sur le sujet et des lacunes des sources dictionnairiques
This dissertation is a diachronic study of the terminology of women’s ready-to-wear fashion in French mail-order catalogs since the introduction of the ready-to-wear concept in France in the early 1950s. Our work focuses on English borrowings and English-influenced neologisms, compared with neologisms in our corpus as a whole.Our goal is two-fold: we wish, first, to assess the influence of English in this terminology, and second, to delineate trends and mechanisms specific to this field. Based on a study of neologisms, necrologisms, and stable terms in our corpus, we examine terminological renewal, its mechanisms, and its motivations.We compared sub-corpora approximately five years apart, each comprising the catalogs from the Spring-Summer and Fall-Winter collections of a given year. The terms were collected and studied manually. They were first studied synchronically, using secondary sources to establish their etymologies, their definitions, and their types, according to a typology adapted from the Office québécois de la langue française’s typology of borrowings. Secondly, terms were analyzed diachronically using a three-part methodological framework, consisting of the terms from our corpus, of the visuals from the catalogs, and of expert opinions. These analyses drew on theories from linguistics and sociology, while also considering economic and other factors, such as historical and societal events.Our analyses enabled us to show the importance of the English language in this field, as well as the importance of terminological renewal, both frequently cited in academic works. Our corpus demonstrated neological activity that goes beyond the dynamics of fashion and that supports the hypothesis of regular generational terminological renewal. Finally, we propose a reflection on the need for work – linguistic research in particular – in the field of fashion, given the lack of studies on the subject and the shortcomings of dictionary sources

This thesis presents a practical scenario for asynchronous logic implementation that would benefit the modern Field-Programmable Gate Arrays (FPGAs) technology in improving reliability. A method based on Asynchronously-Assisted Logic (AAL) blocks is proposed here in order to provide the right degree of variation tolerance, preserve as much of the traditional FPGAs structure as possible, and make use of asynchrony only when necessary or beneficial for functionality. The newly proposed AAL introduces extra underlying hard-blocks that support asynchronous interaction only when needed and at minimum overhead. This has the potential to avoid the obstacles to the progress of asynchronous designs, particularly in terms of area and power overheads. The proposed approach provides a solution that is complementary to existing variation tolerance techniques such as the late-binding technique, but improves the reliability of the system as well as reducing the design’s margin headroom when implemented on programmable logic devices (PLDs) or FPGAs. The proposed method suggests the deployment of configurable AAL blocks to reinforce only the variation-critical paths (VCPs) with the help of variation maps, rather than re-mapping and re-routing. The layout level results for this method's worst case increase in the CLB’s overall size only of 6.3%. The proposed strategy retains the structure of the global interconnect resources that occupy the lion’s share of the modern FPGA’s soft fabric, and yet permits the dual-rail iv completion-detection (DR-CD) protocol without the need to globally double the interconnect resources. Simulation results of global and interconnect voltage variations demonstrate the robustness of the method.

The research question for this study is: how do religious and ethnic identities intersect for second-generation Americans? Is religious identification consistently coupled with strong ethnic identity among second-generation Americans, as posited by the current literature on is this issue, or are there other extant patterns that need to be further examined? I considered this question by comparing religious and non-religious second-generation Americans from Muslim-origin families from a variety of ethnic backgrounds. I interviewed 44 individuals across a range of religious and ethnic identification, and found six main patterns in how ethno-religious identities do and do not map on to one another. I titled these six patterns thusly: "Religion > Ethnicity; Higher Religion, Higher Ethnicity," "Religion > Ethnicity; Higher Religion, Lower Ethnicity," "Religion = Ethnicity," "Religion < Ethnicity," "Somewhat Ethnic, Somewhat Religious," and "Critics of Religion and Ethnicity."The case of second-generation Muslim Americans is particularly interesting, given that what may actually be occurring is the growing importance of a "pan-religious" identity, rather than the continued dominance of specific ethnic identities at the group level. Indeed, the primary function of the congregation vis-à-vis ethnicity may not be to maintain the ascendancy of a particular ethnic identity, as the sociology of religion literature claims; rather, for second-generation Muslims, religiosity may encourage a "pan-ethnicity" based on shared religious identity. This is borne out in the presence of two forms of the "Religion > Ethnicity" category, and the differentiation in how segmented assimilation occurs between the highly religious and the less religious.

The aim of the thesis is the design and evaluation of a generative model based on deep learning for creating symbolic music. Music, and art in general, pose interesting problems from a machine learning standpoint as they have structure and coherence both locally and globally and also have semantic content that goes beyond the mere structural problems. Working on challenges like those can give insight on other problems in the machine learning world. Historically algorithmic music generation focused on structure and was achieved through the use of Markov models or by defining, often manually, a set of strict rules to be followed. In recent years the availability of large amounts of data and cheap computational power led to the resurgence of Artificial Neural Networks (ANN). Deep Learning is machine learning based on ANN with many stacked layers and is improving state of the art in many fields, including generative models. This thesis focuses on Variational Autoencoders(VAE), a type of neural network where the input is mapped to a lower-dimensional code that is fit to a Gaussian distribution and then tries to reconstruct it minimizing the error. The distribution can be easily sampled allowing to generate and interpolate data in the latent space. Autoencoders can use any type of network to encode and decode the input, we will use Convolutional Neural Network (CNN) and Recurrent Neural Netowrks (RNN). Since the quality of music and art in general is deeply subjective and what seems pleasing to one may not be for another we will try to determine the “best” model by conducting a survey and asking the participants to rate their enjoyment of music and whether or not they think each sample to be composed by a human or AI.

This study investigates accent variation in the speech of three generations of two Kuwaiti ethnic groups: Najdis (originally from Saudi Arabia) and Ajamis (originally from Iran). The ethnic groups were chosen due to their varying social status: the Najdis have held a prestigious status in Kuwait for historical reasons, while Ajamis have held the least prestigious status on the social scale. The two groups have over the years gradually come into contact with each other, and this study explores the outcome of dialect contact by focusing on a set of phonological variables which traditionally had accent-specific realisations. The phonological variables (ʤ) (typically realised by Najdis as [j] and by Ajamis as [ʤ]), (s) (realised by Najdis as [s] more often than Ajamis, who use [sʕ] in exclusive co-articulatory environments) and (Ɣ) (realised by Najdis as [q] and by Ajamis as [Ɣ]) were investigated. These variables were analysed in relation to the social variables (of ethnicity, age and gender). Social networks and the correlation between identity and dialect levelling were also considered. Data were collected from 48 Kuwaiti speakers representing the two ethnicities, three ages groups (chosen according to relevant milestones in the history of Kuwait), and a balanced number of males and females. A variety of techniques (picture-naming, map task, interview, and questionnaires) were used to collect data. Results show that the Najdi accent is generally more stable across generations than the Ajamis’. The Ajami accent seems to be moving towards the Najdis’. The accent of the old generation of Ajamis resembles the Najdi accent the least, while the young generation of Ajamis use Najdi variants the most. The female Ajamis are the forefront of this change, followed by young Ajami males. (ʤ) and (s) showed change the most across the Ajami generations, with the young speakers actively avoiding the original Ajami realisations due to their social connotations. Language and linguistic differences used to be the largest barrier against welcoming Ajamis to the Kuwaiti community; the reported accent transformation seems to be playing a major role in bringing the two ethnic groups closer to each other.

Prenatal stress (PNS) has been shown to affect a range of different modalities, like stress responsiveness and affective traits in both animals and humans. Previously, Dr Paula Brunton’s lab has used a novel model of ethologically relevant prenatal social stress and had shown increased stress responsiveness in both first generation (F1) PNS males and females and increased anxiety-like trait in males, together with corresponding changes in mRNA expression for corticotrophin releasing hormone (Crh) and its receptors. The first aim on this project was to further explore the phenotype of PNS offspring created using this model in social context. F1 PNS females, but not males, displayed an impairment in social memory in comparison to control females, which was supported by lower vasopressin receptor type 1a (Avpr1a) mRNA expression in the anterior part of lateral septum and bed nucleus of stria terminalis. Acute stress exposure immediately prior to the social memory test, impaired social memory in control males and females, but had no effect in PNS males and markedly improved performance in PNS females. This facilitated learning in the PNS females was supported by the finding of higher Avpr1a mRNA expression in both target regions in the brain. Finally, olfactory memory for social but not non-social odours was also impaired in PNS females, compared to control females, indicating that deficits in social memory in PNS females are specific to social odours and not in the detection and/or processing of all odours. It has been shown previously that phenotypes observed in PNS animals can also be seen following disrupted maternal care in the early post-partum period and that stress can affect maternal behaviour. To investigate this possibility in the current model a maternal behaviour observation protocol was developed. Dams were observed during the first postnatal week, three times/day in 90 min blocks. Stressed dams showed an increase in pup-directed behaviours, together with an increase in arched back nursing specifically, compared to control dams. Furthermore, studies have shown that maternal behaviour patterns can be transferred from mother to daughters, therefore this possibility was also investigated here. There were no differences in maternal behaviour between F1 control and F1 PNS dams. The maternal behaviour experiment for the F1 PNS dams created a unique opportunity to study their offspring (F2). F2 PNS rats had lower body weights than their control counterparts throughout their lifetimes, while not differing significantly in their calorie intake. Increased anxiety-like behaviour was also observed in both the F2 males and females (but only during proestrous and estrous stages of their cycle). These changes were supported in males by increased Crh and Crh receptor type 1 and decreased Crh receptor type 2 mRNA expression in discrete regions of the amygdala. Furthermore, F2 PNS females exhibited exaggerated, and males attenuated ACTH and corticosterone secretion in response to acute stress, compared with controls. The reduced stress response in F2 PNS males was supported by higher glucocorticoid receptor (GR, Nr3c1) mRNA expression in field CA1 of hippocampus. In F2 PNS females, increased stress responses were associated with increased Crh and Avp mRNA expression in the medial parvocellular division of the paraventricular nucleus of the hypothalamus and lower basal Nr3c1 and mineralocorticoid receptor (MR, Nr3c2) mRNA expression in the hippocampus. As increased stress and anxiety-like responses have been linked to a depressive phenotype that possibility was also investigated. No changes were found in either sucrose preference or floating/swimming behaviour in the forced swim test between the F2 PNS and control rats, in either sex. Finally, the variation in individual stress responsiveness and anxiety-like trait and the relationship between these phenotypes was investigated in an outbred male Sprague Dawley population. It was found that three of the most commonly used anxiety tests: open field test, light dark box and elevated plus maze do not correlate as well with each other as could be expected. Secondly plasma corticosterone concentrations 30min after the onset of acute restraint stress were positively correlated with the amount of time the rats spent in the anxiogenic environments, showing perhaps counter-intuitively, that the higher the stress responses the less anxious the male rat is. The behavioural tests were also used as a selection procedure to compare gene expression by microarray in the amygdala of high and low anxious rats and hypothalamus of high and low stress-responsive rats. To summarise, stress during pregnancy has profound effects on the dams’ immediate maternal behaviour, as well as neuroendocrine and behavioural effects in both the F1 and F2 offspring. Furthermore, there is evidence of inter-individual variation in stress responsiveness and anxiety-like behaviour in an outbred rat population. This data could lead to further understanding of the origins of inter-individual variation and appreciation of the effect of stress throughout the life course.

The traditional paradigm of baseflow generation assumes a uniform water table contributes baseflow evenly across a watershed. This thesis considers an alternate paradigm in which baseflow originates from a mix of localized sources that drain at different rates. Four forested headwater catchments across the United States were examined for spatial variability in baseflow sources by analyzing fractional baseflow contribution from each subcatchment relative to the catchment outlet. This revealed that subcatchment flow contributions changed dynamically through time, supporting the idea of different drainage rates in different places. A parallel linear reservoir model, which is predicated on heterogeneity in flow sources and not groundwater hydraulics, was used to simulate results consistent with observations in some of the study catchments. These results support the idea that in some locations baseflow recession may be better explained by landscape spatial heterogeneity than by aquifer hydraulics.

Thesis advisor: Gabor T. Marth
Improvements in molecular and computational technologies have driven and will continue to drive advances in our understanding of genetic variation and its relationship to phenotypic diversity. Over the last three years, several new DNA sequencing technologies have been developed that greatly improve upon the cost and throughput of the capillary DNA sequencing technologies that were used to sequence the first human genome. The economy of these so‐called “next‐generation” technologies has enabled researchers to conduct genome‐wide studies in genetic variation that were previously intractable or too expensive. However, because the new technologies employ novel molecular techniques, the resulting sequence data is quite different from the capillary sequences to which the genomics field is accustomed. Moreover, the vast amounts of sequence data that these technologies produce present novel statistical and computational challenges in order to make even the simplest observations. The focus of my dissertation has been the development of novel computational and analytical methods that facilitate genome‐wide studies in genetic variation with traditional capillary sequencers and with new sequencing technologies. I present a novel method that produces more accurate error estimates for sequence data from one of these next‐generation sequencing technologies. I also present two studies that illustrate the utility of two such technologies for genome‐wide polymorphism discovery studies in Drosophila melanogaster and Caenorhabditis elegans. These studies accurately estimate the degree of genetic diversity in the fruitfly and nematode, respectively. I later describe how new sequencing approaches can be used to accelerate the mapping of causal genetic mutations in forward geetic screens. Lastly, I remark on where I believe these technologies will lead future studies in human genetic variation and describe their relevance to several of my future research interests
Thesis (PhD) — Boston College, 2008
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology

Thesis (MSc)--University of Stellenbosch, 2004.
ENGLISH ABSTRACT: Geographic variation in the presence/absence of generation glands in females of the cordylus-niger-oelofseni complex was described and correlated with climatic variables. Preserved and live specimens from 96 localities in the area south of 32°30' S and west of 19°45' E in the Western Cape, South Africa, were examined for the presence or absence of generation glands. Females from western coastal localities and from the Cape Fold Mountains generally lack generation glands, while females from inland lowland localities generally possess glands. A GIS analysis was performed to determine mean annual minimum temperature, mean annual maximum temperature, potential evaporation, mean annual precipitation, mean annual fog and mean annual cloud cover measured at 14:00 for each locality. Discriminant function and canonical analyses showed a highly significant correlation between the presence and absence of generation glands and five of the six climatic variables. It is suggested that the high incidence of fog and lower temperatures experienced along the west coast as a result of the cold Benguela Current, and the high incidence of orographic fog and cloud cover in the Cape Fold Mountains may affect energy allocation in females. In order to maintain their reproductive output, females may be forced to invest less energy in secondary sexual characters such as generation glands. Interspecific variation in the location, occurrence, number, and age of gland differentiation was investigated for cordylid lizards. For several species, data were obtained from the literature and for others data were obtained from material housed in the Ellerman Collection of the University of Stellenbosch. Cordylus cordylus and C. cataphractus were used for an evaluation of inter- and intrapopulation variation. Data for C. cordylus were obtained from five populations on the coastal lowlands of the Western Cape, while data on C. cataphractus come from the literature. The sex, snout-vent length, and number of generation glands were recorded for a representative sample of lizards at each locality. While in all species generation glands were located in the femoral region, Cordylus giganteus and C. microlepidotus had additional generation glands elsewhere on the body. It is suggested that additional generation glands in these species may be related to an increased need for chemical communication in a low-visibility environment in the case of C. giganteus, and in low population densities in the case of C. microlepidotus. Generation glands are present in all cordylid males, but females of some species may lack these glands. All cordylids display sexual dimorphism with regards to the presence and number of generation glands, with males having significantly more glands than females, indicating that these glands may play a more important role in males than in females. Low sexual dimorphism in at least two species suggests that generation glands may be equally important in both sexes of these species. In females, the presence of generation glands is closely regulated by climate. There is no indication of differences in generation gland profile between ground-dwelling and rock-dwelling species, except that in at least three ground-dwelling species, generation glands are already present at birth. In other species these glands differentiate only later in life. In the males of most species, generation glands start to differentiate prior to or at sexual maturity with a drastic increase in number when asymptotic body size is reached. The considerable inter- and intrapopulation variation in gland number in females, but not in males, underscores the hypothesis that the presence of generation glands in females is energy-linked and closely regulated by climate. An opposite geographic pattern of generation gland number in C. cataphractus, suggests that other factors than climate must be responsible for a difference in gland number and a difference in population density is suggested as explanation. To test for differences in aggression levels, females with and those without generation glands were staged in two experiments. In one experiment, females from different localities were staged against each other, while females from the same locality were paired in another experiment. No significant difference in aggression levels between females with and those without generation glands were observed in both experiments. It is suggested that generation glands do not exclusively function in territorial marking, but rather as a scent enhancer for femoral gland secretions. Inorder to elucidate the functional significance of generation glands, male response to female gland stimuli was investigated for 12 male C. cordylus. Males were presented with different female gland secretions (femoral, generation, and femoral and generation gland secretion combined) and water was used as a control. Total number of tongue-flicks and number of tongue-flicks directed at the secretion were counted. No significant difference was observed in the number of tongue-flicks between the different treatment groups. Males did, however, display leg-waving and head-rubbing behaviour. At present, the behaviour displayed by male C. cordylus in the presence of female gland stimuli, is unclear. The general absence of tongue-flicking of sandpaper labelled by female gland stimuli may be because of a flaw in the experimental design or because the experiment was conducted outside the breeding season. The display ofleg-waving and head-rubbing behaviour, however, suggests that cordylids do not exclusively rely on tongue-flicking for detection of conspecifics. The real function of generation glands thus still remains unresolved and further studies are needed to clarify this.
AFRIKAANSE OPSOMMING: Geografiese variasie in die aan-/afwesigheid van generasiekliere in wyfies van die cordylus-niger-oelofseni kompleks is beskryf en met klimaatsveranderlikes gekorreleer. Gepreserveerde en lewende materiaal, afkomstig van 96 lokaliteite in die area suid van 32°30' S en wes van 19°45'0 in die Wes-Kaap, Suid-Afrika, is vir die aan- ofafwesigheid van generasiekliere ondersoek. Generasiekliere is oor die algemeen afwesig in wyfies van westelike kuslokaliteite en die Kaapse Plooiberge, terwyl dit aanwesig is in wyfies van die binnelandse laagland lokaliteite. 'n GIS-analise is gedoen om die gemiddelde jaarlikse minimum temperatuur, gemiddelde jaarlikse maksimum temperatuur, potensiële verdamping, gemiddelde jaarlikse neerslag, gemiddelde jaarlikse mis en gemiddelde jaarlikse wolkbedekking, gemeet teen 14:00, vir elke lokaliteit te bepaal. Diskriminantefunksie en kanonieke analises toon 'n hoogs beduidende korrelasie tussen die aan- en afwesigheid van kliere en vyf van die ses klimaatsveranderlikes. Daar word voorgestel dat die hoë voorkoms van mis en lae temperature wat langs die weskus ervaar word as gevolg van die koue Benguela Seestroom, en die hoë voorkoms van orografiese mis en wolkbedekking in die Kaapse Plooiberge, die energie-toekenning in wyfies beïnvloed. Om hulle voortplantingsuitset te handhaaf, word wyfies moontlik gedwing om minder energie in sekondêre geslagskenmerke, soos generasiekliere, te belê. Interspesifieke variasie in die posisie, voorkoms, aantal en tyd van klierontwikkeling is vir verskeie gordelakkedisspesies ondersoek. Data vir verskeie spesies is vanuit die literatuur verkry, terwyl data vir ander spesies vanafmaterial in die Ellerman-versameling van die Universiteit van Stellenbosch verkry is. Cordylus cordylus en C. cataphractus is vir 'n evaluering van inter- en intrapopulasie variasie gebruik. Data vir C. cordylus is vanafvyfpopulasie wat op die kuslaaglande van die Wes-Kaap voorkom, ingesamel, terwyl data oor C. cataphractus vanuit die literatuur verkry is. Geslag, snoet-kloaak-lengte en die aantal generasiekliere is aangeteken vir 'n verteenwoordigende aantal individue van elke populasie. Terwyl generasiekliere in die femorale wyk van alle spesies aangetref word, het Cordylus giganteus en C. microlepidotus ook addisionele generasiekliere in ander dele van die liggaam. Daar is tot die gevolgtrekking gekom dat addisionele generasiekliere in hierdie spesies moontlik verwant is aan 'n groter behoefte aan chemiese kommunikasie in 'n lae sigbaarheidsomgewing in die geval van C. giganteus, en in 'n lae populasiedigtheid in die geval van C. microlepidotus. Generasiekliere word in alle gordelakkedis mannetjies aangetref, maar kan afwesig wees in wyfies van sommige spesies. Alle gordelakkedisse toon geslagsdimorfisme met betrekking tot die aanwesigheid en aantal generasiekliere, en mannetjies het beduidend meer kliere as wyfies, wat daarop dui dat hierdie kliere moontlik 'n meer belangrike rol by mannetjies as by wyfies speel. Lae geslagsdimorfisme inten minste twee spesies stel voor dat generasiekliere moontlik ewe belangrik in beide geslagte van hierdie spesies kan wees. In wyfies word die aanwesigheid van generasiekliere sterk deur klimaat gereguleer. Daar is geen aanduiding van verskille in generasieklierprofiel tussen grondbewonende en rotsbewonende spesies nie, behalwe dat generasiekliere reeds by geboorte teenwoordig is in ten minste drie grondbewonende spesies. In ander spesies ontwikkel hierdie kliere eers later. In mannetjies van die meeste spesies, begin generasiekliere voor oftydens geslagsrypheid ontwikkel, met 'n drastiese toename in aantal kliere wanneer asimptotiese liggaamsgrootte bereik word. Die aansienlike inter- en intrapopulasie variasie in aantal kliere in wyfies, maar nie in mannetjies nie, ondersteun die hipotese dat die teenwoordigheid van generasiekliere in wyfies aan energie gekoppel is en deur klimaat gereguleer word. 'n Teenoorgestelde geografiese patroon in die aantal generasiekliere in C. cataphractus, stel voor dat ander faktore as klimaat vir die verskil in aantal kliere verantwoordelik is en 'n verskil in populasiedigtheid word as verklaring voorgestel. Om vir verskille in aggressievlakke te toets, is wyfies met en wyfies sonder generasiekliere is teenoor mekaar getoets in twee eksperimente. In een eksperiment is wyfies van verskillende lokaliteite teenoor mekaar getoets, en in 'n ander eksperiment is wyfies van dieselfde lokaliteit teenoor mekaar getoets. Inbeide eksperimente is geen beduidende verskille is in die aggressievlakke van wyfies nie waargeneem nie. Daar word voorgestel dat generasiekliere nie uitsluitlik in gebiedsafbakening funksioneer nie, maar dat dit eerder as reukversterker vir die femorale kliere dien. Om die funksie van generasiekliere vas te stel, is die reaksie van 12 mannetjie C. cordylus op klierstimuli van wyfies getoets. Verskillende kliersekresies (femoraal, generasie, en femoraal en generasie gekombineerd) van wyfies is mannetjies voorgelê, en water is as 'n kontrole gebruik. Totale aantal tongskiete en aantal tongskiete wat na die sekresie gerig is, is getel. Geen beduidende verskil in die aantal tongskiete is tussen die verskillende groepe waargeneem nie. Mannetjies het egter beenwaai- en kopvryfgedrag getoon. Die rede vir die gedrag wat deur C. cordylus mannetjies in die teenwoordigheid van klierstimuli van wyfies vertoon word, is egter tans onduidelik. Die algemene afwesigheid van tongskiete na skuurpapier wat met klierstimuli van wyfies gemerk is, mag moontlik wees as gevolg van 'n fout in die eksperimentele ontwerp of omdat die eksperiment buite die paarseisoen uitgevoer is. Die vertoning van beenwaai- en kopvryfgedrag stel egter voor dat gordelakkedisse nie uitsluitlik op tongskiete staatmaak om lede van dieselfde spesie waar te neem nie. Die ware funksie van generasiekliere is dus steeds onopgelos en verdere studies word benodig om dit duidelikheid hieroor te kry.

RNA viruses include several notable human pathogens including HIV, hepatitis C virus, West Nile virus, influenza, and Ebola virus. This group of viruses includes viruses with incredibly diverse genome structures, such as single-stranded genomes, double-stranded genomes, multipart genomes, negative-stranded genomes, and positive-stranded genomes. They also exist as heterogeneous populations that can mutate and rapidly evolve due to their error-prone polymerases. These errors then accumulate as they are passed down through generation. They can, therefore, be used as a historical marker for genetic relationships. If these errors result in a change of fitness for the virus they can then be used to locate areas in the genome that are undergoing selection pressures.

In this work, I use these principles to examine what changes are necessary for Ebola virus to infect boa constrictor cells and how high priority RNA viruses mutate as a function of routine viral passaging and propagation. In Chapter 2, I show that Ebola virus requires no additional mutations in order to replicate efficiently in boa constrictor cells. In Chapter 3, I show that SNV analysis can be used to track the identity and passage history of different RNA viruses.

L'exploitation de la variation clonale est une des voies d'amélioration utilisée chez un grand nombre de plantes d'intérêts agronomiques telles que la pomme de terre, le café et la vigne. En effet, après plusieurs cycles de reproduction végétative, des caractéristiques agronomiques stables apparaissent donnant naissance à une diversité phénotypique remarquable, appelée « diversité clonale ». Chez la vigne, cette diversité clonale est d'une importance majeure pour les viticulteurs puisqu'elle permet une amélioration variétale sans changer d'identité de cépage en conformité avec la réglementation fixée par Appellations d'Origine Protégée. L'hypothèse la plus parcimonieuse expliquant cette diversité phénotypique clonale est l'accumulation de mutations somatiques au cours des cycles de reproduction végétative. L'objectif de cette thèse a été de dresser un panorama le plus exhaustif possible des différents polymorphismes moléculaires entre les génomes de plusieurs clones. Dans un premier temps trois clones de Pinot ont été séquencés par la technique 454 GS-FLX puis dans un second temps 11 clones de quatre cépages ont été séquencés la technique Illumina HiSeq 2000. Afin d'analyser la grande quantité de données obtenues, nous avons construit un pipeline d'analyse (Bacchus pipeline) permettant d'identifier tous les types de polymorphismes moléculaires entre les différents génomes.Nos résultats permettent, pour la première fois un inventaire exhaustif des polymorphismes moléculaires dans un contexte multiplication végétatif. L'ensemble des mutations polymorphes entre deux clones a pu être identifié, SNPs, indels (2,5 SNPs et 11,5 indels par Mb en moyenne) ainsi que des variations d'ordre structural (larges insertions ou délétions) représentant la classe la plus fréquente (129 évènements par Mb entre deux clones en moyenne). Afin d'évaluer le polymorphisme d'insertion généré par ces éléments nous en avons étudié quatre par une approche S-SAP sur plusieurs niveaux de diversité (inter-espèces, inter-cépages, inter-clones et entre plusieurs tissus d'un même individu). L'analyse phylogénétique au niveau des espèces est conforme à celle réalisée avec d'autres types de marqueurs moléculaires (SSR, SNP). Cependant, une forte instabilité de ces insertions a été confirmée entre les clones et entre les tissus d'un même d'individu. L'identification des clones par une méthodologie moléculaire serait d'une grande importance pour la filère. Pour cet objectif, nos résultats indiquent que les mutations de types SNP et petits indels qui sont certes moins fréquentes que les variations structurales mais qui sont plus stables semblent plus pertinentes pour la mise en place d'une méthodologie d'identification des clones
Clonal variation is considered as an effective contribution to breeding programs of vegetatively propagated species with major agronomical interest such as banana, potato, coffee and grape. Indeed, after several propagation cycles, stable and heritable phenotypic variations appear giving rise to a phenotypic variation termed “clonal diversity”. This clonal diversity is very important for wine-growers because it allows preserving cultivars identity in the strict respect of Appellation (A.O.P) wines specifications The most parsimonious hypothesis explaining clonal phenotypic diversity is the accumulation of somatic mutations. The objective of my thesis was to provide a broad description of molecular polymorphisms in the context of vegetative propagation. Three clones were first sequenced by 454 GS-FLX technology and eleven clones were then sequenced with Illumina Hiseq2000 technique. To analyse the high quantity of data obtained, we built a pipeline (Bacchus pipeline) allowing the identification of all existing molecular polymorphisms between different genomes.All polymorphism types were observed: indels and SNPs which have a low polymorphism frequency (2.5 SNPs and 11.5 indels per Mb between two clones in average) and structural variations (large insertions or deletions) which have a high polymorphism frequency (129 per Mb between two clones in average) but are unstable. To evaluate stability and polymorphism level of these transposable elements, we have studied 4 elements using S-SAP method at different diversity levels (inter-species, inter-cultivars, inter-clones and between organs/tissues of a single individual). Our interspecific phylogenetic analysis is similar to other phylogenies performed with SSR or SNPs markers. However, we confirm the high instability of these elements between clones and between tissues in single individuals.Clone identification through molecular methods would be of high significance for the wine industry. SNP or small indels mutations are less frequent but more stable than structural variation and could be used for accurate clone identification

New sequencing strategies have redefined the concept of “high-throughput sequencing” and many companies, researchers, and recent reviews use the term “Next-Generation Sequencing” (NGS) instead of high-throughput sequencing. These advances have introduced a new era in genomics and bioinformatics⁠⁠. During my years as PhD student I have developed various software, algorithms and procedures for the analysis of Nest Generation sequencing data required for distinct biological research projects and collaborations in which our research group was involved. The tools and algorithms are thus presented in their appropriate biological contexts. Initially I dedicated myself to the development of scripts and pipelines which were used to assemble and annotate the mitochondrial genome of the model plant Vitis vinifera. The sequence was subsequently used as a reference to study the RNA editing of mitochondrial transcripts, using data produced by the Illumina and SOLiD platforms. I subsequently developed a new approach and a new software package for the detection of of relatively small indels between a donor and a reference genome, using NGS paired-end (PE) data and machine learning algorithms. I was able to show that, suitable Paired End data, contrary to previous assertions, can be used to detect, with high confidence, very small indels in low complexity genomic contexts. Finally I participated in a project aimed at the reconstruction of the genomic sequences of 2 distinct strains of the biotechnologically relevant fungus Fusarium. In this context I performed the sequence assembly to obtain the initial contigs and devised and implemented a new scaffolding algorithm which has proved to be particularly efficient.

A complex trait is a trait or disease that is controlled by both genetic and environmental factors, along with their interactions. Trait architecture encompasses the genetic variants and environmental causes of variation in the trait or disease, their effects on the trait or disease and the mechanism by which these factors interact at molecular and organism levels. It is important to understand trait architecture both from a biological viewpoint and a health perspective. In this thesis, I laid emphasis on exploring the influence of familial environmental factors on complex trait architecture alongside the genetic components. I performed a variety of studies to explore the architecture of anthropometric and cardio-metabolic traits, such as height, body mass index, high density lipoprotein content of blood and blood pressure, using a cohort of 20,000 individuals of recent Scottish descent and their phenotype measurements, Single Nucleotide Polymorphism (SNP) data and genealogical information. I extended a method of variance component analysis that could simultaneously estimate SNP-associated heritability and total heritability whilst considering familial environmental effects shared among siblings, couples and nuclear family members. I found that most missing heritability could be explained by including closely related individuals in the analysis and accounting for these close relationships; and that, on top of genetics, couple and sibling environmental effects are additional significant contributors to the complex trait variation investigated. Subsequently, I accounted for couple and sibling environmental effects in Genome- Wide Association Study (GWAS) and prediction models. Results demonstrated that by adding additional couple and sibling information, both GWAS performance and prediction accuracy were boosted for most traits investigated, especially for traits related to obesity. Since couple environmental effects as modelled in my study might, in fact, reflect the combined effect of assortative mating and shared couple environment, I explored further the dissection of couple effects according to their origin. I extended assortative mating theory by deriving the expected resemblance between an individual and in-laws of his first-degree relatives. Using the expected resemblance derived, I developed a novel pedigree study which could jointly estimate the heritability and the degree of assortative mating. I have shown in this thesis that, for anthropometric and cardio-metabolic traits, environmental factors shared by siblings and couples seem to have important effects on trait variation and that appropriate modelling of such effects may improve the outcome of genetic analyses and our understanding of the causes of trait variation. My thesis also points out that future studies on exploring trait architecture should not be limited to genetics because environment, as well as mate choice, might be a major contributor to trait variation, although trait architecture varies from trait to trait.

Given a sentence, a paraphrase generation system produces a sentence that says the same thing but usually in a different way. The paraphrase generation problem can be formulated in the machine translation paradigm; instead of translation of English to a foreign language, the system translates an English sentence (for example) to another English sentence. Quirk et al. (2004) demonstrated this approach to generate almost 90% acceptable paraphrases. However, most of the sentences had little variation from the original input sentence. Leveraging syntactic information, this thesis project presents an approach that successfully generated more varied paraphrase sentences than the approach of Quirk et al. while maintaining coverage of the proportion of acceptable paraphrases generated. The ParaMeTer system (Paraphrasing by MT) identifies syntactic chunks in paraphrase sentences and substitutes labels for those chunks. This enables the system to generalize movements that are more syntactically plausible, as syntactic chunks generally capture sets of words that can change order in the sentence without losing grammaticality. ParaMeTer then uses statistical phrase-based MT techniques to learn alignments for the words and chunk labels alike. The baseline system followed the same pattern as the Quirk et al. system - a statistical phrase-based MT system. Human judgments showed that the syntactic approach and baseline both achieve approximately the same ratio of fluent, acceptable paraphrase sentences per fluent sentences. These judgments also showed that the ParaMeTer system has more phrase rearrangement than the baseline system. Though the baseline has more within-phrase alteration, future modifications such as a chunk-only translation model should improve ParaMeTer's variation for phrase alteration as well.

This thesis is a sociolinguistic investigation into aspects of non-phonological variation in a group of preadolescents recorded in outer east London. Focusing on the analysis of selected grammatical variables, it aims to explore the nature and development of linguistic variation in an age group which has not figured prominently in the foundational sociolinguistic literature. The study is embedded within a variationist framework, and examines how the distribution of vernacular variables selected from different levels of the grammar can provide important insights into the maturing sociolinguistic competence of preadolescent speakers. The distribution of specific grammatical variables is correlated with the broad social dimensions of age and gender in order to examine the social and linguistic constraints which operate on aspects of variation in this age group. Furthermore, the findings which emerge from this study are contextualized in relation to patterns of variation used by older speakers, and are more broadly situated with regard to related patterns of variation in other dialects of English. Another primary aim of the study is to contribute to empirical characterisations of grammatical variation in southeastern England, an area in which there has been little systematic quantitative investigation of non-phonological variation. Given that London has been identified in the sociolinguistic literature as the site of considerable dialect levelling and a major locus of linguistic innovation, the study explores preadolescents' active participation in some of the burgeoning linguistic changes that are affecting not only southeasten dialects, but also other contemporary varieties of English.

In the current global market, there are plenty solutions for the savings of energy in the different areas of consumption in buildings: Green roofs and walls, cool roofs, daylighting, motion sensors, and others but there are very few sources of renewable energy at the reach of a common person in residential (smaller) scale. Photovoltaic systems are the most well-know and reliable process of harvesting energy at this small scale. The relationship between energy demand and energy production when installing a photovoltaics system in a residence is one of the main drivers while making a decision at the time of purchasing a system. However, architectural decisions in early stages may influence, enhance or even decrease the possible energy generation and interior performance, thus influencing the possible return of investment. This study evaluates the possible architectural variations that may be beneficial or disadvantegous at a particular city and other circumstances. From, roof, angle, location, roof articulation, layout articulation , shading devices and others, this paper shows a spectrum of convenient and inconvenient projects due to current conditions like climate, solar radiation, typical construction, electricity rates and government incentives. As a conclusion a hierarchy of architectural elements when being used with photovoltaics is developed to demonstrate that a common user can strategically play with architectural features of his/her house to take the most out of the system.

We developed a pipeline to identify the copy number polymorphisms (CNPs) in the Northern Swedish population using whole genome sequencing (WGS) data. Two different methodologies were applied to discover CNPs in more than 1,000 individuals. We also studied the association between the identified CNPs with the expression level of 438 plasma proteins collected in the same population. The identified CNPs were summarized and filtered as a population copy number matrix for 1,021 individuals in 243,987 non-overlapping CNP loci. For the 872 individuals with both WGS and plasma protein biomarkers data, we conducted linear regression analyses with age and sex as covariance. From the analyses, we detected 382 CNP loci, clustered in 30 collapsed copy number variable regions (CNVRs) that were significantly associated with the levels of 17 plasma protein biomarkers (p < 4.68×10-10).

Hydropower contributes around 20% to the world electricity supply and is considered as the most important, clean, emissions free and economical renewable energy source.  Total installed capacity of Hydropower generation is approximately 777GW in the world (2998TWh/year). Furthermore, estimated technically feasible hydropower potential in the world is 14000TWh/year. The hydropower is the major renewable energy source in many countries and running at a higher plant-factor. Bearing overheating is one of the major problems for continues operations of hydropower plants. Objective of this work is to model and simulate dynamic variation of temperatures of bearings (generator guide bearing, turbine guide bearing, thrust bearing) of a hydropower generating unit. The temperature of a bearing is  depends on multiple variables such as temperatures of ambient air, cooling water and cooling water flow-rate, initial bearing temperatures, duration of operation  and electrical load. Aim of this study is to minimize the failures of hydropower plants due bearing temperature variations and to improve the plant-factor. The bearing heat exchange system of a hydropower plant is multi-input (MI) and multi-output (MO) system with complex nonlinear characteristics. The heat transfer pattern is compel in nature and involves with large number of variables. Therefore, it is difficult to use conventional modelling methods to model a system of this nature. So that Neural Network (NN) method has been selected as the best where past input and output data is available, and the input characteristics can be mapped in order to develop a model. In this report a neural network model is developed to model the hydropower plant, using Matlab neural network tool box and matlab as the implementation language.

The goal of this thesis is to explore a new clustering algorithm, VAE-Clustering, and examine if it can be applied to find differences in the distribution of stock returns and augment the distribution of a current portfolio of stocks and see how it performs in different market conditions. The VAE-clustering method is as mentioned a newly introduced method and not widely tested, especially not on time series. The first step is therefore to see if and how well the clustering works. We first apply the algorithm to a dataset containing monthly time series of the power demand in Italy. The purpose in this part is to focus on how well the method works technically. When the model works well and generates proper results with the Italian Power Demand data, we move forward and apply the model on stock return data. In the latter application we are unable to find meaningful clusters and therefore unable to move forward towards the goal of the thesis. The results shows that the VAE-clustering method is applicable for time series. The power demand have clear differences from season to season and the model can successfully identify those differences. When it comes to the financial data we hoped that the model would be able to find different market regimes based on time periods. The model is though not able distinguish different time periods from each other. We therefore conclude that the VAE-clustering method is applicable on time series data, but that the structure and setting of the financial data in this thesis makes it to hard to find meaningful clusters. The major finding is that the VAE-clustering method can be applied to time series. We highly encourage further research to find if the method can be successfully used on financial data in different settings than tested in this thesis.
Syftet med den här avhandlingen är att utforska en ny klustringsalgoritm, VAE-Clustering, och undersöka om den kan tillämpas för att hitta skillnader i fördelningen av aktieavkastningar och förändra distributionen av en nuvarande aktieportfölj och se hur den presterar under olika marknadsvillkor. VAE-klusteringsmetoden är som nämnts en nyinförd metod och inte testad i stort, särskilt inte på tidsserier. Det första steget är därför att se om och hur klusteringen fungerar. Vi tillämpar först algoritmen på ett datasätt som innehåller månatliga tidsserier för strömbehovet i Italien. Syftet med denna del är att fokusera på hur väl metoden fungerar tekniskt. När modellen fungerar bra och ger tillfredställande resultat, går vi vidare och tillämpar modellen på aktieavkastningsdata. I den senare applikationen kan vi inte hitta meningsfulla kluster och kan därför inte gå framåt mot målet som var att simulera olika marknader och se hur en nuvarande portfölj presterar under olika marknadsregimer. Resultaten visar att VAE-klustermetoden är väl tillämpbar på tidsserier. Behovet av el har tydliga skillnader från säsong till säsong och modellen kan framgångsrikt identifiera dessa skillnader. När det gäller finansiell data hoppades vi att modellen skulle kunna hitta olika marknadsregimer baserade på tidsperioder. Modellen kan dock inte skilja olika tidsperioder från varandra. Vi drar därför slutsatsen att VAE-klustermetoden är tillämplig på tidsseriedata, men att strukturen på den finansiella data som undersöktes i denna avhandling gör det svårt att hitta meningsfulla kluster. Den viktigaste upptäckten är att VAE-klustermetoden kan tillämpas på tidsserier. Vi uppmuntrar ytterligare forskning för att hitta om metoden framgångsrikt kan användas på finansiell data i andra former än de testade i denna avhandling

This research was conducted to expand the understanding of the role of the X chromosome in common and familial typical migraine. The primary objective of this study was to identify new X chromosomal genetic targets that cause migraine. Overall this research has identified nine genetic targets of interest. Various obstacles were encountered throughout this study, but the knowledge gained for overcoming these obstacles are invaluable for implementation and improvement of future genetic studies investigating the X chromosome.

The discovery of DNA has been one of the biggest catalysts in genomic research. Sequencing has enabled us to access the wealth of information encoded in DNA and has provided the basis for ground-breaking achievements such as the first complete human genome sequence. Furthermore, it has tremendously advanced our understanding of life-threatening genetic disorders and bacterial and viral infections. With the recent advent of next generation sequencing (NGS) technologies, sequencing became accessible to the majority of researchers and made metagenomic sequencing widely available. However, to realise its true potential, sophisticated and tailor-made bioinformatic programs are essential to translate the collected data into meaningful information. My thesis explored the potential of resolving fine-scale variation in NGS data. The identification and correction of artificial fine-scale variation in the form of biases and errors is imperative in order to draw valid conclusions. Furthermore, resolving natural fine-scale variation in the form of single nucleotide polymorphisms (SNPs) and closely related species or strains is critical for the development of effective treatments and the characterisation of diseases. In recent years, Illumina has emerged as the global market leader in DNA sequencing. However, biases and errors associated with this high-throughput sequencing technology are still poorly understood which has precluded the development of effective noise removal algorithms. In addition, many programs were not designed for Illumina data or metagenomic sequencing. Therefore, a better understanding of the idiosyncrasies encountered in Illumina data is essential and programs must be tested and benchmarked on realistic and reliable in silico data sets to reveal not only their true capacities but also their limitations. I conducted the largest in vivo study of Illumina error profiles in combination with state-of-the-art library preparation methods to date. For the first time, a direct connection between experimental design factors and systematic errors was established, providing detailed insight into the nature of Illumina errors. Further, I tested various error removal techniques and developed a sophisticated Illumina amplicon noise removal algorithm, enabling researchers to choose optimal processing strategies for their particular data sets. In addition, I devised several simulation tools that accurately reflect artificial and natural fine-scale variation. This includes a flexible and efficient read simulation program which is the only program that can directly reflect the impact of experimental design factors. Furthermore, I developed a program simulating the evolution of a virus into a quasi-species. These programs formed the basis for two comprehensive benchmarking studies that revealed the capacities and limitations of viral haplotype reconstruction programs and taxonomic classification programs, respectively. My work furthers our knowledge of Illumina sequencing errors and will facilitate more accurate and effective analyses of sequencing data sets.

This thesis describes the development and use of a new class of molecular tools called Selector probes, and its potential for investigations of genetic variation. The Selector technology provides multiplex amplification of targeted DNA sequences with a high specificity, and an enrichment factor in the same order of magnitude as PCR. A common feature in this thesis work is to focus the analysis on DNA regions of interest. For example, this technique can be implemented in analysing candidate regions found by whole genome studies that need validation (global to local analysis), and applications requiring detection of rare alleles (common to rare allele), important in for example cancer samples. An assay is presented that allows for fast and simple quantification of relative copy-number variations. The method was proven to be able to detect aneuploidy in chromosome 13, 18, 21 and X, with a resolution enough to distinguish between 4 and 5 copies. The method was successfully applied to solve a biological question regarding a copy-number variation, that explains the Ridge phenotype typical for the dog bread Rhodesian Ridgebacks. The Selector strategy was able to detect and map a tandem duplication with a size of 133 kb, which was characterized with base-pair resolution. A readout platform that facilitates simultaneous digital quantitative analysis of a large numbers of biomolecules is further introduced. The work involves arraying amplified product from successful selection and decoding each molecule by hybridization of fluorophore labeled oligonucleotides. Finally, a genome partitioning method which is applied upstream of next generation sequencing platforms is presented. It is shown that the method provides successful enrichment with 98 % coverage and 94 % specificity and high enrichment uniformity. The technique was applied for mutation analysis of 26 cancer-related genes in tumor cell-lines and tissue.

A list of genes have been identified to carry mutations causing familial ALS such as SOD1, TARDBP, C9orf72. But for sporadic ALS, which is 90% of all ALS cases, the underlying genetic variants are still largely unknown. There are multiple genome-wide association study (GWAS) for sporadic ALS, but usually a large number nominated SNP can hardly be replicated in larger cohort analysis. Also majority of GWAS SNP lie within noncoding region of genome, imposing a huge challenge to study their biological role in ALS pathology. With the rapid development of next-generation sequencing technology, we are able to sequence exome and whole-genome of a large number of ALS patients to search for novel genetic variants and their potential biological function. Here by analyzing exam data, we discovered two novel or extremely rare missense mutations of DPP6 from a Mestizo Mexican ALS family. We showed the two mutations could exert loss-of-function effect by affecting electrophysiological properties of Potassium channels as well as the membrane localization of DPP6. To our knowledge this is the first report of DPP6 nonsynonymous mutations in familial ALS patients. In addition, by analyzing whole-genome data, we discovered strong linkage disequilibrium between SNP rs12608932, a repeatedly significant ALS GWAS signal, and one polymorphic TGGA tetra-nucleotide tandem repeat, which is further flanked by large TGGA repetitive sequences. We also demonstrated rs12608932 risk allele is associated with reduced UNC13A expression level in human cerebellum and UNC13A knockout could lead to shorter survival in SOD1-G93A ALS mice. Thus the TGGA repeat might be the real underlying genetic variation that confer risk to sporadic ALS.

Computer games have always become more and more advanced. One of the biggest reasons to its rapid evolution is the use of procedural content generation (PCG), which is used to generate game content automatically. However, there is one type of games that is more unexplored when it comes to PCG, namely motion games. Motion games are games where the player interacts with the game by moving his own body rather than using a gamepad, mouse or keyboard. Thanks to that, motion games are a healthier alternative to regular games, and this thesis therefore explores the possibilities to use PCG to develop more exciting motion games. The focus lies on achieving variation and progression since both of those are important concepts closely related to PCG. An exploratory case study is also conducted to examine how the derived guidelines work in a real game. The result concluded is that the guidelines seem to work well, but that all of them are not easily adapted to every game. Different game genres therefore call for different guidelines to be used.

Este documento apresenta um estudo em nível de mestrado na área de Geração de Língua Natural (GLN), enfocando a questão da variação humana na tarefa de Geração de Expressões de Referência (GER). O trabalho apresenta um levantamento bibliográfico sobre o tema, a criação de dois algoritmos de GER e a construção de um novo córpus de expressões de referência. Modelos computacionais de GER baseados nos algoritmos criados foram implementados em versões que incorporam e não incorporam a variação humana e empregados em uma série de experimentos de GER em sete córpus de expressões de referência. Resultados comprovam a hipótese inicial de que algoritmos de GER que levam em conta a variação humana podem gerar expressões de referência mais próximas a descrições de seres humanos do que algoritmos que não levam esta questão em conta. Além disso, confirmou-se que algoritmos de GER baseados em técnicas de aprendizado de máquina mostram-se superiores a algoritmos de GER consagrados e amplamente utilizados na literatura, como o algoritmo Incremental.
This work concerns a MSc Project in the field of Natural Language Generation (NLG), focusing on the issue of human variation in the Referring Expression Generation task (REG). The study presents a literature review on the topic, the proposal of two REG algorithms and the construction of a new corpus of referring expressions. Based on these algorithms, two REG models are implemented: with and without taking human variation. These models are employed in a series of REG experiments using seven referring expression corpora. Results confirm the initial hypothesis that REG algorithms that take speaker variation into account outperform existing algorithms that generate speaker-independent descriptions. Moreover, the present study confirms that algorithms based on machine learning techniques overperform existing algorithms, as the Dale and Reiter\'s Incremental algorithm.

Considerable effort has been devoted to finding reliable methods of correcting noisy RGB-D images captured with unreliable depth-sensing technologies. Supervised neural networks have been shown to be capable of RGB-D image correction, but require copious amounts of carefully-corrected ground-truth data to train effectively. Data collection is laborious and time-intensive, especially for large datasets, and generation of ground-truth training data tends to be subject to human error. It might be possible to train an effective method on a relatively smaller dataset using synthetically damaged depth-data as input to the network, but this requires some understanding of the latent noise distribution of the respective camera. It is possible to augment datasets to a certain degree using naive noise generation, such as random dropout or Gaussian noise, but these tend to generalize poorly to real data. A superior method would imitate real camera noise to damage input depth images realistically so that the network is able to learn to correct the appropriate depth-noise distribution.We propose a novel noise-generating CNN capable of producing realistic noise customized to a variety of different depth-noise distributions. In order to demonstrate the effects of synthetic augmentation, we also contribute a large novel RGB-D dataset captured with the Intel RealSense D415 and D435 depth cameras. This dataset pairs many examples of noisy depth images with automatically completed RGB-D images, which we use as proxy for ground-truth data. We further provide an automated depth-denoising pipeline which may be used to produce proxy ground-truth data for novel datasets. We train a modified sparse-to-dense depth-completion network on splits of varying size from our dataset to determine reasonable baselines for improvement. We determine through these tests that adding more noisy depth frames to each RGB-D image in the training set has a nearly identical impact on depth-completion training as gathering more ground-truth data. We leverage these findings to produce additional synthetic noisy depth images for each RGB-D image in our baseline training sets using our noise-generating CNN. Through use of our augmentation method, it is possible to achieve greater than 50% error reduction on supervised depth-completion training, even for small datasets.

Deploying wind power to a larger extent is one solution to reduce negative environmental impacts of electric power supply. However, various challenges are connected with increasing wind power penetration levels. From the perspective of transmission system operators, this includes balancing of varying as well as - to some extent - uncertain generation levels. From the perspective of power generating companies, changes in the generation mix will affect the market's merit order and, hence, their profits. This thesis focuses on provision and use of flexibility in the Nordic electricity market. First, this thesis studies wind power variations and accuracy of wind power forecasts in Sweden using statistical methods. Even though today’s wind penetration levels are still low in Sweden, power systems and electricity markets have to cope with these characteristics of variations and forecast errors to a larger extent in future. Second, it investigates to which extent an increased exchange and use of flexibility that is available in the intraday time-frame could efficiently facilitate system balancing and whether this would also be profitable from the power generating companies' perspective. Here, a simulation model is developed that reflects important aspects of production planning and trading decisions in the intraday time-frame. In a first case study, it is shown that the benefits of internal rescheduling strongly depend on the costs to adjust production plans in the intraday time-frame as compared to real-time. In a second case study, it becomes evident that trading flexibility in the intraday time-frame can reduce the need for system balancing more efficiently than internal rescheduling within each balance responsible party. Motivated by the positive gains of intraday trading and the challenge of appropriately modelling continuous intraday markets, trading activity and price development on Elbas is investigated. The results provide insights into trading behaviour on a continuous intraday market and show that trading is not always in accordance to the power system's physical situation. To the extent to which better information and adaptations in the market design could improve the market participants' base for trading decisions, policy recommendations and further research questions areas suggested.
Att använda vindkraft i en större utsträckning är en möjlighet att minska elproduktionens negativa miljöpåverkan. Det finns dock också olika utmaningar med stora mängder vindkraft. Från ett systemperspektiv gäller det till exempel att hålla balansen mellan tillförsel och konsumtion av el. Från elproducenternas perspektiv bör vindkraftens påverkan på elmarknaden nämnas eftersom det påverka aktörernas vinster. Avhandlingen titta närmare in i hur man kan få tillgång till mer flexibilitet på produktionssidan. Avhandlingen består av tre delar. För det första undersöks variationer och prognosfel av vindkraft i Sverige med hjälp av statistiska metoder. Även om andel vindkraft hittills är låg i Sverige, behöver elsystemet och elmarknader i framtiden hantera samma egenskaper av själva variationer och prognosfel som idag men i en större utsträckning. För det andra undersöks hur den flexibiliteten som finns i tidshorisonten några timmar innan leveranstimmen kan utnyttjas för att integrera vindkraften på ett sätt som är både fördelaktigt från systemets och från aktörernas perspektiv. Undersökningen sker med hjälp av en simuleringsmodell som omfattar viktiga delar i produktionsplanering och intradayhandel. I en fallstudie uppvisas att vinster av intern omplanering är i högsta grad beroende på kostnadsskillnaden mellan omplanering några timmar innan leveranstimmen och anpassning av körscheman under själva leveranstimmen. Resultat av ytterligare en fallstudie uppvisar att det är betydligt billigare och mer effektivt att använda intradayhandel istället för intern omplanering för att utnyttja den befintliga flexibiliteten och för att reducera obalanser som systemoperatörer annars behöver ta hand om under leveranstimmen. Detta är en anledning till att undersöka handelsmönster på Elbas som är en intradaymarknad med kontinuerlig handel. En annan anledning till den här tredje delen är utmaningarna i att modellera kontinuerlig intradayhandel. Studien beskriver handelsaktiviteten på Elbas och hur priserna utvecklas under handelstiden. Ett resultat är att handeln inte alltid återspeglar den fysiska situationen i elsystemet. I den utsträckningen som ett snabbare informationsflöde och förändringar i marknadsdesignen kunde förbättrar aktörernas underlag för intradayhandel, föreslås förbättringar och öppna forskningsfrågor.

QC 20150911

Elektra 36141: Korttidsplanering av vatten-värmekraftsystem vid stora mängder vindkraft: System-perspektivet

This thesis is settled within the STOCKMAPPING project, which represents one of the studies that were developed in the framework of RITMARE Flagship project. The main goals of STOCKMAPPING were the creation of a genomic mapping for stocks of demersal target species and the assembling of a database of population genomic, in order to identify stocks and stocks boundaries. The thesis focuses on three main objectives representing the core for the initial assessment of the methodologies and structure that would be applied to the entire STOCKMAPPING project: individuation of an analytical design to identify and locate stocks and stocks boundaries of Mullus barbatus, application of a multidisciplinary approach to validate biological methods and an initial assessment and improvement for the genotyping by sequencing technique utilized (2b-RAD). The first step is the individuation of an analytical design that has to take in to account the biological characteristics of red mullet and being representative for STOCKMAPPING commitments. In this framework a reduction and selection steps was needed due to budget reduction. Sampling areas were ranked according the individuation of four priorities. To guarantee a multidisciplinary approach the biological data associated to the collected samples were used to investigate differences between sampling areas and GSAs. Genomic techniques were applied to red mullet for the first time so an initial assessment of molecular protocols for DNA extraction and 2b-RAD processing were needed. At the end 192 good quality DNAs have been extracted and eight samples have been processed with 2b-RAD. Utilizing the software Stacks for sequences analyses a great number of SNPs markers among the eight samples have been identified. Several tests have been performed changing the main parameter of the Stacks pipeline in order to identify the most explicative and functional sets of parameters.

Il est intuitif qu’avec de nouveaux outils, il devient possible d’explorer de nouveaux domaines de la physique. Les champs électromagnétiques ultra-rapides sont l’un de ces outils, ils permettent de sonder la matière à de nouvelles échelles de temps, à la fois pour développer de nouvelles applications et pour la recherche fondamentale. Néanmoins, ces champs constituent en eux-mêmes un phénomène méritant d’être analysé et étudié. Le travail présenté ici est divisé en deux parties, dont la première s’occupe de la génération et amplification de lasers ultracourtes. L’amplification paramétrique optique est discutée dans les différentes configurations, notamment dans le cas où le signal a une dérivé angulaire spectrale. On discute aussi deux oscillateurs à blocage de mode en phase. Ont présente aussi une nouvelle manière d’étudier son comportement en fonction des dimensions de la sous-cavité. La mesure de ces phénomènes représente également un défi en raison de l’échelle temporelle extrêmement réduite à laquelle ces phénomènes se produisent, échelle bien trop petite pour des méthodes de mesure traditionnelles. Dans ce manuscrit, nous avons abordé deux techniques de mesure bien connues: l’autocorrélation interférométrique (IAC) du second ordre et la corrélation croisée du 3ème ordre (TOCC). Avec l’IAC et une mesure de la puissance spectrale du champ, il est possible de reconstruire intégralement le champ électrique tandis que le TOCC associé à l’autocorrélation en intensité détermine le profil en intensité de manière unique, et ont présente des algorithmes que font la reconstruction avec un haut contraste. Nous avons par ailleurs étudié la réalisation d’une nouvelle configuration de corrélateur croisé monocoup
It is intuitive that with new tools to analyze nature, new domains can be explored. Ultrafast electromagnetic fields are one of those tools, as they allow the probing of matter on new time scales, both for new applications and for basic research. However they are on their own right an important phenomenon that deserves to be analyzed, studied and probed. This work is divided in two parts one that deals with the generation and amplification of ultrashort pulses the second with the diagnostics of these lasers. We present a home-built tunable, narrow spectrum CPA amplification chain. We study the features of optical parametric amplification in several configurations. We made simulations regarding the amplification of a seed pulse that is angularly chirped, we also make some analytical calculations based on the same principle. Two mode-locked oscillators are presented one is a sub-12 fs laser oscillator used to produce the seed of the amplification chain, the second is a sub-6 fs laser oscillator. We describe the first laser oscillator in great detail. We devise and discuss models that can explain the parameters of the sub-cavity and the ability of these lasers to enter into mode-locking (ML), we compare the simulation results precise experimental measures made on the sub-6 fs oscillator. The measurement of ultrafast phenomena is also very challenging because their time scale is too short for common electronic devices. We have examined known measurements, such as third order cross correlations (TOCC) and interferometric second order autocorrelations (IAC) and obtained new analysis methods and new facts that broaden their usefulness. In particular, we have fully reconstructed the spectral phase of a pulse using an IAC trace and its power spectrum. We also prove that the existence of a TOCC plus an intensity autocorrelation is sufficient to retrieve the intensity profile of a pulse we present initial results on reconstruction algorithms, that might be able to do this with a high temporal contrast. We end this thesis with a study on simulation and implementation of a new configuration for single shot correlation measurements

Crop performance depends on genotype, the environment in which the crop is grown, and interaction between genotype and environment. A measure of these effects is important in determining adaptation and in recommending crop genotypes to growers. In instances where hybrid seed has been introduced into developing countries, which often traditionally save seed for the next planting, determining the adaptation of genotypes and making accurate recomendations may be difficult. This experiment evaluated 15 commercial hybrid grain sorghums (Sorghum bicolor (L.) Moench), along with their segregating F₂ and F₃ generations, for adaptation to variable moisture environments. Grain yield per entry in all tests was the main phenotypic character used to measure adaptation in environments differing in mean moisture stress. Grain yield was also the main characteristic used to observe changes through generations F₁ to F₃.There was an expected decrease in yield with decreased irrigation, and with advanced generations. A close association was observed between mean 3-year grain yield of the selected hybrids and their F₂ and F₃ progenies when grown in the same environment.

An important goal of biology is to understand the key mechanisms of evolution underlying the diversity of living organisms on Earth. In that respect, the recent innovations in the field of new generation sequencing technologies (NGS) are bringing new and exciting opportunities. This thesis presents results obtained with these tools in the specific context of the study of two sister species of cold-adapted leaf beetles, Gonioctena intermedia and G. quinquepunctata. More specifically, this work is focused around four research directions: the two first explore methods of statistical inference using a spatially explicit model of coalescence, by (1) evaluating the potential of various summary statistics to discriminate phylogeographic hypotheses, and (2) investigating the dispersal abilities of a montane leaf beetle, G. quinquepunctata, using an original method that avoids using summary statistics. The third research direction focuses on the adaptation to cold conditions in this montane leaf beetle, by testing the association between genetic polymorphism across tens of thousands of genetic markers and altitude in samples collected at various elevation levels in the Vosges (France). Finally, the fourth, and last, research axis presents the discovery of mitochondrial heteroplasmy, i.e. the presence in an individual of multiple copies of the mitochondrial genome, in natural populations of G. intermedia. We illustrate, here, how NGS technologies could help identify this phenomenon, probably underestimated in animals, on a large scale.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished

This thesis appears in three parts: Modules I, II, & III. The purpose of these units was to argue that Generation 1.5 (G1.5) learners are a distinct group of English language learners with unique ways of representing themselves in academic writing, and to identify those salient linguistic differences among G1.5, traditional ESL, and NS student writers. Using multiple methodologies, the text explores the discourse patterns of G1.5 students in their academic writing. Elements in each section include: Module I: o A discussion and literature review of research on Generation 1.5 students and design criteria for an extended corpus study. Module II: o A pilot study of early results from a corpus study comparing G1.5, ESL, and NES student academic writing, with a focus of pronoun and modal use. Module III: o A study involving surveys and interviews to evaluate what both students and instructors consider good academic writing and expect of student essays. o Corpus data from G1.5, ESL, and NS student corpora to determine lexicogrammatical and syntactic patterns in G1.5 student writers and how they differ from both ESL and NS students. Salient features are analyzed using a framework where features are mapped onto an adapted version of Halliday‘s (2004) three macrofunctions of language, allowing for an analysis of semantic and lexico-grammatical features in terms of ideational, interpersonal, and textual positioning. o Case studies of three essays to test corpus results and a framework of selfrepresentation against individual performance. The resulting text concludes that G1.5 students‘ self-representation in writing is distinct from other student writers, and manifests in their semantic choices, narrative style, and elements of a hybrid of academic and personal/interpersonal writing.

Next Generation Sequencing (NGS) technologies enable Deoxyribonucleic Acid (DNA) or Ribonucleic Acid (RNA) sequencing to be done at volumes and speeds several orders of magnitude faster than Sanger (dideoxy termination) based methods and have enabled the development of novel experiment types that would not have been practical before the advent of the NGS-based machines. The dramatically increased throughput of these new protocols requires significant changes to the algorithms used to process and analyze the results. In this thesis, I present novel algorithms used for Chromatin Immunoprecipitation and Sequencing (ChIP-Seq) as well as the structures required and challenges faced for working with Single Nucleotide Variations (SNVs) across a large collection of samples, and finally, I present the results obtained when performing an NGS based analysis of eight mammary ductal carcinoma cell lines and four matched normal cell lines.

Studying genetic diversity in natural and domestic populations is of major importance in evolutionary biology. The recent advent of next generation sequencing (NGS) technologies has dramatically changed the scope of these studies, enabling researchers to study genetic diversity in a whole-genome context. This thesis details examples of studies using NGS data to: (i) characterize evolutionary forces shaping the genome of the Atlantic herring, (ii) detect the genetic basis of speciation and domestication in the rabbit, and, (iii) identify mutations associated with skeletal atavism in Shetland ponies. The Atlantic herring (Clupea harengus) is the most abundant teleost species inhabiting the North Atlantic. Herring has seasonal reproduction and is adapted to a wide range of salinity (3-35‰) throughout the Baltic Sea and Atlantic Ocean. By using NGS data and whole-genome screening of 20 populations, we revealed the underlying genetic architecture for both adaptive features. Our results demonstrated that differentiated genomic regions have evolved by natural selection and genetic drift has played a subordinate role. The European rabbit (Oryctolagus cuniculus) is native to the Iberian Peninsula, where two rabbit subspecies with partial reproductive isolation have evolved. We performed whole genome sequencing to characterize regions of reduced introgression. Our results suggest key role of gene regulation in triggering genetic incompatibilities in the early stages of reproductive isolation. Moreover, we studied gene expression in testis and found misregulation of many genes in backcross progenies that often show impaired male fertility. We also scanned whole genome of wild and domestic populations and identified differentiated regions that were enriched for non-coding conserved elements. Our results indicated that selection has acted on standing genetic variation, particularly targeting genes expressed in the central nervous system. This finding is consistent with the tame behavior present in domestic rabbits, which allows them to survive and reproduce under the stressful non-natural rearing conditions provided by humans. In Shetland ponies, abnormally developed ulnae and fibulae characterize a skeletal deformity known as skeletal atavism. To explore the genetic basis of this disease, we scanned the genome using whole genome resequencing data. We identified two partially overlapping large deletions in the pseudoautosomal region (PAR) of the sex chromosomes that remove the entire coding sequence of the SHOX gene and part of CRLF2 gene. Based on this finding, we developed a diagnostic test that can be used as a tool to eradicate this inherited disease in horses.