De todas as adaptações que as plantas sofreram durante a evolução, a aquisição do sistema vascular à 400 milhões de anos atrás, foi sem dúvida um evento decisivo para sua bem sucedida existência na terra. A madeira é considerada o mais importante recurso natural de energia renovável e o setor econômico baseado na produção florestal cresce a cada ano. Inúmeros fatores como rápida taxa de crescimento, grande produção de biomassa, adaptabilidade a diversos ambientes e solos, boa qualidade de madeira para produção de uma ampla gama de produtos e presença de celulose de fibra curta, ideal para a produção de papel e celulose, contribuíram para o grande sucesso das espécies de Eucalyptus e tornaram o Brasil o maior produtor mundial de celulose de fibra curta utilizando o eucalipto como matéria prima. Devido à reconhecida importância econômica e também ambiental das árvores, o desenvolvimento do sistema vascular se tornou um importante e fascinante processo biológico para se estudar. No entanto, existe ainda pouco conhecimento sobre os processos celulares, moleculares e bioquímicos envolvidos na formação da madeira. Dessa forma, no presente trabalho foi utilizada a técnica de SAGE (Serial Analysis of Gene Expression) para caracterizar o perfil transcricional do caule de plantas de E. grandis com 6 meses de idade. A partir do sequenciamento de 826 clones, foi possível analisar 2.274 tags/genes, sendo que 989 (43,5%) genes puderam ser identificados e ter uma possível função atribuída. Genes que codificam enzimas e proteínas muito importantes durante o processo de formação da madeira, como aqueles relacionados à biossíntese e deposição da parede celular e organização do citoesqueleto, apresentaram elevada expressão, sendo possível ainda sugerir a ocorrência de possíveis mecanismos comuns de controle transcricional para grupos de genes funcionalmente relacionados. A posterior comparação com as proteínas identificadas por espectrometria de massas através do sistema LC-MS/MS a partir do mesmo material biológico mostrou que muitos desses genes representam também as proteínas mais abundantes. Juntamente com outros projetos que vêm sendo desenvolvidos no laboratório, o presente trabalho contribuiu para a construção de um banco de dados local com informações do transcritoma e do proteoma de diferentes idades e tecidos, fornecendo uma visão global sobre os genes envolvidos no processo de formação da madeira e possivelmente responsáveis pelo rápido crescimento nas espécies de Eucalyptus, indicando importantes alvos para futuros programas de melhoramento. / From the numerous adaptations that plants have developed during evolution, the acquisition of the vascular system some 400 million years ago was been a decisive event for their successful existence on earth. Wood is considered the most important natural resource of renewable energy and the Forest-based economical sector grows every year. Several factors like the fast growth rate, large biomass production, adaptability to a wide range of environments and soils, good wood quality for the production of a wide range of products and the presence of short cellulose fiber, suitable for pulp and paper production, have contributed to the great success of Eucalyptus species making Brazil the main producer of short cellulose fiber using eucalypt as raw material. Due to the recognized economical and also environmental importance of trees, the development of the vascular system became an important and fascinating biological process to study. However, little is known about the cellular, molecular and biochemical processes involved in wood formation. In this way, in the current work SAGE (Serial Analysis of Gene Expression) technique was used to characterize the transcriptional profile in stems of 6 months old Eucalyptus grandis. From the sequencing of 826 clones, it was possible to analyse 2,274 tags/genes, and 989 (43,5%) genes could be identified and to have a possible function attributed. Genes that code for enzymes and proteins important for wood formation process, like those related to cell wall biosynthesis and deposition, and cytoskeleton organization had high expression, making it possible to suggest the occurrence of a common transcriptional control for a few functionally related genes. The posterior comparison with the set of proteins identified by LC ESI-MS/MS from the same biological material showed that some of these genes also represent the most abundant proteins. Taken together with other projects that are being developed in the laboratory, the present work contributed for the construction of a local data-base with transcriptome and proteome information from different ages and tissues, giving a global vision of the genes involved in the wood formation process and potentially responsible for the fast growth in the Eucalyptus species, indicating important targets for future breedings programs.

Abstract Iterative receiver techniques, multiple-input – multiple-output (MIMO) processing, and orthogonal frequency division multiplexing (OFDM) are amongst the key physical layer technologies when aiming at higher spectral efficiency for a wireless communication system. Special focus is put on iterative detection, decoding, and channel estimation for a MIMO-OFDM system. After designing separately efficient algorithms for the detection, channel decoding, and channel estimation, the objective is to optimize them to work together through optimizing the activation schedules for soft-in soft-out (SfISfO) components. A list parallel interference cancellation (PIC) detector is derived to approximate an a posteriori probability (APP) algorithm with reduced complexity and minimal loss of performance. It is shown that the list PIC detector with good initialization outperforms the K-best list sphere detector (LSD) in the case of small list sizes, whereas the complexities of the algorithms are of the same order. The convergence of the iterative detection and decoding is improved by using a priori information to also recalculate the candidate list, aside from the log-likelihood ratios (LLRs) of the coded bits. Unlike in pilot based channel estimation, the least-squares (LS) channel estimator based on symbol decisions requires a matrix inversion in MIMO-OFDM. The frequency domain (FD) space-alternating generalized expectation-maximization (SAGE) channel estimator calculates the LS estimate iteratively, avoiding the matrix inversion with constant envelope modulation. The performance and computational complexity of the FD-SAGE channel estimator are compared to those of pilot based LS channel estimation with minimum mean square error (MMSE) post-processing exploiting the time correlation of the channel. A time domain (TD) SAGE channel estimator is derived to avoid the matrix inversion in channel estimation based on symbol decisions for MIMO-OFDM systems also with non-constant envelope modulation. An obvious problem, with more than two blocks in an iterative receiver, is to find the optimal activation schedule of the different blocks. It is proposed to use extrinsic information transfer (EXIT) charts to characterize the behavior of the receiver blocks and to find out the optimal activation schedule for them. A semi-analytical expression of the EXIT function is derived for the LS channel estimator. An algorithm is proposed to generate the EXIT function of the APP algorithm as a function of the channel estimate’s mutual information (MI). Surface fitting is used to get closed form expressions for the EXIT functions of the APP algorithm and the channel decoder. Trellis search algorithms are shown to find the convergence with the lowest possible complexity using the EXIT functions. With the proposed concept, the activation scheduling can be adapted to prevailing channel circumstances and unnecessary iterations will be avoided.

À l'heure actuelle, les résultats périnataux en France demeurent parmi les moins satisfaisants en Europe malgré une très forte médicalisation. Les autorités de santé affirment reconnaître l'influence de la prise en charge et de l'accompagnement pendant la grossesse, l'accouchement et la période néonatale sur l'état de santé de la mère et de l'enfant mais l'offre de soins peine à s'élargir. Contrairement à ce que prévoient les lois concernant le libre choix du praticien en France, les parturientes ne sont pas à même de choisir le professionnel de santé qui les accompagnera lors de leur accouchement. De même, les sages-femmes, contrairement à ce qu'impose leur code de déontologie, ne sont pas en mesure de garantir à leurs patientes ni les conditions, ni le lieu de leur accouchement. De surcroît, peu d'entre elles exercent leur profession de façon autonome tout en pratiquant le plein exercice de leur fonction. En centrant cette recherche anthropologique sur l'expérience des femmes et des sages-femmes dans leurs relations autour de la naissance et de l'accouchement, l'objectif de cette étude qualitative est de faire la lumière sur les tenants et les aboutissants de l'uniformisation de l'offre de soins. Dans un premier temps sont abordés les différents types d'accompagnement proposés aux femmes aujourd'hui ainsi que la place qu'y occupent les sages-femmes. Dans un second temps, l'étude de l'accompagnement global permet l'examen de la prise en charge des patientes et de ses liens de causalité avec les relations interprofessionnelles. Ainsi sont révélés les impacts de cette pratique sur le soutien à la parentalité et la nécessité d'une diversification de l'offre de soins. / Currently, the perinatal results in France remain among the least satisfactory in Europe in spite of a very strong medicalization. However, health authorities acknowledge the influence of maternity care during pregnancy, childbirth and neonatal period on the state of health of the mother and the child but health services hardly increase. Contrary to what French law says on free choice of practitioner, parturient women cannot choose the health professional who will assist them during labor. Likewise, midwives cannot guarantee their patients the place and conditions of childbirth, contrary to their code of ethics. In addition, few of them have the opportunity to work in an independent way and at the same time fully practice their profession. By focusing this anthropological research on women's and midwives' experience in their relationships around childbirth, the aims of this qualitative study are to clarify the ins and outs of the standardization of health services. Initially, the various types of care provided to women today and the place granted to midwives are discussed. Secondly, possible causal links between interprofessional relations and maternity care are searched for through the study of comprehensive care. So are revealed the impacts of a close and trusting relationship in supporting parenthood and of a diversification of health services.

The human genome contains tens of thousands of gene loci which code for an even greater number of protein and RNA products. The highly complex temporal and spatial expression of these genes makes possible all the biological processes of life. Altered gene expression by mutation or deregulation is fundamental for the development of many human diseases. The ultimate aim of this thesis was to identify gene expression changes relevant to cancer. The advent of genome-wide expression profiling techniques, such as microarrays, has provided powerful new tools to identify such changes and researchers are now faced with an explosion of gene expression data. Processing, comparing and integrating these data present major challenges. I approached these challenges by developing and assessing novel methods for cross-platform analysis of expression data, scalable subspace clustering, and curation of experimental gene regulation data from the published literature. I found that combining results from different expression platforms increases reliability of coexpression predictions. However, I also observed that global correlation between platforms was generally low, and few gene pairs reached reasonable thresholds for high-confidence coexpression. Therefore, I developed a novel subspace clustering algorithm, able to identify coexpressed genes in experimental subsets of very large gene expression datasets. Biological assessment against several metrics indicates that this algorithm performs well. I also developed a novel meta-analysis method to identify consistently reported genes from differential expression studies when raw data are unavailable. This method was applied to thyroid cancer, producing a ranked list of significantly over-represented genes. Tissue microarray analysis of some of these candidates and others identified a number of promising biomarkers for diagnostic and prognostic classification of thyroid cancer. Finally, I present ORegAnno (www.oreganno.org), a resource for the community-driven curation of experimentally verified regulatory sequences. This resource has proven a great success with ~30,000 sequences entered from over 900 publications by ~50 contributing users. These data, methods and resources contribute to our overall understanding of gene regulation, gene expression, and the changes that occur in cancer. Such an understanding should help identify new cancer mechanisms, potential treatment targets, and have significant diagnostic and prognostic implications. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

Greater sage-grouse (Centrocercus urophasianus) are a species of conservation concern throughout their range including the state of Idaho. Little is known about the size of areas used by female sage-grouse during the breeding and nesting seasons, fidelity of females to those areas, or fidelity of female sage-grouse to specific leks or nest sites. The recent miniaturization of global positioning system (GPS) transmitting devices allows for a more thorough analysis of this behavior. We placed GPS transmitters on 234 female sage-grouse in Idaho, USA, from 2015 to 2019. We monitored 145 nest attempts, 15 of which occurred in consecutive years, from 130 female sage-grouse (Centrocercus urophasianus) with GPS transmitters to document movements and space-use during nesting. We quantified the length and direction of off-nest excursion distances for all 145 nest attempts. Also, for the 15 consecutive nest attempts, we compared the excursion distances for each bird, each year. The mean distance for an off-nest excursion across all study areas was 93.7 m (n = 145, SD = 57.9, range = 15.5 to 275.8 m). Rayleigh’s test of uniformity indicated that eight of 145 nest attempts had off-nest excursions that were not in a consistent direction. Mean excursion distances in the consecutive year were longer than those of the initial year (T = -3.1, n = 15, p-value = 0.013), and females with smaller excursion distances in the initial year also had smaller excursion distances in the consecutive year. We also quantified size of breeding areas for 50 female sage-grouse and identified factors that influenced breeding-area size. For 18 of those females, we quantified size and fidelity to breeding areas and leks between successive years. We generated 95% brownian bridge estimates of breeding-area size for each bird and counted the number of leks those females visited. To quantify breeding-area fidelity for the 18 females, we overlaid 95% brownian bridge estimates for females with consecutive breeding attempts, calculated percent overlap, and documented number of leks visited each year. Median size of breeding areas for all females was 21 km2 (interquartile range = 7.8 to 59.3 km2). Each bird visited a mean of 2 leks (SD = 1.2, range = 1 to 6 leks). Between years, breeding areas overlapped for all 18 females, and size of breeding areas did not differ between the first and second year (W-value = 61, p-value = 0.49). For those 18 females, only 7 visited the same lek in consecutive years, and none visited more than one common lek in consecutive years. Our results indicate that females use large areas while breeding and nesting and exhibit strong fidelity to those areas. Our results provide novel information on the breeding and nesting ecology of this species that will help agencies that manage sage-grouse and their habitat.

No description available.

Translocations have been used as a management strategy to successfully augment declining native wildlife populations. Greater sage-grouse (Centrocercus urophasianus; sage-grouse) population declines on Anthro Mountain, Utah prompted managers to translocate sage-grouse and test protocols from a successful translocation project in Strawberry Valley, Utah. Sage-grouse from Parker Mountain, Utah were used as the source population for Anthro Mountain and Strawberry Valley translocations. Sixty hens were translocated to Anthro Mountain in 2009 and 2010; I monitored vital rates of the 60 translocated hens and 32 resident hens from 2009-2012. My objective was to determine the overall success of the translocation 4 years after the initial release and compare vital rates to the source population and Strawberry Valley.In Chapter 2, I determined that survival varied by study area and hen age but was not affected by residency status. Annual survival of Anthro Mountain hens was lower than Parker Mountain and Strawberry Valley hens. Adult hen survival in all three populations was higher than yearling survival.In Chapter 3, I determined that the translocation contributed to population growth. Adult resident and previously translocated hens had the highest reproductive success, followed by resident yearlings, newly translocated adults, and newly translocated yearlings. Lek counts increased from 2009-2013 and a new lek was discovered in 2011. Survival was not affected by residency status or age, but varied greatly by year and season. Mean monthly survival was lowest in the fall; this differs from range-wide trends.In Chapter 4, I determined that translocated hens adapted to the release area. They exhibited similar seasonal movements and used similar habitats as residents. The home range size of resident and translocated hens was comparable; however, previously translocated hens had smaller home ranges than newly released hens.Despite landscape level differences between the source and release areas, translocated hens assimilated to the population and contributed to population growth. Although the translocation was successful, the low vital rate estimates are cause for concern. The low estimates suggest that factors such as predation, habitat quality and quantity, and anthropogenic influences may be problematic for this isolated population.

Greater sage-grouse (Centrocercus urophasianus) adult and juvenile survival have been identified as critical demographic parameters. However, little is known regarding the dynamics of juvenile sage-grouse. From 2008-2010, I used radio-telemetry and 2 transmitter types to monitor 91 juvenile sage-grouse. Program MARK was used to analyze survival data. Over-winter survival was 0.802 - 0.982 and 0.687 - 0.969 for females and males, respectively. Fall survival rates were 0.522 - 0.623 for females and 0.332 - 0.449 for males. Survival from fall through winter was 0.418 - 0.616 for females and 0.228 - 0.435 for males. For both years combined, the probability predation caused death was 0.705, and probability harvest caused death was 0.159. The probability unreported harvest caused death was 0.091. Sex (p= 0.103) and transmitter type (p = 0.09) affected survival. Back-mounted transmitters negatively affected survival and their use should be avoided to minimize experimental bias.

Changes to vegetation architecture within a natural habitat can have profound impacts upon ecological community function, but the relative influence of vegetation architecture itself and potential indirect influences of associated food resources are often difficult to disentangle. I present the results of a three-year study designed to address the community level impacts of changes in big sagebrush (Artemisia tridentata) architecture and associated prey availability upon the ground-dwelling arthropod community. Three experimental sagebrush architecture treatments (low, intermediate, and high foliage density) and two levels of prey insect availability treatment (natural and baited/increased prey availability) were imposed in a sage-steppe ecosystem. The ground-dwelling spider (top predators) and insect (prey) response to all combinations of the six treatments were assessed through abundances in pitfall traps. Chapter 2 demonstrates that changes in a single shrub’s architecture did not markedly impact prey arthropod availability on the ground, though an overall increase in arthropod abundance was detected within baited shrubs. This indicates changes to vegetation architecture do not impact prey insect availability for ground-dwelling spiders. Thus, changes in shrub architecture and not the associated prey base directly alter the ground-dwelling spider community. Chapter 3 shows that architectural manipulation of a single sagebrush directly influences the ability of certain ground-dwelling spider guilds to persist beneath the shrub. Data within Chapters 2 and 3 support the conclusion that vegetation architecture directly affects ground-dwelling spider community structure and composition. Finally, Chapter 4 explores how the relative impacts of vegetation architecture and prey availability upon ecological communities can shift depending upon the spatial context in which the manipulations take place, given the differences in mobility of species within the grounddwelling spider and insect prey communities. Within this study, Diurnal and Nocturnal Wanderers responded to manipulations in prey availability at a larger spatial context (patches of 15 shrubs) while more stationary Trappers and Ambushers did not. Through simultaneous manipulation of vegetation architecture (Artemisia tridentata, big sagebrush) and associated insect prey base in different spatial contexts, this dissertation demonstrates that vegetation architecture directly affects ground-dwelling spider community organization at the species and guild levels of diversity. Shifts in spider (predator) functional diversity can ultimately impact arthropod decomposer and herbivore populations, influencing fundamental ecosystem processes such as decomposition and productivity.

Due to loss of habitat, Gunnison sage-grouse (Centrocercus minimus) currently occupy 8.5% of their presumed historical range. One population survives in Utah, occurring in San Juan County. The Gunnison Sage-grouse Rangewide Conservation Plan and the San Juan County Gunnison Sage-grouse Conservation Plan recommended management strategies to address identified conservation threats to the Utah population. I addressed three conservation strategies identified in the plans: 1) creation and enhancement of brood-rearing areas; 2) assessment of habitat conditions within the Gunnison Sage-grouse Conservation Area; and 3) prevention or reduction of perching events by avian predators on distribution line power poles. From 2007-2009, I addressed the conservation strategy of creating mesic brood-rearing areas in Conservation Reserve Program fields and native sagebrush areas by evaluating the role of irrigation and dormant season cattle grazing on habitat. Vegetation and arthropod diversity in irrigated versus non-irrigated plots did not differ (p>0.01). Conservation Reserve Program plots exhibited greater arthropod abundance and cover of perennial grass than the native sagebrush plots, but lower diversity of perennial grasses and abundance and diversity of forbs (p<0.01). The second conservation strategy I addressed was the completion of an assessment of habitat conditions within the Gunnison Sage-grouse Conservation Area. I measured vegetation conditions within habitat occupied and unoccupied by Gunnison sage-grouse. Cover and height of grasses exceeded guidelines for occupied and unoccupied habitats. Forb cover was below recommended guidelines in occupied habitat. Sagebrush cover was below guidelines for winter habitat. Habitat restoration efforts should focus on retaining existing sagebrush cover and establishment of sagebrush, forb, and grass cover within Conservation Reserve Program fields. The third conservation strategy I evaluated was the retrofitting of distribution line power poles with perch deterrents to discourage avian predators from perching. I evaluated the efficacy of five perch deterrents. The perch deterrents did not mitigate potential avian predators from perching. A deterrent designed for insulators, in combination with physical deterrents we tested, has potential to prevent perching. These studies provided a sound first step that can be built upon by the Monticello/Dove Creek Local Working Group to improve habitat conditions, reduce the threat of avian predation, and plan future conservation activities within the Conservation Area.